20473f03adfc10172e8cc39b23656e077aece62e braney Mon Feb 7 14:48:45 2022 -0800 add GENCODE V39 log files to doc diff --git src/hg/makeDb/doc/ucscGenes/hg38.gencodeV39.log src/hg/makeDb/doc/ucscGenes/hg38.gencodeV39.log new file mode 100644 index 0000000..ecfffc9 --- /dev/null +++ src/hg/makeDb/doc/ucscGenes/hg38.gencodeV39.log @@ -0,0 +1,3674 @@ +==== doBioCyc.log ==== ++ mkdir /hive/data/genomes/hg38/bed/gencodeV39/build/bioCyc ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build/bioCyc ++ grep -E -v '^#' /hive/data/outside/bioCyc/210823/humancyc/23.0/data/genes.col ++ grep -E -v '^#' /hive/data/outside/bioCyc/210823/humancyc/23.0/data/pathways.col ++ awk '-F\t' '{if (140 == NF) { printf "%s\t\t\n", $0; } else { print $0}}' ++ kgBioCyc1 -noEnsembl genes.tab pathways.tab knownGeneV39 bioCycPathway.tab bioCycMapDesc.tab +Got 17428 elements in genes.tab ++ hgLoadSqlTab knownGeneV39 bioCycPathway /cluster/home/braney/kent/src/hg/lib/bioCycPathway.sql ./bioCycPathway.tab +Scanning through 1 files ++ hgLoadSqlTab knownGeneV39 bioCycMapDesc /cluster/home/braney/kent/src/hg/lib/bioCycMapDesc.sql ./bioCycMapDesc.tab +Scanning through 1 files ++ echo 'BuildBioCyc successfully finished' +BuildBioCyc successfully finished +==== doBlast.log ==== ++ rm -rf /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp ++ mkdir /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp ++ ls -l /hive/data/genomes/hg38/bed/gencodeV39/build/ucscGenes.faa +-rw-rw-r-- 1 braney genecats 48813438 Jan 17 08:24 /hive/data/genomes/hg38/bed/gencodeV39/build/ucscGenes.faa ++ ls -l /hive/data/genomes/mm39/bed/gencodeVM27/build/ucscGenes.faa +-rw-rw-r-- 1 braney genecats 30565721 Aug 5 10:32 /hive/data/genomes/mm39/bed/gencodeVM27/build/ucscGenes.faa ++ ls -l /hive/data/genomes/rn6/bed/ensGene.95/ensembl.faa +-rw-rw-r-- 1 braney genecats 15893238 Mar 11 2019 /hive/data/genomes/rn6/bed/ensGene.95/ensembl.faa ++ ls -l /hive/data/genomes/danRer11/bed/ensGene.95/ensembl.faa +-rw-rw-r-- 1 braney genecats 28003563 Mar 11 2019 /hive/data/genomes/danRer11/bed/ensGene.95/ensembl.faa ++ ls -l /hive/data/genomes/dm6/bed/ensGene.95/ensembl.faa +-rw-rw-r-- 1 braney genecats 20545656 Mar 11 2019 /hive/data/genomes/dm6/bed/ensGene.95/ensembl.faa ++ ls -l /hive/data/genomes/ce11/bed/ws245Genes/ws245Pep.faa +-rw-rw-r-- 1 jcasper protein 11513083 Mar 30 2016 /hive/data/genomes/ce11/bed/ws245Genes/ws245Pep.faa ++ ls -l /hive/data/genomes/sacCer3/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa +-rw-rw-r-- 1 hiram genecats 3135195 Sep 2 2011 /hive/data/genomes/sacCer3/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa ++ cat ++ rm -rf /hive/users/braney/scratch/brHgNearBlastp ++ doHgNearBlastp.pl -noLoad -clusterHub=ku -distrHost=hgwdev -dbHost=hgwdev -workhorse=hgwdev config.ra +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev mkdir /hive/users/braney/scratch/brHgNearBlastp +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split +faSplit sequence /hive/data/genomes/hg38/bed/gencodeV39/build/ucscGenes.faa 1000 /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_ +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_knownGeneV39.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_knownGeneV39.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.formatdb +cd /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.formatdb +/cluster/bin/blast/x86_64/blast-2.2.20/bin/formatdb -i /hive/data/genomes/hg38/bed/gencodeV39/build/ucscGenes.faa -t knownGeneV39 -n knownGeneV39 +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.knownGeneV39/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.knownGeneV39/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.knownGeneV39 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0000.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0001.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0002.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0003.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0004.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0005.fa 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/hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0918.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0919.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0920.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0921.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0922.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0923.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0924.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0925.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0926.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0927.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0928.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0929.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0930.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0931.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0932.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0933.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0934.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0935.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0936.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0937.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0938.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0939.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0940.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0941.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0942.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0943.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +944 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.knownGeneV39/batch +944 jobs in batch +9437 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 944 +================ +Checking job status 0 minutes after launch +944 jobs in batch +10381 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +944 jobs in batch +20088 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +944 jobs in batch +20088 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +944 jobs in batch +19573 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +944 jobs in batch +18904 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +944 jobs in batch +18401 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 7 minutes after launch +944 jobs in batch +17760 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 9 minutes after launch +944 jobs in batch +16997 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 11 minutes after launch +944 jobs in batch +16054 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 14 minutes after launch +944 jobs in batch +15010 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 17 minutes after launch +944 jobs in batch +13861 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 20 minutes after launch +944 jobs in batch +12586 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 23 minutes after launch +944 jobs in batch +11194 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +944 jobs in batch +11194 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 944 of 944 jobs +CPU time in finished jobs: 200725s 3345.41m 55.76h 2.32d 0.006 y +IO & Wait Time: 3211s 53.52m 0.89h 0.04d 0.000 y +Average job time: 216s 3.60m 0.06h 0.00d +Longest finished job: 1286s 21.43m 0.36h 0.01d +Submission to last job: 1367s 22.78m 0.38h 0.02d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.knownGeneV39/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_mm39.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_mm39.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/mm39.formatdb +cd /hive/users/braney/scratch/brHgNearBlastp/mm39.formatdb +/cluster/bin/blast/x86_64/blast-2.2.20/bin/formatdb -i /hive/data/genomes/mm39/bed/gencodeVM27/build/ucscGenes.faa -t mm39 -n mm39 +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.mm39/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.mm39/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.mm39 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0000.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0001.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0002.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0003.fa 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/hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0916.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0917.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0918.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0919.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0920.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0921.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0922.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0923.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0924.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0925.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0926.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0927.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0928.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0929.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0930.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0931.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0932.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0933.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0934.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0935.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0936.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0937.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0938.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0939.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0940.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0941.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0942.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0943.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +944 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.mm39/batch +944 jobs in batch +11044 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 944 +================ +Checking job status 0 minutes after launch +944 jobs in batch +11879 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +944 jobs in batch +11678 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +944 jobs in batch +11352 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +944 jobs in batch +10978 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +944 jobs in batch +10452 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +944 jobs in batch +9777 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 7 minutes after launch +944 jobs in batch +8968 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 9 minutes after launch +944 jobs in batch +8049 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 11 minutes after launch +944 jobs in batch +6905 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 14 minutes after launch +944 jobs in batch +5736 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +944 jobs in batch +5736 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 944 of 944 jobs +CPU time in finished jobs: 115763s 1929.38m 32.16h 1.34d 0.004 y +IO & Wait Time: 2626s 43.77m 0.73h 0.03d 0.000 y +Average job time: 125s 2.09m 0.03h 0.00d +Longest finished job: 695s 11.58m 0.19h 0.01d +Submission to last job: 801s 13.35m 0.22h 0.01d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.mm39/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/mm39.split +faSplit sequence /hive/data/genomes/mm39/bed/gencodeVM27/build/ucscGenes.faa 1000 /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_ +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.mm39.knownGeneV39/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.mm39.knownGeneV39/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.mm39.knownGeneV39 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0000.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0001.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0002.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0003.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0004.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0005.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0006.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0007.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0008.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0009.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0010.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0011.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0012.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0013.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0014.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0015.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0016.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0017.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0018.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0019.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0020.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0021.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0022.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0023.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0024.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0025.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0026.fa /hive/users/braney/scratch/brHgNearBlastp/mm39.split/mm39_0027.fa 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+942 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.mm39.knownGeneV39/batch +942 jobs in batch +5592 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 942 +================ +Checking job status 0 minutes after launch +942 jobs in batch +6404 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +942 jobs in batch +6155 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +942 jobs in batch +5837 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +942 jobs in batch +5421 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +942 jobs in batch +4842 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +942 jobs in batch +4140 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 7 minutes after launch +942 jobs in batch +3382 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 9 minutes after launch +942 jobs in batch +12109 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 11 minutes after launch +942 jobs in batch +11111 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +942 jobs in batch +11111 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 942 of 942 jobs +CPU time in finished jobs: 113442s 1890.70m 31.51h 1.31d 0.004 y +IO & Wait Time: 2652s 44.20m 0.74h 0.03d 0.000 y +Average job time: 123s 2.05m 0.03h 0.00d +Longest finished job: 540s 9.00m 0.15h 0.01d +Submission to last job: 565s 9.42m 0.16h 0.01d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.mm39.knownGeneV39/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_rn6.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_rn6.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/rn6.formatdb +cd /hive/users/braney/scratch/brHgNearBlastp/rn6.formatdb +/cluster/bin/blast/x86_64/blast-2.2.20/bin/formatdb -i /hive/data/genomes/rn6/bed/ensGene.95/ensembl.faa -t rn6 -n rn6 +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.rn6/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.rn6/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.rn6 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0000.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0001.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0002.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0003.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0004.fa 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/hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0917.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0918.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0919.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0920.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0921.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0922.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0923.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0924.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0925.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0926.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0927.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0928.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0929.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0930.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0931.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0932.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0933.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0934.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0935.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0936.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0937.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0938.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0939.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0940.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0941.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0942.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0943.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +944 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.rn6/batch +944 jobs in batch +10989 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 944 +================ +Checking job status 0 minutes after launch +944 jobs in batch +11841 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +944 jobs in batch +11588 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +944 jobs in batch +11140 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +944 jobs in batch +10627 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +944 jobs in batch +9924 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +944 jobs in batch +9188 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 7 minutes after launch +944 jobs in batch +8341 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 9 minutes after launch +944 jobs in batch +7412 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +944 jobs in batch +7412 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 944 of 944 jobs +CPU time in finished jobs: 64469s 1074.48m 17.91h 0.75d 0.002 y +IO & Wait Time: 2610s 43.50m 0.73h 0.03d 0.000 y +Average job time: 71s 1.18m 0.02h 0.00d +Longest finished job: 404s 6.73m 0.11h 0.00d +Submission to last job: 473s 7.88m 0.13h 0.01d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.rn6/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/rn6.split +faSplit sequence /hive/data/genomes/rn6/bed/ensGene.95/ensembl.faa 1000 /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_ +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.rn6.knownGeneV39/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.rn6.knownGeneV39/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.rn6.knownGeneV39 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0000.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0001.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0002.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0003.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0004.fa 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/hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0950.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0951.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0952.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0953.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0954.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0955.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0956.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0957.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0958.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0959.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0960.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0961.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0962.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0963.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0964.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0965.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0966.fa /hive/users/braney/scratch/brHgNearBlastp/rn6.split/rn6_0967.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +968 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.rn6.knownGeneV39/batch +968 jobs in batch +7314 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 968 +================ +Checking job status 0 minutes after launch +968 jobs in batch +8157 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +968 jobs in batch +7931 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +968 jobs in batch +7554 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +968 jobs in batch +7006 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +968 jobs in batch +6322 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +968 jobs in batch +5526 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +968 jobs in batch +5522 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 968 of 968 jobs +CPU time in finished jobs: 62287s 1038.11m 17.30h 0.72d 0.002 y +IO & Wait Time: 2618s 43.64m 0.73h 0.03d 0.000 y +Average job time: 67s 1.12m 0.02h 0.00d +Longest finished job: 113s 1.88m 0.03h 0.00d +Submission to last job: 309s 5.15m 0.09h 0.00d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.rn6.knownGeneV39/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_danRer11.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_danRer11.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/danRer11.formatdb +cd /hive/users/braney/scratch/brHgNearBlastp/danRer11.formatdb +/cluster/bin/blast/x86_64/blast-2.2.20/bin/formatdb -i /hive/data/genomes/danRer11/bed/ensGene.95/ensembl.faa -t danRer11 -n danRer11 +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.danRer11/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.danRer11/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.danRer11 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0000.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0001.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0002.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0003.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0004.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0005.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0006.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0007.fa 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/hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0932.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0933.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0934.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0935.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0936.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0937.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0938.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0939.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0940.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0941.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0942.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0943.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +944 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.danRer11/batch +944 jobs in batch +5380 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 944 +================ +Checking job status 0 minutes after launch +944 jobs in batch +6210 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +944 jobs in batch +5980 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +944 jobs in batch +5513 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +944 jobs in batch +5087 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +944 jobs in batch +4514 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +944 jobs in batch +3698 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 7 minutes after launch +944 jobs in batch +2587 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 9 minutes after launch +944 jobs in batch +1342 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 11 minutes after launch +944 jobs in batch +45 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +944 jobs in batch +45 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 944 of 944 jobs +CPU time in finished jobs: 110527s 1842.12m 30.70h 1.28d 0.004 y +IO & Wait Time: 2682s 44.70m 0.74h 0.03d 0.000 y +Average job time: 120s 2.00m 0.03h 0.00d +Longest finished job: 606s 10.10m 0.17h 0.01d +Submission to last job: 667s 11.12m 0.19h 0.01d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.danRer11/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/danRer11.split +faSplit sequence /hive/data/genomes/danRer11/bed/ensGene.95/ensembl.faa 1000 /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_ +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.danRer11.knownGeneV39/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.danRer11.knownGeneV39/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.danRer11.knownGeneV39 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0000.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0001.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0002.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0003.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0004.fa 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/hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0954.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0955.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0956.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0957.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0958.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0959.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0960.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0961.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0962.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0963.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0964.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0965.fa /hive/users/braney/scratch/brHgNearBlastp/danRer11.split/danRer11_0966.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +967 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.danRer11.knownGeneV39/batch +967 jobs in batch +43 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 967 +================ +Checking job status 0 minutes after launch +967 jobs in batch +1009 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +967 jobs in batch +1007 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +967 jobs in batch +998 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +967 jobs in batch +142 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +967 jobs in batch +37 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +967 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +967 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 967 of 967 jobs +CPU time in finished jobs: 110174s 1836.23m 30.60h 1.28d 0.003 y +IO & Wait Time: 2829s 47.15m 0.79h 0.03d 0.000 y +Average job time: 117s 1.95m 0.03h 0.00d +Longest finished job: 277s 4.62m 0.08h 0.00d +Submission to last job: 283s 4.72m 0.08h 0.00d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.danRer11.knownGeneV39/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_dm6.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_dm6.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/dm6.formatdb +cd /hive/users/braney/scratch/brHgNearBlastp/dm6.formatdb +/cluster/bin/blast/x86_64/blast-2.2.20/bin/formatdb -i /hive/data/genomes/dm6/bed/ensGene.95/ensembl.faa -t dm6 -n dm6 +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.dm6/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.dm6/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.dm6 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/hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0923.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0924.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0925.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0926.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0927.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0928.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0929.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0930.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0931.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0932.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0933.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0934.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0935.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0936.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0937.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0938.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0939.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0940.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0941.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0942.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0943.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +944 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.dm6/batch +944 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 944 +================ +Checking job status 0 minutes after launch +944 jobs in batch +976 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +944 jobs in batch +975 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +944 jobs in batch +425 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +944 jobs in batch +56 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +944 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +944 jobs in batch +28 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +944 jobs in batch +28 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 944 of 944 jobs +CPU time in finished jobs: 74867s 1247.78m 20.80h 0.87d 0.002 y +IO & Wait Time: 2758s 45.97m 0.77h 0.03d 0.000 y +Average job time: 82s 1.37m 0.02h 0.00d +Longest finished job: 249s 4.15m 0.07h 0.00d +Submission to last job: 257s 4.28m 0.07h 0.00d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.dm6/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/dm6.split +faSplit sequence /hive/data/genomes/dm6/bed/ensGene.95/ensembl.faa 1000 /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_ +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.dm6.knownGeneV39/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.dm6.knownGeneV39/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.dm6.knownGeneV39 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0000.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0001.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0002.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0003.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0004.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0005.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0006.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0007.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0008.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0009.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0010.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0011.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0012.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0013.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0014.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0015.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0016.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0017.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0018.fa 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/hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0964.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0965.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0966.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0967.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0968.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0969.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0970.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0971.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0972.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0973.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0974.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0975.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0976.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0977.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0978.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0979.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0980.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0981.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0982.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0983.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0984.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0985.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0986.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0987.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0988.fa /hive/users/braney/scratch/brHgNearBlastp/dm6.split/dm6_0989.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +990 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.dm6.knownGeneV39/batch +990 jobs in batch +28 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 990 +================ +Checking job status 0 minutes after launch +990 jobs in batch +1018 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +990 jobs in batch +1016 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +990 jobs in batch +191 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +990 jobs in batch +30 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +990 jobs in batch +26 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +990 jobs in batch +26 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 990 of 990 jobs +CPU time in finished jobs: 65545s 1092.42m 18.21h 0.76d 0.002 y +IO & Wait Time: 2792s 46.53m 0.78h 0.03d 0.000 y +Average job time: 69s 1.15m 0.02h 0.00d +Longest finished job: 178s 2.97m 0.05h 0.00d +Submission to last job: 180s 3.00m 0.05h 0.00d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.dm6.knownGeneV39/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_ce11.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_ce11.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/ce11.formatdb +cd /hive/users/braney/scratch/brHgNearBlastp/ce11.formatdb +/cluster/bin/blast/x86_64/blast-2.2.20/bin/formatdb -i /hive/data/genomes/ce11/bed/ws245Genes/ws245Pep.faa -t ce11 -n ce11 +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.ce11/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.ce11/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.ce11 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0000.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0001.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0002.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0003.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0004.fa 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/hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0929.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0930.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0931.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0932.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0933.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0934.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0935.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0936.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0937.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0938.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0939.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0940.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0941.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0942.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0943.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +944 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.ce11/batch +944 jobs in batch +26 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 944 +================ +Checking job status 0 minutes after launch +944 jobs in batch +970 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +944 jobs in batch +724 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +944 jobs in batch +31 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +944 jobs in batch +25 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +944 jobs in batch +25 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 944 of 944 jobs +CPU time in finished jobs: 35970s 599.50m 9.99h 0.42d 0.001 y +IO & Wait Time: 2706s 45.10m 0.75h 0.03d 0.000 y +Average job time: 41s 0.68m 0.01h 0.00d +Longest finished job: 111s 1.85m 0.03h 0.00d +Submission to last job: 120s 2.00m 0.03h 0.00d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.ce11/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/ce11.split +faSplit sequence /hive/data/genomes/ce11/bed/ws245Genes/ws245Pep.faa 1000 /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_ +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.ce11.knownGeneV39/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.ce11.knownGeneV39/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.ce11.knownGeneV39 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0000.fa 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/hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0946.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0947.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0948.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0949.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0950.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0951.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0952.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0953.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0954.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0955.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0956.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0957.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0958.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0959.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0960.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0961.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0962.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0963.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0964.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0965.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0966.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0967.fa /hive/users/braney/scratch/brHgNearBlastp/ce11.split/ce11_0968.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +969 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.ce11.knownGeneV39/batch +969 jobs in batch +25 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 969 +================ +Checking job status 0 minutes after launch +969 jobs in batch +994 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +969 jobs in batch +328 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +969 jobs in batch +25 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +969 jobs in batch +21 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +969 jobs in batch +21 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 969 of 969 jobs +CPU time in finished jobs: 34781s 579.69m 9.66h 0.40d 0.001 y +IO & Wait Time: 2807s 46.78m 0.78h 0.03d 0.000 y +Average job time: 39s 0.65m 0.01h 0.00d +Longest finished job: 97s 1.62m 0.03h 0.00d +Submission to last job: 100s 1.67m 0.03h 0.00d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.ce11.knownGeneV39/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_sacCer3.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doFormat_sacCer3.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/sacCer3.formatdb +cd /hive/users/braney/scratch/brHgNearBlastp/sacCer3.formatdb +/cluster/bin/blast/x86_64/blast-2.2.20/bin/formatdb -i /hive/data/genomes/sacCer3/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa -t sacCer3 -n sacCer3 +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.sacCer3/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.sacCer3/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.sacCer3 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0000.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0001.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0002.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0003.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0004.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0005.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0006.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0007.fa 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/hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0920.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0921.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0922.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0923.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0924.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0925.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0926.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0927.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0928.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0929.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0930.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0931.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0932.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0933.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0934.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0935.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0936.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0937.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0938.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0939.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0940.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0941.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0942.fa /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split/knownGeneV39_0943.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +944 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.sacCer3/batch +944 jobs in batch +21 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 944 +================ +Checking job status 0 minutes after launch +944 jobs in batch +965 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +944 jobs in batch +21 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +944 jobs in batch +21 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 944 of 944 jobs +CPU time in finished jobs: 8713s 145.22m 2.42h 0.10d 0.000 y +IO & Wait Time: 2634s 43.90m 0.73h 0.03d 0.000 y +Average job time: 12s 0.20m 0.00h 0.00d +Longest finished job: 28s 0.47m 0.01h 0.00d +Submission to last job: 39s 0.65m 0.01h 0.00d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.sacCer3/loadPairwise.csh +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev nice /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/doSplit.csh +mkdir /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split +faSplit sequence /hive/data/genomes/sacCer3/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa 1000 /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_ +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.sacCer3.knownGeneV39/doBlastp.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' ku /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.sacCer3.knownGeneV39/doBlastp.csh +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.sacCer3.knownGeneV39 +mkdir out +chmod a+x blastSome +ls -1S /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0000.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0001.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0002.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0003.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0004.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0005.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0006.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0007.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0008.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0009.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0010.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0011.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0012.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0013.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0014.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0015.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0016.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0017.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0018.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0019.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0020.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0021.fa 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/hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0958.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0959.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0960.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0961.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0962.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0963.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0964.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0965.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0966.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0967.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0968.fa /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split/sacCer3_0969.fa +gensub2 split.lst single gsub spec +para make spec +Checking input files +970 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.sacCer3.knownGeneV39/batch +970 jobs in batch +21 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 970 +================ +Checking job status 0 minutes after launch +970 jobs in batch +972 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +970 jobs in batch +21 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! +para time +970 jobs in batch +21 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 970 of 970 jobs +CPU time in finished jobs: 8786s 146.43m 2.44h 0.10d 0.000 y +IO & Wait Time: 2673s 44.55m 0.74h 0.03d 0.000 y +Average job time: 12s 0.20m 0.00h 0.00d +Longest finished job: 25s 0.42m 0.01h 0.00d +Submission to last job: 32s 0.53m 0.01h 0.00d +Estimated complete: 0s 0.00m 0.00h 0.00d +# chmod a+x /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.sacCer3.knownGeneV39/loadPairwise.csh +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.split +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/knownGeneV39.formatdb +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/mm39.split +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/mm39.formatdb +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/rn6.split +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/rn6.formatdb +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/danRer11.split +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/danRer11.formatdb +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/dm6.split +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/dm6.formatdb +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/ce11.split +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/ce11.formatdb +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/sacCer3.split +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rm -rf /hive/users/braney/scratch/brHgNearBlastp/sacCer3.formatdb +# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev rmdir /hive/users/braney/scratch/brHgNearBlastp + + *** All done! + *** -noLoad was specified -- you can run this script manually to load knownGeneV39 tables: + run.knownGeneV39.knownGeneV39/loadPairwise.csh + + *** -noLoad was specified -- you can run these scripts manually to load knownGeneV39 tables: + run.knownGeneV39.mm39/loadPairwise.csh + run.knownGeneV39.rn6/loadPairwise.csh + run.knownGeneV39.danRer11/loadPairwise.csh + run.knownGeneV39.dm6/loadPairwise.csh + run.knownGeneV39.ce11/loadPairwise.csh + run.knownGeneV39.sacCer3/loadPairwise.csh + + *** -noLoad was specified -- you can run these scripts manually to load knownGeneV39BlastTab in query databases: + run.mm39.knownGeneV39/loadPairwise.csh + run.rn6.knownGeneV39/loadPairwise.csh + run.danRer11.knownGeneV39/loadPairwise.csh + run.dm6.knownGeneV39/loadPairwise.csh + run.ce11.knownGeneV39/loadPairwise.csh + run.sacCer3.knownGeneV39/loadPairwise.csh + + ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.knownGeneV39 ++ ./loadPairwise.csh +cd /hive/data/genomes/hg38/bed/gencodeV39/build/hgNearBlastp/run.knownGeneV39.knownGeneV39 +hgLoadBlastTab knownGeneV39 knownBlastTab -maxPer=1000 -bestOnly out/knownGeneV39_0000.tab out/knownGeneV39_0001.tab out/knownGeneV39_0002.tab out/knownGeneV39_0003.tab out/knownGeneV39_0004.tab out/knownGeneV39_0005.tab out/knownGeneV39_0006.tab out/knownGeneV39_0007.tab out/knownGeneV39_0008.tab out/knownGeneV39_0009.tab out/knownGeneV39_0010.tab out/knownGeneV39_0011.tab out/knownGeneV39_0012.tab out/knownGeneV39_0013.tab out/knownGeneV39_0014.tab out/knownGeneV39_0015.tab out/knownGeneV39_0016.tab out/knownGeneV39_0017.tab out/knownGeneV39_0018.tab out/knownGeneV39_0019.tab out/knownGeneV39_0020.tab out/knownGeneV39_0021.tab out/knownGeneV39_0022.tab 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run.knownGeneV39.knownGeneV39/out/knownGeneV39_0936.tab run.knownGeneV39.knownGeneV39/out/knownGeneV39_0937.tab run.knownGeneV39.knownGeneV39/out/knownGeneV39_0938.tab run.knownGeneV39.knownGeneV39/out/knownGeneV39_0939.tab run.knownGeneV39.knownGeneV39/out/knownGeneV39_0940.tab run.knownGeneV39.knownGeneV39/out/knownGeneV39_0941.tab run.knownGeneV39.knownGeneV39/out/knownGeneV39_0942.tab run.knownGeneV39.knownGeneV39/out/knownGeneV39_0943.tab ++ gzip run.ce11.knownGeneV39/all.tab run.danRer11.knownGeneV39/all.tab run.dm6.knownGeneV39/all.tab run.knownGeneV39.ce11/all.tab run.knownGeneV39.danRer11/all.tab run.knownGeneV39.dm6/all.tab run.knownGeneV39.sacCer3/all.tab run.sacCer3.knownGeneV39/all.tab ++ echo 'BuildBlast successfully finished' +BuildBlast successfully finished +==== doFoldUtr.log ==== ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build ++ rm -rf rnaStruct ++ mkdir -p rnaStruct ++ cd rnaStruct ++ ln -s /cluster/data/hg38/hg38.2bit knownGeneV39.2bit ++ mkdir -p utr3/split utr5/split utr3/fold utr5/fold +++ pwd ++ utrFa -nibPath=/hive/data/genomes/hg38/bed/gencodeV39/build/rnaStruct knownGeneV39 knownGene utr3 utr3/utr.fa +chrUn_KI270394v1 +chrUn_KI270392v1 +chrUn_KI270423v1 +chrUn_KI270385v1 +chrUn_KI270539v1 +chrUn_KI270312v1 +chrUn_KI270336v1 +chrUn_KI270419v1 +chrUn_KI270329v1 +chrUn_KI270379v1 +chrUn_KI270378v1 +chrUn_KI270335v1 +chrUn_KI270337v1 +chrUn_KI270376v1 +chrUn_KI270395v1 +chrUn_KI270412v1 +chrUn_KI270310v1 +chrUn_KI270544v1 +chrUn_KI270388v1 +chrUn_KI270466v1 +chrUn_KI270389v1 +chrUn_KI270516v1 +chrUn_KI270393v1 +chrUn_KI270429v1 +chrUn_KI270334v1 +chrUn_KI270583v1 +chrUn_KI270340v1 +chrUn_KI270338v1 +chrUn_KI270316v1 +chrUn_KI270422v1 +chrUn_KI270373v1 +chrUn_KI270305v1 +chrUn_KI270391v1 +chrUn_KI270387v1 +chrUn_KI270580v1 +chrUn_KI270548v1 +chrUn_KI270372v1 +chrUn_KI270330v1 +chrUn_KI270384v1 +chrUn_KI270383v1 +chrUn_KI270465v1 +chrUn_KI270386v1 +chrUn_KI270363v1 +chrUn_KI270396v1 +chrUn_KI270425v1 +chrUn_KI270529v1 +chrUn_KI270381v1 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+chr11_KI270827v1_alt +chrX_ML143383v1_fix +chr17_JH159147v1_alt +chr2_KI270773v1_alt +chrUn_KI270757v1 +chr9_GL383540v1_alt +chr6_ML143351v1_fix +chr22_KI270739v1_random +chr22_KB663609v1_alt +chr21_GL383580v2_alt +chr6_KI270802v1_alt +chr12_KI270833v1_alt +chr6_KI270758v1_alt +chr16_KZ208921v1_alt +chrUn_KI270756v1 +chr6_KQ090017v1_alt +chr21_KI270872v1_alt +chr5_GL383532v1_alt +chr2_ML143342v1_fix +chr10_KN538366v1_fix +chr12_KN538370v1_fix +chr17_JH159148v1_alt +chr16_GL383557v1_alt +chr5_ML143350v1_fix +chr17_GL383566v1_alt +chr4_KQ090013v1_alt +chrUn_KI270538v1 +chr5_GL000208v1_random +chrUn_KI270435v1 +chr18_KZ208922v1_fix +chrUn_KI270748v1 +chr2_GL582966v2_alt +chr22_GL383583v2_alt +chr15_ML143369v1_fix +chr22_KI270738v1_random +chr19_KV575254v1_alt +chr11_KI270721v1_random +chr19_KV575257v1_alt +chr22_KQ759762v1_fix +chrY_KN196487v1_fix +chr5_GL383530v1_alt +chr22_KI270877v1_alt +chr8_KZ559107v1_alt +chr13_KI270843v1_alt +chr22_KI270737v1_random +chr18_GL383568v1_alt +chr3_KZ559104v1_fix +chr11_KI270902v1_alt +chr17_KI270859v1_alt +chr11_KN196481v1_fix +chr3_KI270783v1_alt +chr12_KQ090023v1_alt +chr1_KI270760v1_alt +chr2_KI270768v1_alt +chr1_GL383519v1_alt +chr2_KI270771v1_alt +chr18_KI270864v1_alt +chr4_KI270787v1_alt +chrUn_KI270438v1 +chr17_KI270730v1_random +chr3_KI270781v1_alt +chr21_GL383581v2_alt +chr17_KZ559114v1_alt +chr20_KI270869v1_alt +chr7_GL383534v2_alt +chr12_KI270834v1_alt +chr4_KI270785v1_alt +chr2_KI270769v1_alt +chr12_GL383549v1_alt +chr1_KN196474v1_fix +chr19_KI270918v1_alt +chr13_KQ090025v1_alt +chr2_GL383522v1_alt +chr6_GL383533v1_alt +chr4_ML143348v1_fix +chr5_KI270793v1_alt +chr7_KI270807v1_alt +chr1_KI270708v1_random +chr20_GL383577v2_alt +chr5_KI270898v1_alt +chr5_KI270795v1_alt +chr8_KI270815v1_alt +chr2_KI270772v1_alt +chr17_GL383564v2_alt +chr8_KI270819v1_alt +chr9_KQ090019v1_alt +chr16_KI270854v1_alt +chr5_KZ208910v1_alt +chr2_KI270770v1_alt +chr8_KI270901v1_alt +chrUn_GL000214v1 +chr17_KI270907v1_alt +chr17_ML143374v1_fix +chr2_KI270775v1_alt +chrUn_KI270519v1 +chr12_GL383552v1_alt +chr5_KN196477v1_alt +chr6_KV766194v1_fix +chr1_KZ208905v1_alt +chr2_KZ208908v1_alt +chr11_KV766195v1_fix +chr1_KQ458382v1_alt +chr8_KI270814v1_alt +chr7_KV880764v1_fix +chr2_GL383521v1_alt +chr21_KI270873v1_alt +chrX_KI270881v1_alt +chr22_KQ759761v1_alt +chr8_KI270818v1_alt +chr19_KV575260v1_alt +chr2_ML143341v1_fix +chr13_KN538373v1_fix +chrUn_KI270750v1 +chrUn_KI270751v1 +chr22_KI270731v1_random +chr6_KI270799v1_alt +chr12_GL383553v2_alt +chr22_KN196486v1_alt +chr2_KI270716v1_random +chr12_KZ559112v1_alt +chr11_GL383547v1_alt +chr17_KV575245v1_fix +chr3_GL000221v1_random +chr19_KI270888v1_alt +chr19_GL383574v1_alt +chr22_KQ458387v1_alt +chr22_KN196485v1_alt +chr19_KV575258v1_alt +chr8_KV880766v1_fix +chr19_KI270884v1_alt +chr17_KI270910v1_alt +chrUn_KI270741v1 +chr18_KI270911v1_alt +chr7_KI270804v1_alt +chr7_KI270806v1_alt +chrUn_KI270749v1 +chr13_ML143364v1_fix +chr4_KI270788v1_alt +chr8_KI270817v1_alt +chr19_KV575251v1_alt +chr18_GL383572v1_alt +chr19_KV575255v1_alt +chrUn_GL000218v1 +chr2_KI270893v1_alt +chr2_KI270715v1_random +chr2_KI270767v1_alt +chrUn_GL000220v1 +chr1_KI270892v1_alt +chr3_KI270782v1_alt +chr22_GL383582v2_alt +chr3_KI270895v1_alt +chr9_GL383539v1_alt +chr18_KZ559116v1_alt +chr3_KI270934v1_alt +chr4_KQ090014v1_alt +chr9_KQ090018v1_alt +chr19_KV575246v1_alt +chr3_KZ559101v1_alt +chr3_KI270936v1_alt +chrUn_GL000213v1 +chr4_GL383527v1_alt +chr5_KI270794v1_alt +chr18_GL383570v1_alt +chr22_KI270734v1_random +chr8_KZ208914v1_fix +chr11_ML143357v1_fix +chr3_KI270937v1_alt +chr3_KQ031386v1_fix +chr1_KI270761v1_alt +chr1_KZ208904v1_alt +chr1_KN196473v1_fix +chr3_KI270924v1_alt +chr19_KV575253v1_alt +chr21_KI270874v1_alt +chr12_GL877875v1_alt +chr18_GL383569v1_alt +chr18_KI270863v1_alt +chr19_KV575248v1_alt +chr13_KQ090024v1_alt +chrUn_KI270744v1 +chr13_KI270841v1_alt +chr16_KQ031390v1_alt +chr12_GL383550v2_alt +chr19_KI270931v1_alt +chr19_KV575247v1_alt +chr19_GL383575v2_alt +chr19_KI270883v1_alt +chr19_KI270933v1_alt +chr19_KI270915v1_alt +chr19_KI270891v1_alt +chr19_KI270889v1_alt +chr19_KI270919v1_alt +chr11_ML143360v1_fix +chr19_KI270885v1_alt +chr19_KV575259v1_alt +chr9_GL383541v1_alt +chr14_KZ208919v1_alt +chr7_KZ559106v1_alt +chr5_KI270796v1_alt +chr14_KI270725v1_random +chr3_JH636055v2_alt +chr5_GL383531v1_alt +chr3_KI270777v1_alt +chr18_KI270912v1_alt +chr2_KI270776v1_alt +chr22_KQ458388v1_alt +chr12_KZ208918v1_alt +chr1_KI270706v1_random +chr6_KI270800v1_alt +chr3_KZ208909v1_alt +chr1_KI270712v1_random +chr22_KI270928v1_alt +chrUn_GL000216v2 +chr4_ML143347v1_fix +chr9_KI270719v1_random +chr11_KI270830v1_alt +chr19_GL000209v2_alt +chr19_KV575252v1_alt +chr17_KI270860v1_alt +chr5_KI270792v1_alt +chrUn_GL000219v1 +chr10_GL383545v1_alt +chrUn_GL000224v1 +chr22_KI270733v1_random +chr7_KQ031388v1_fix +chr13_KI270839v1_alt +chr3_GL383526v1_alt +chr14_KI270845v1_alt +chr11_KZ559111v1_alt +chr10_KI270824v1_alt +chr2_KZ208907v1_alt +chr22_KI270736v1_random +chr11_KQ090022v1_fix +chr1_GL383518v1_alt +chrUn_GL000195v1 +chr20_KI270870v1_alt +chr12_GL383551v1_alt +chr3_KI270784v1_alt +chr19_KI270890v1_alt +chr19_KI270916v1_alt +chr1_KI270765v1_alt +chr10_KQ090020v1_alt +chr17_GL000205v2_random +chr6_KB021644v2_alt +chr11_KI270826v1_alt +chr19_KI270929v1_alt +chr22_KI270878v1_alt +chr1_KN196472v1_fix +chrUn_KI270742v1 +chr19_KI270922v1_alt +chrX_KV766199v1_alt +chr19_GL383576v1_alt +chr10_KI270825v1_alt +chr19_KI270923v1_alt +chr7_KI270899v1_alt +chr19_KI270917v1_alt +chr11_JH159137v1_alt +chr14_GL000194v1_random +chr13_KI270840v1_alt +chr16_GL383556v1_alt +chr12_ML143362v1_fix +chr14_KI270722v1_random +chr3_KZ559105v1_alt +chr5_KI270791v1_alt +chr15_KI270906v1_alt +chr17_KI270861v1_alt +chr11_KQ759759v1_fix +chr3_KI270935v1_alt +chr6_KI270797v1_alt +chr3_KZ559102v1_alt +chr19_KI270920v1_alt +chr18_GL383571v1_alt +chrUn_KI270747v1 +chr19_KI270930v1_alt +chr11_JH159136v1_alt +chr21_GL383579v2_alt +chr14_GL000009v2_random +chr11_KN538368v1_alt +chr11_KI270829v1_alt +chr19_KI270886v1_alt +chr18_KQ458385v1_alt +chr19_KI270914v1_alt +chr3_KI270779v1_alt +chr4_KQ983258v1_alt +chr4_KI270789v1_alt +chr13_KN538371v1_fix +chr2_KN538362v1_fix +chr19_KI270887v1_alt +chr7_KI270809v1_alt +chr4_GL000008v2_random +chrY_KZ208924v1_fix +chr7_KI270805v1_alt +chr11_KI270832v1_alt +chrUn_KI270743v1 +chr14_GL000225v1_random +chr12_KN196482v1_fix +chr1_KQ458384v1_alt +chr2_KI270894v1_alt +chr11_KI270903v1_alt +chr3_ML143343v1_alt +chr19_KI270932v1_alt +chr11_ML143359v1_fix +chr11_KI270927v1_alt +chr4_KI270790v1_alt +chr19_KV575256v1_alt +chr2_KI270774v1_alt +chr17_GL383565v1_alt +chr3_KI270780v1_alt +chr5_GL949742v1_alt +chr8_KI270926v1_alt +chr4_KQ983257v1_fix +chr18_KZ559115v1_fix +chr16_KI270855v1_alt +chr19_KI270867v1_alt +chr4_ML143344v1_fix +chr17_KI270858v1_alt +chr4_KQ090015v1_alt +chr12_KI270835v1_alt +chr19_KV575250v1_alt +chr6_KZ208911v1_fix +chr4_KI270786v1_alt +chr15_KI270849v1_alt +chr6_KQ090016v1_fix +chr17_KV766197v1_alt +chr3_KI270778v1_alt +chr19_KI270882v1_alt +chr7_ML143352v1_fix +chr1_KI270766v1_alt +chr22_KI270875v1_alt +chr15_KI270851v1_alt +chr22_KI270876v1_alt +chr14_ML143368v1_alt +chr10_KQ090021v1_fix +chr8_KV880767v1_fix +chr16_KQ090027v1_alt +chr6_KN196478v1_fix +chr11_ML143358v1_fix +chr16_ML143373v1_fix +chr7_KI270808v1_alt +chr6_KI270798v1_alt +chrX_KI270913v1_alt +chr4_ML143349v1_fix +chr17_KV766198v1_alt +chr10_KN196480v1_fix +chr17_JH159146v1_alt +chr1_KQ983255v1_alt +chr11_KZ559109v1_fix +chr17_KI270729v1_random +chr17_KV766196v1_fix +chr19_KI270921v1_alt +chr8_KI270812v1_alt +chrX_KI270880v1_alt +chr18_GL383567v1_alt +chr8_KI270811v1_alt +chr10_ML143355v1_fix +chr19_KV575249v1_alt +chr15_GL383554v1_alt +chr11_KI270831v1_alt +chr12_ML143361v1_fix +chr8_KI270813v1_alt +chr11_KZ559110v1_alt +chr3_KZ559103v1_alt +chr22_KI270879v1_alt +chr11_KZ559108v1_fix +chr1_KN538361v1_fix +chr8_KI270816v1_alt +chr3_KN196476v1_fix +chr13_KI270838v1_alt +chr10_GL383546v1_alt +chr12_KQ759760v1_fix +chr8_KI270900v1_alt +chr6_KQ031387v1_fix +chr14_KI270844v1_alt +chr17_KI270909v1_alt +chr15_KI270848v1_alt +chr1_KZ208906v1_fix +chr9_KN196479v1_fix +chr4_ML143345v1_fix +chr1_KQ458383v1_alt +chr1_KI270762v1_alt +chr13_KN538372v1_fix +chr5_KV575243v1_alt +chr2_KN538363v1_fix +chr1_GL383520v2_alt +chr15_ML143370v1_fix +chr19_KN196484v1_fix +chr3_KQ031385v1_fix +chr8_KI270810v1_alt +chr17_GL383563v3_alt +chr4_GL383528v1_alt +chr4_KI270896v1_alt +chr19_GL383573v1_alt +chr15_GL383555v2_alt +chr17_KI270862v1_alt +chrUn_KI270442v1 +chr15_ML143372v1_fix +chr14_ML143367v1_fix +chrX_ML143381v1_fix +chr19_KQ458386v1_fix +chr18_KQ090028v1_fix +chr12_GL877876v1_alt +chr13_ML143366v1_fix +chr3_KV766192v1_fix +chr22_ML143380v1_fix +chr3_KN538364v1_fix +chr10_KN538367v1_fix +chr4_KV766193v1_alt +chr1_KI270759v1_alt +chr15_KI270850v1_alt +chr9_KI270823v1_alt +chr15_KI270727v1_random +chr3_KN196475v1_fix +chr10_ML143354v1_fix +chr1_KN538360v1_fix +chr22_ML143378v1_fix +chr1_KQ031383v1_fix +chr7_KV880765v1_fix +chr15_KI270852v1_alt +chr16_KZ559113v1_fix +chr2_KQ031384v1_fix +chr19_ML143376v1_fix +chr21_ML143377v1_fix +chr2_KQ983256v1_alt +chr12_KN538369v1_fix +chr1_KV880763v1_alt +chr4_KI270925v1_alt +chr12_KI270904v1_alt +chr4_GL000257v2_alt +chr7_KZ208912v1_fix +chr8_KI270822v1_alt +chr5_KV575244v1_fix +chr7_KZ208913v1_alt +chr14_KZ208920v1_fix +chr19_GL949747v2_alt +chr19_GL949753v2_alt +chr6_KI270801v1_alt +chr1_KI270763v1_alt +chr8_KI270821v1_alt +chr19_GL949752v1_alt +chr19_GL949746v1_alt +chr19_GL949751v2_alt +chr12_KZ208916v1_fix +chr19_GL949748v2_alt +chr19_GL949750v2_alt +chr19_KI270938v1_alt +chr19_GL949749v2_alt +chr7_KI270803v1_alt +chr5_KI270897v1_alt +chr14_KI270846v1_alt +chr17_KI270908v1_alt +chr14_KI270847v1_alt +chr5_GL339449v2_alt +chr17_GL000258v2_alt +chr16_KI270728v1_random +chr16_KV880768v1_fix +chr15_KQ031389v1_alt +chr16_KI270853v1_alt +chr17_KI270857v1_alt +chr6_GL000252v2_alt +chr6_GL000255v2_alt +chr6_GL000250v2_alt +chr6_GL000253v2_alt +chr6_GL000251v2_alt +chr6_GL000254v2_alt +chr6_GL000256v2_alt +chr15_KN538374v1_fix +chr15_KI270905v1_alt +chr15_ML143371v1_fix +chr8_KZ208915v1_fix +chr21 +chr22 +chrY +chr19 +chr20 +chr18 +chr17 +chr16 +chr15 +chr14 +chr13 +chr12 +chr10 +chr11 +chr9 +chr8 +chrX +chr7 +chr6 +chr5 +chr4 +chr3 +chr2 +chr1 +++ pwd ++ utrFa -nibPath=/hive/data/genomes/hg38/bed/gencodeV39/build/rnaStruct knownGeneV39 knownGene utr5 utr5/utr.fa +chrUn_KI270394v1 +chrUn_KI270392v1 +chrUn_KI270423v1 +chrUn_KI270385v1 +chrUn_KI270539v1 +chrUn_KI270312v1 +chrUn_KI270336v1 +chrUn_KI270419v1 +chrUn_KI270329v1 +chrUn_KI270379v1 +chrUn_KI270378v1 +chrUn_KI270335v1 +chrUn_KI270337v1 +chrUn_KI270376v1 +chrUn_KI270395v1 +chrUn_KI270412v1 +chrUn_KI270310v1 +chrUn_KI270544v1 +chrUn_KI270388v1 +chrUn_KI270466v1 +chrUn_KI270389v1 +chrUn_KI270516v1 +chrUn_KI270393v1 +chrUn_KI270429v1 +chrUn_KI270334v1 +chrUn_KI270583v1 +chrUn_KI270340v1 +chrUn_KI270338v1 +chrUn_KI270316v1 +chrUn_KI270422v1 +chrUn_KI270373v1 +chrUn_KI270305v1 +chrUn_KI270391v1 +chrUn_KI270387v1 +chrUn_KI270580v1 +chrUn_KI270548v1 +chrUn_KI270372v1 +chrUn_KI270330v1 +chrUn_KI270384v1 +chrUn_KI270383v1 +chrUn_KI270465v1 +chrUn_KI270386v1 +chrUn_KI270363v1 +chrUn_KI270396v1 +chrUn_KI270425v1 +chrUn_KI270529v1 +chrUn_KI270381v1 +chrUn_KI270303v1 +chrUn_KI270508v1 +chrUn_KI270417v1 +chrUn_KI270424v1 +chrUn_KI270418v1 +chrUn_KI270304v1 +chrUn_KI270530v1 +chrUn_KI270518v1 +chrUn_KI270302v1 +chrUn_KI270315v1 +chrUn_KI270509v1 +chrUn_KI270420v1 +chrUn_KI270375v1 +chrUn_KI270390v1 +chrUn_KI270510v1 +chrUn_KI270414v1 +chrUn_KI270411v1 +chrUn_KI270374v1 +chrUn_KI270333v1 +chrUn_KI270371v1 +chrUn_KI270364v1 +chrUn_KI270587v1 +chrUn_KI270528v1 +chrUn_KI270593v1 +chrUn_KI270517v1 +chrUn_KI270362v1 +chrUn_KI270467v1 +chrUn_KI270468v1 +chrUn_KI270382v1 +chrUn_KI270320v1 +chrUn_KI270584v1 +chrUn_KI270590v1 +chrUn_KI270507v1 +chrUn_KI270522v1 +chrUn_KI270591v1 +chrUn_KI270588v1 +chrUn_KI270515v1 +chrUn_KI270582v1 +chrUn_KI270581v1 +chr13_ML143363v1_fix +chrUn_KI270521v1 +chrUn_KI270448v1 +chrUn_KI270511v1 +chrUn_KI270366v1 +chr22_ML143379v1_fix +chrUn_KI270311v1 +chr10_KN538365v1_fix +chrX_ML143384v1_fix +chrUn_GL000226v1 +chrM +chrX_ML143385v1_fix +chrUn_KI270322v1 +chrUn_KI270512v1 +chr9_ML143353v1_fix +chrUn_KI270752v1 +chrX_ML143382v1_fix +chrUn_KI270579v1 +chr1_KI270707v1_random +chr13_KN196483v1_fix +chr8_KI270820v1_alt +chrUn_KI270755v1 +chrY_KI270740v1_random +chr13_KI270842v1_alt +chrUn_KI270317v1 +chr9_KI270718v1_random +chr14_KI270723v1_random +chr9_KI270720v1_random +chr14_KI270724v1_random +chr9_KI270717v1_random +chr12_KI270837v1_alt +chr1_KI270710v1_random +chrUn_KI270754v1 +chr1_KI270713v1_random +chr22_KI270732v1_random +chr1_KI270714v1_random +chrUn_KI270745v1 +chr1_KI270711v1_random +chr22_KI270735v1_random +chr19_KI270866v1_alt +chr14_KI270726v1_random +chrUn_KI270589v1 +chr1_KZ559100v1_fix +chr11_ML143356v1_fix +chrY_KZ208923v1_fix +chr1_KI270764v1_alt +chr19_KI270865v1_alt +chr4_ML143346v1_fix +chr12_KI270836v1_alt +chr17_ML143375v1_fix +chr20_KI270871v1_alt +chr16_KQ090026v1_alt +chr9_GL383542v1_alt +chr19_KI270868v1_alt +chrUn_KI270753v1 +chr21_GL383578v2_alt +chr16_KI270856v1_alt +chr12_KZ208917v1_fix +chr13_ML143365v1_fix +chrUn_KI270746v1 +chr1_KI270709v1_random +chr11_KI270827v1_alt +chrX_ML143383v1_fix +chr17_JH159147v1_alt +chr2_KI270773v1_alt +chrUn_KI270757v1 +chr9_GL383540v1_alt +chr6_ML143351v1_fix +chr22_KI270739v1_random +chr22_KB663609v1_alt +chr21_GL383580v2_alt +chr6_KI270802v1_alt +chr12_KI270833v1_alt +chr6_KI270758v1_alt +chr16_KZ208921v1_alt +chrUn_KI270756v1 +chr6_KQ090017v1_alt +chr21_KI270872v1_alt +chr5_GL383532v1_alt +chr2_ML143342v1_fix +chr10_KN538366v1_fix +chr12_KN538370v1_fix +chr17_JH159148v1_alt +chr16_GL383557v1_alt +chr5_ML143350v1_fix +chr17_GL383566v1_alt +chr4_KQ090013v1_alt +chrUn_KI270538v1 +chr5_GL000208v1_random +chrUn_KI270435v1 +chr18_KZ208922v1_fix +chrUn_KI270748v1 +chr2_GL582966v2_alt +chr22_GL383583v2_alt +chr15_ML143369v1_fix +chr22_KI270738v1_random +chr19_KV575254v1_alt +chr11_KI270721v1_random +chr19_KV575257v1_alt +chr22_KQ759762v1_fix +chrY_KN196487v1_fix +chr5_GL383530v1_alt +chr22_KI270877v1_alt +chr8_KZ559107v1_alt +chr13_KI270843v1_alt +chr22_KI270737v1_random +chr18_GL383568v1_alt +chr3_KZ559104v1_fix +chr11_KI270902v1_alt +chr17_KI270859v1_alt +chr11_KN196481v1_fix +chr3_KI270783v1_alt +chr12_KQ090023v1_alt +chr1_KI270760v1_alt +chr2_KI270768v1_alt +chr1_GL383519v1_alt +chr2_KI270771v1_alt +chr18_KI270864v1_alt +chr4_KI270787v1_alt +chrUn_KI270438v1 +chr17_KI270730v1_random +chr3_KI270781v1_alt +chr21_GL383581v2_alt +chr17_KZ559114v1_alt +chr20_KI270869v1_alt +chr7_GL383534v2_alt +chr12_KI270834v1_alt +chr4_KI270785v1_alt +chr2_KI270769v1_alt +chr12_GL383549v1_alt +chr1_KN196474v1_fix +chr19_KI270918v1_alt +chr13_KQ090025v1_alt +chr2_GL383522v1_alt +chr6_GL383533v1_alt +chr4_ML143348v1_fix +chr5_KI270793v1_alt +chr7_KI270807v1_alt +chr1_KI270708v1_random +chr20_GL383577v2_alt +chr5_KI270898v1_alt +chr5_KI270795v1_alt +chr8_KI270815v1_alt +chr2_KI270772v1_alt +chr17_GL383564v2_alt +chr8_KI270819v1_alt +chr9_KQ090019v1_alt +chr16_KI270854v1_alt +chr5_KZ208910v1_alt +chr2_KI270770v1_alt +chr8_KI270901v1_alt +chrUn_GL000214v1 +chr17_KI270907v1_alt +chr17_ML143374v1_fix +chr2_KI270775v1_alt +chrUn_KI270519v1 +chr12_GL383552v1_alt +chr5_KN196477v1_alt +chr6_KV766194v1_fix +chr1_KZ208905v1_alt +chr2_KZ208908v1_alt +chr11_KV766195v1_fix +chr1_KQ458382v1_alt +chr8_KI270814v1_alt +chr7_KV880764v1_fix +chr2_GL383521v1_alt +chr21_KI270873v1_alt +chrX_KI270881v1_alt +chr22_KQ759761v1_alt +chr8_KI270818v1_alt +chr19_KV575260v1_alt +chr2_ML143341v1_fix +chr13_KN538373v1_fix +chrUn_KI270750v1 +chrUn_KI270751v1 +chr22_KI270731v1_random +chr6_KI270799v1_alt +chr12_GL383553v2_alt +chr22_KN196486v1_alt +chr2_KI270716v1_random +chr12_KZ559112v1_alt +chr11_GL383547v1_alt +chr17_KV575245v1_fix +chr3_GL000221v1_random +chr19_KI270888v1_alt +chr19_GL383574v1_alt +chr22_KQ458387v1_alt +chr22_KN196485v1_alt +chr19_KV575258v1_alt +chr8_KV880766v1_fix +chr19_KI270884v1_alt +chr17_KI270910v1_alt +chrUn_KI270741v1 +chr18_KI270911v1_alt +chr7_KI270804v1_alt +chr7_KI270806v1_alt +chrUn_KI270749v1 +chr13_ML143364v1_fix +chr4_KI270788v1_alt +chr8_KI270817v1_alt +chr19_KV575251v1_alt +chr18_GL383572v1_alt +chr19_KV575255v1_alt +chrUn_GL000218v1 +chr2_KI270893v1_alt +chr2_KI270715v1_random +chr2_KI270767v1_alt +chrUn_GL000220v1 +chr1_KI270892v1_alt +chr3_KI270782v1_alt +chr22_GL383582v2_alt +chr3_KI270895v1_alt +chr9_GL383539v1_alt +chr18_KZ559116v1_alt +chr3_KI270934v1_alt +chr4_KQ090014v1_alt +chr9_KQ090018v1_alt +chr19_KV575246v1_alt +chr3_KZ559101v1_alt +chr3_KI270936v1_alt +chrUn_GL000213v1 +chr4_GL383527v1_alt +chr5_KI270794v1_alt +chr18_GL383570v1_alt +chr22_KI270734v1_random +chr8_KZ208914v1_fix +chr11_ML143357v1_fix +chr3_KI270937v1_alt +chr3_KQ031386v1_fix +chr1_KI270761v1_alt +chr1_KZ208904v1_alt +chr1_KN196473v1_fix +chr3_KI270924v1_alt +chr19_KV575253v1_alt +chr21_KI270874v1_alt +chr12_GL877875v1_alt +chr18_GL383569v1_alt +chr18_KI270863v1_alt +chr19_KV575248v1_alt +chr13_KQ090024v1_alt +chrUn_KI270744v1 +chr13_KI270841v1_alt +chr16_KQ031390v1_alt +chr12_GL383550v2_alt +chr19_KI270931v1_alt +chr19_KV575247v1_alt +chr19_GL383575v2_alt +chr19_KI270883v1_alt +chr19_KI270933v1_alt +chr19_KI270915v1_alt +chr19_KI270891v1_alt +chr19_KI270889v1_alt +chr19_KI270919v1_alt +chr11_ML143360v1_fix +chr19_KI270885v1_alt +chr19_KV575259v1_alt +chr9_GL383541v1_alt +chr14_KZ208919v1_alt +chr7_KZ559106v1_alt +chr5_KI270796v1_alt +chr14_KI270725v1_random +chr3_JH636055v2_alt +chr5_GL383531v1_alt +chr3_KI270777v1_alt +chr18_KI270912v1_alt +chr2_KI270776v1_alt +chr22_KQ458388v1_alt +chr12_KZ208918v1_alt +chr1_KI270706v1_random +chr6_KI270800v1_alt +chr3_KZ208909v1_alt +chr1_KI270712v1_random +chr22_KI270928v1_alt +chrUn_GL000216v2 +chr4_ML143347v1_fix +chr9_KI270719v1_random +chr11_KI270830v1_alt +chr19_GL000209v2_alt +chr19_KV575252v1_alt +chr17_KI270860v1_alt +chr5_KI270792v1_alt +chrUn_GL000219v1 +chr10_GL383545v1_alt +chrUn_GL000224v1 +chr22_KI270733v1_random +chr7_KQ031388v1_fix +chr13_KI270839v1_alt +chr3_GL383526v1_alt +chr14_KI270845v1_alt +chr11_KZ559111v1_alt +chr10_KI270824v1_alt +chr2_KZ208907v1_alt +chr22_KI270736v1_random +chr11_KQ090022v1_fix +chr1_GL383518v1_alt +chrUn_GL000195v1 +chr20_KI270870v1_alt +chr12_GL383551v1_alt +chr3_KI270784v1_alt +chr19_KI270890v1_alt +chr19_KI270916v1_alt +chr1_KI270765v1_alt +chr10_KQ090020v1_alt +chr17_GL000205v2_random +chr6_KB021644v2_alt +chr11_KI270826v1_alt +chr19_KI270929v1_alt +chr22_KI270878v1_alt +chr1_KN196472v1_fix +chrUn_KI270742v1 +chr19_KI270922v1_alt +chrX_KV766199v1_alt +chr19_GL383576v1_alt +chr10_KI270825v1_alt +chr19_KI270923v1_alt +chr7_KI270899v1_alt +chr19_KI270917v1_alt +chr11_JH159137v1_alt +chr14_GL000194v1_random +chr13_KI270840v1_alt +chr16_GL383556v1_alt +chr12_ML143362v1_fix +chr14_KI270722v1_random +chr3_KZ559105v1_alt +chr5_KI270791v1_alt +chr15_KI270906v1_alt +chr17_KI270861v1_alt +chr11_KQ759759v1_fix +chr3_KI270935v1_alt +chr6_KI270797v1_alt +chr3_KZ559102v1_alt +chr19_KI270920v1_alt +chr18_GL383571v1_alt +chrUn_KI270747v1 +chr19_KI270930v1_alt +chr11_JH159136v1_alt +chr21_GL383579v2_alt +chr14_GL000009v2_random +chr11_KN538368v1_alt +chr11_KI270829v1_alt +chr19_KI270886v1_alt +chr18_KQ458385v1_alt +chr19_KI270914v1_alt +chr3_KI270779v1_alt +chr4_KQ983258v1_alt +chr4_KI270789v1_alt +chr13_KN538371v1_fix +chr2_KN538362v1_fix +chr19_KI270887v1_alt +chr7_KI270809v1_alt +chr4_GL000008v2_random +chrY_KZ208924v1_fix +chr7_KI270805v1_alt +chr11_KI270832v1_alt +chrUn_KI270743v1 +chr14_GL000225v1_random +chr12_KN196482v1_fix +chr1_KQ458384v1_alt +chr2_KI270894v1_alt +chr11_KI270903v1_alt +chr3_ML143343v1_alt +chr19_KI270932v1_alt +chr11_ML143359v1_fix +chr11_KI270927v1_alt +chr4_KI270790v1_alt +chr19_KV575256v1_alt +chr2_KI270774v1_alt +chr17_GL383565v1_alt +chr3_KI270780v1_alt +chr5_GL949742v1_alt +chr8_KI270926v1_alt +chr4_KQ983257v1_fix +chr18_KZ559115v1_fix +chr16_KI270855v1_alt +chr19_KI270867v1_alt +chr4_ML143344v1_fix +chr17_KI270858v1_alt +chr4_KQ090015v1_alt +chr12_KI270835v1_alt +chr19_KV575250v1_alt +chr6_KZ208911v1_fix +chr4_KI270786v1_alt +chr15_KI270849v1_alt +chr6_KQ090016v1_fix +chr17_KV766197v1_alt +chr3_KI270778v1_alt +chr19_KI270882v1_alt +chr7_ML143352v1_fix +chr1_KI270766v1_alt +chr22_KI270875v1_alt +chr15_KI270851v1_alt +chr22_KI270876v1_alt +chr14_ML143368v1_alt +chr10_KQ090021v1_fix +chr8_KV880767v1_fix +chr16_KQ090027v1_alt +chr6_KN196478v1_fix +chr11_ML143358v1_fix +chr16_ML143373v1_fix +chr7_KI270808v1_alt +chr6_KI270798v1_alt +chrX_KI270913v1_alt +chr4_ML143349v1_fix +chr17_KV766198v1_alt +chr10_KN196480v1_fix +chr17_JH159146v1_alt +chr1_KQ983255v1_alt +chr11_KZ559109v1_fix +chr17_KI270729v1_random +chr17_KV766196v1_fix +chr19_KI270921v1_alt +chr8_KI270812v1_alt +chrX_KI270880v1_alt +chr18_GL383567v1_alt +chr8_KI270811v1_alt +chr10_ML143355v1_fix +chr19_KV575249v1_alt +chr15_GL383554v1_alt +chr11_KI270831v1_alt +chr12_ML143361v1_fix +chr8_KI270813v1_alt +chr11_KZ559110v1_alt +chr3_KZ559103v1_alt +chr22_KI270879v1_alt +chr11_KZ559108v1_fix +chr1_KN538361v1_fix +chr8_KI270816v1_alt +chr3_KN196476v1_fix +chr13_KI270838v1_alt +chr10_GL383546v1_alt +chr12_KQ759760v1_fix +chr8_KI270900v1_alt +chr6_KQ031387v1_fix +chr14_KI270844v1_alt +chr17_KI270909v1_alt +chr15_KI270848v1_alt +chr1_KZ208906v1_fix +chr9_KN196479v1_fix +chr4_ML143345v1_fix +chr1_KQ458383v1_alt +chr1_KI270762v1_alt +chr13_KN538372v1_fix +chr5_KV575243v1_alt +chr2_KN538363v1_fix +chr1_GL383520v2_alt +chr15_ML143370v1_fix +chr19_KN196484v1_fix +chr3_KQ031385v1_fix +chr8_KI270810v1_alt +chr17_GL383563v3_alt +chr4_GL383528v1_alt +chr4_KI270896v1_alt +chr19_GL383573v1_alt +chr15_GL383555v2_alt +chr17_KI270862v1_alt +chrUn_KI270442v1 +chr15_ML143372v1_fix +chr14_ML143367v1_fix +chrX_ML143381v1_fix +chr19_KQ458386v1_fix +chr18_KQ090028v1_fix +chr12_GL877876v1_alt +chr13_ML143366v1_fix +chr3_KV766192v1_fix +chr22_ML143380v1_fix +chr3_KN538364v1_fix +chr10_KN538367v1_fix +chr4_KV766193v1_alt +chr1_KI270759v1_alt +chr15_KI270850v1_alt +chr9_KI270823v1_alt +chr15_KI270727v1_random +chr3_KN196475v1_fix +chr10_ML143354v1_fix +chr1_KN538360v1_fix +chr22_ML143378v1_fix +chr1_KQ031383v1_fix +chr7_KV880765v1_fix +chr15_KI270852v1_alt +chr16_KZ559113v1_fix +chr2_KQ031384v1_fix +chr19_ML143376v1_fix +chr21_ML143377v1_fix +chr2_KQ983256v1_alt +chr12_KN538369v1_fix +chr1_KV880763v1_alt +chr4_KI270925v1_alt +chr12_KI270904v1_alt +chr4_GL000257v2_alt +chr7_KZ208912v1_fix +chr8_KI270822v1_alt +chr5_KV575244v1_fix +chr7_KZ208913v1_alt +chr14_KZ208920v1_fix +chr19_GL949747v2_alt +chr19_GL949753v2_alt +chr6_KI270801v1_alt +chr1_KI270763v1_alt +chr8_KI270821v1_alt +chr19_GL949752v1_alt +chr19_GL949746v1_alt +chr19_GL949751v2_alt +chr12_KZ208916v1_fix +chr19_GL949748v2_alt +chr19_GL949750v2_alt +chr19_KI270938v1_alt +chr19_GL949749v2_alt +chr7_KI270803v1_alt +chr5_KI270897v1_alt +chr14_KI270846v1_alt +chr17_KI270908v1_alt +chr14_KI270847v1_alt +chr5_GL339449v2_alt +chr17_GL000258v2_alt +chr16_KI270728v1_random +chr16_KV880768v1_fix +chr15_KQ031389v1_alt +chr16_KI270853v1_alt +chr17_KI270857v1_alt +chr6_GL000252v2_alt +chr6_GL000255v2_alt +chr6_GL000250v2_alt +chr6_GL000253v2_alt +chr6_GL000251v2_alt +chr6_GL000254v2_alt +chr6_GL000256v2_alt +chr15_KN538374v1_fix +chr15_KI270905v1_alt +chr15_ML143371v1_fix +chr8_KZ208915v1_fix +chr21 +chr22 +chrY +chr19 +chr20 +chr18 +chr17 +chr16 +chr15 +chr14 +chr13 +chr12 +chr10 +chr11 +chr9 +chr8 +chrX +chr7 +chr6 +chr5 +chr4 +chr3 +chr2 +chr1 ++ faSplit sequence utr3/utr.fa 10000 utr3/split/s ++ faSplit sequence utr5/utr.fa 10000 utr5/split/s ++ ls -1 utr3/split ++ ls -1 utr5/split ++ cd utr3 ++ cat ++ gensub2 in.lst single template jobList ++ cp template ../utr5 ++ cd ../utr5 ++ gensub2 in.lst single template jobList ++ ssh ku 'cd /hive/data/genomes/hg38/bed/gencodeV39/build/rnaStruct/utr3; para make jobList' +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +Checking input files +9707 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/rnaStruct/utr3/batch +9707 jobs in batch +10381 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 9707 +================ +Checking job status 0 minutes after launch +9707 jobs in batch +20088 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +9707 jobs in batch +20088 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +9707 jobs in batch +19635 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +9707 jobs in batch +19376 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +9707 jobs in batch +18763 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +9707 jobs in batch +18250 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 7 minutes after launch +9707 jobs in batch +17593 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 9 minutes after launch +9707 jobs in batch +16851 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 11 minutes after launch +9707 jobs in batch +15905 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 14 minutes after launch +9707 jobs in batch +14798 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 17 minutes after launch +9707 jobs in batch +13699 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 20 minutes after launch +9707 jobs in batch +12447 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 23 minutes after launch +9707 jobs in batch +11982 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 26 minutes after launch +9707 jobs in batch +10539 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 30 minutes after launch +9707 jobs in batch +8862 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 34 minutes after launch +9707 jobs in batch +6929 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 38 minutes after launch +9707 jobs in batch +5866 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 43 minutes after launch +9707 jobs in batch +3866 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 48 minutes after launch +9707 jobs in batch +11434 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 53 minutes after launch +9707 jobs in batch +9779 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 58 minutes after launch +9707 jobs in batch +7433 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 63 minutes after launch +9707 jobs in batch +5747 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 68 minutes after launch +9707 jobs in batch +4274 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 73 minutes after launch +9707 jobs in batch +1328 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 78 minutes after launch +9707 jobs in batch +141 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 83 minutes after launch +9707 jobs in batch +157 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 88 minutes after launch +9707 jobs in batch +388 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 93 minutes after launch +9707 jobs in batch +25 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 98 minutes after launch +9707 jobs in batch +184 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 103 minutes after launch +9707 jobs in batch +20 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 108 minutes after launch +9707 jobs in batch +17 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 113 minutes after launch +9707 jobs in batch +12 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 118 minutes after launch +9707 jobs in batch +10 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 123 minutes after launch +9707 jobs in batch +8 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 128 minutes after launch +9707 jobs in batch +6 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 133 minutes after launch +9707 jobs in batch +4 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 138 minutes after launch +9707 jobs in batch +3 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 143 minutes after launch +9707 jobs in batch +3 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 148 minutes after launch +9707 jobs in batch +2 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 153 minutes after launch +9707 jobs in batch +1 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 158 minutes after launch +9707 jobs in batch +1 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 163 minutes after launch +9707 jobs in batch +1 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 168 minutes after launch +9707 jobs in batch +1 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 173 minutes after launch +9707 jobs in batch +33 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 178 minutes after launch +9707 jobs in batch +33 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 183 minutes after launch +9707 jobs in batch +33 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 188 minutes after launch +9707 jobs in batch +33 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 193 minutes after launch +9707 jobs in batch +33 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 198 minutes after launch +9707 jobs in batch +33 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 203 minutes after launch +9707 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! ++ ssh ku 'cd /hive/data/genomes/hg38/bed/gencodeV39/build/rnaStruct/utr5; para make jobList' +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +Checking input files +8994 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/rnaStruct/utr5/batch +8994 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 8994 +================ +Checking job status 0 minutes after launch +8994 jobs in batch +9026 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +8994 jobs in batch +8921 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +8994 jobs in batch +8438 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +8994 jobs in batch +7771 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +8994 jobs in batch +6966 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +8994 jobs in batch +5974 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 7 minutes after launch +8994 jobs in batch +4849 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 9 minutes after launch +8994 jobs in batch +3498 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 11 minutes after launch +8994 jobs in batch +2044 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 14 minutes after launch +8994 jobs in batch +197 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 17 minutes after launch +8994 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! ++ ssh ku 'cd /hive/data/genomes/hg38/bed/gencodeV39/build/rnaStruct/utr3; para time' +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +9707 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 9707 of 9707 jobs +CPU time in finished jobs: 1602568s 26709.47m 445.16h 18.55d 0.051 y +IO & Wait Time: 111029s 1850.48m 30.84h 1.29d 0.004 y +Average job time: 177s 2.94m 0.05h 0.00d +Longest finished job: 11486s 191.43m 3.19h 0.13d +Submission to last job: 12120s 202.00m 3.37h 0.14d +Estimated complete: 0s 0.00m 0.00h 0.00d ++ ssh ku 'cd /hive/data/genomes/hg38/bed/gencodeV39/build/rnaStruct/utr5; para time' +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +8994 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +Completed: 8994 of 8994 jobs +CPU time in finished jobs: 24376s 406.26m 6.77h 0.28d 0.001 y +IO & Wait Time: 314375s 5239.59m 87.33h 3.64d 0.010 y +Average job time: 38s 0.63m 0.01h 0.00d +Longest finished job: 287s 4.78m 0.08h 0.00d +Submission to last job: 921s 15.35m 0.26h 0.01d +Estimated complete: 0s 0.00m 0.00h 0.00d ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build/rnaStruct/utr5 ++ hgLoadRnaFold knownGeneV39 foldUtr5 fold +Parsed 94478 files ++ cd ../utr3 ++ hgLoadRnaFold -warnEmpty knownGeneV39 foldUtr3 fold +ENST00000262160.11 is empty, skipping + +ENST00000519966.5 is empty, skipping + +Parsed 91084 files ++ rm -r split fold err batch.bak ++ cd ../utr5 ++ rm -r split fold err batch.bak ++ echo 'BuildFoldUtr successfully finished' +BuildFoldUtr successfully finished +==== doKnown.log ==== ++ source ./buildEnv.sh +++ export db=hg38 +++ db=hg38 +++ export GENCODE_VERSION=V39 +++ GENCODE_VERSION=V39 +++ export PREV_GENCODE_VERSION=V38 +++ PREV_GENCODE_VERSION=V38 +++ export dir=/hive/data/genomes/hg38/bed/gencodeV39/build +++ dir=/hive/data/genomes/hg38/bed/gencodeV39/build +++ export genomes=/hive/data/genomes +++ genomes=/hive/data/genomes +++ export tempDb=knownGeneV39 +++ tempDb=knownGeneV39 +++ export oldKnownDb=knownGeneV38 +++ oldKnownDb=knownGeneV38 +++ export oldDb=hg38 +++ oldDb=hg38 +++ export kent=/cluster/home/braney/kent +++ kent=/cluster/home/braney/kent +++ export spDb=sp180404 +++ spDb=sp180404 +++ export cpuFarm=ku +++ cpuFarm=ku +++ export oldGeneDir=/cluster/data/hg38/bed/gencodeV38/build +++ oldGeneDir=/cluster/data/hg38/bed/gencodeV38/build +++ export oldGeneBed=/cluster/data/hg38/bed/gencodeV38/build/ucscGenes.bed +++ oldGeneBed=/cluster/data/hg38/bed/gencodeV38/build/ucscGenes.bed +++ export Db=Hg38 +++ Db=Hg38 +++ export xdb=mm39 +++ xdb=mm39 +++ export Xdb=Mm39 +++ Xdb=Mm39 +++ export ydb=canFam4 +++ ydb=canFam4 +++ export zdb=rheMac8 +++ zdb=rheMac8 +++ export ratDb=rn6 +++ ratDb=rn6 +++ export RatDb=Rn6 +++ RatDb=Rn6 +++ export fishDb=danRer11 +++ fishDb=danRer11 +++ export flyDb=dm6 +++ flyDb=dm6 +++ export wormDb=ce11 +++ wormDb=ce11 +++ export yeastDb=sacCer3 +++ yeastDb=sacCer3 +++ export tempFa=/hive/data/genomes/hg38/bed/gencodeV39/build/ucscGenes.faa +++ tempFa=/hive/data/genomes/hg38/bed/gencodeV39/build/ucscGenes.faa +++ export genomes=/hive/data/genomes +++ genomes=/hive/data/genomes +++ export xdbFa=/hive/data/genomes/mm39/bed/gencodeVM27/build/ucscGenes.faa +++ xdbFa=/hive/data/genomes/mm39/bed/gencodeVM27/build/ucscGenes.faa +++ export ratFa=/hive/data/genomes/rn6/bed/ensGene.95/ensembl.faa +++ ratFa=/hive/data/genomes/rn6/bed/ensGene.95/ensembl.faa +++ export fishFa=/hive/data/genomes/danRer11/bed/ensGene.95/ensembl.faa +++ fishFa=/hive/data/genomes/danRer11/bed/ensGene.95/ensembl.faa +++ export flyFa=/hive/data/genomes/dm6/bed/ensGene.95/ensembl.faa +++ flyFa=/hive/data/genomes/dm6/bed/ensGene.95/ensembl.faa +++ export wormFa=/hive/data/genomes/ce11/bed/ws245Genes/ws245Pep.faa +++ wormFa=/hive/data/genomes/ce11/bed/ws245Genes/ws245Pep.faa +++ export yeastFa=/hive/data/genomes/sacCer3/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa +++ yeastFa=/hive/data/genomes/sacCer3/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa +++ export scratchDir=/hive/users/braney/scratch +++ scratchDir=/hive/users/braney/scratch +++ export blastTab=hgBlastTab +++ blastTab=hgBlastTab +++ export xBlastTab=mmBlastTab +++ xBlastTab=mmBlastTab +++ export rnBlastTab=rnBlastTab +++ rnBlastTab=rnBlastTab +++ export dbHost=hgwdev +++ dbHost=hgwdev +++ export ramFarm=ku +++ ramFarm=ku +++ export cpuFarm=ku +++ cpuFarm=ku +++ export bioCycDir=/hive/data/outside/bioCyc/210823/humancyc/23.0/data +++ bioCycDir=/hive/data/outside/bioCyc/210823/humancyc/23.0/data +++ export multizDir=/cluster/data/hg38/bed/multiz100way +++ multizDir=/cluster/data/hg38/bed/multiz100way +++ export mz=multiz100way +++ mz=multiz100way +++ export gnfU133TableLookup=knownToU133 +++ gnfU133TableLookup=knownToU133 +++ export 'gnfU95TablesFixed=hgFixed.gnfHumanU95MedianRatio hgFixed.gnfHumanU95Exps' +++ gnfU95TablesFixed='hgFixed.gnfHumanU95MedianRatio hgFixed.gnfHumanU95Exps' +++ export gnfU95TableLookup=knownToU95 +++ gnfU95TableLookup=knownToU95 +++ export 'gnfAtlasTablesFixed=hgFixed.gnfHumanAtlas2MedianRatio hgFixed.gnfHumanAtlas2MedianExps' +++ gnfAtlasTablesFixed='hgFixed.gnfHumanAtlas2MedianRatio hgFixed.gnfHumanAtlas2MedianExps' +++ export gnfAtlasTableLookup=knownToGnfAtlas2 +++ gnfAtlasTableLookup=knownToGnfAtlas2 +++ export hprd_website=http://www.hprd.org/edownload/ +++ hprd_website=http://www.hprd.org/edownload/ +++ export hprd_tar=HPRD_FLAT_FILES_041310 +++ hprd_tar=HPRD_FLAT_FILES_041310 +++ export hprd_file=FLAT_FILES_072010/HPRD_ID_MAPPINGS.txt +++ hprd_file=FLAT_FILES_072010/HPRD_ID_MAPPINGS.txt ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build ++ buildCore.sh +++ hgsql hgFixed -Ne 'select releaseNotes from knownId where releaseNotes='\''hg38 V39'\''' ++ version= ++ test '' '!=' '' ++ hgsql -e 'select * from wgEncodeGencodeCompV39' --skip-column-names hg38 ++ cut -f 2-16 ++ genePredToBed stdin tmp ++ hgsql -e 'select * from wgEncodeGencodePseudoGeneV39' --skip-column-names hg38 ++ cut -f 2-16 ++ genePredToBed stdin tmp2 ++ sort -k1,1 -k2,2n tmp tmp2 ++ gzip -c ++ rm tmp tmp2 +++ hgsql hgFixed -Ne 'select end+1 from knownId where end = (select maX(end) from knownId)' ++ lastEndId=5542772 ++ test '' == '' ++ zcat gencodeV39.bed.gz ++ awk '{print $4}' ++ sort ++ hgsql hg38 -Ne 'select name,alignId from knownGene' ++ sort ++ kgAllocId EnstToUC.txt newGencodeName.txt 5542772 stdout ++ sort -u +++ awk '{print $2}' out.txt ++ newEndId=5551768 ++ touch oldToNew.tab ++ rm EnstToUC.txt newGencodeName.txt out.txt ++ hgsql hgFixed -Ne 'insert into knownId values (5542772, 5551768, "hg38 V39")' ++ zcat gencodeV39.bed.gz ++ hgsql '' ++ echo 'create database knownGeneV39' ++ makeGencodeKnownGene -justKnown hg38 knownGeneV39 V39 txToAcc.tab ++ hgsql hg38 -Ne 'create view knownGeneV39.chromInfo as select * from chromInfo' ++ hgsql hg38 -Ne 'create view knownGeneV39.trackDb as select * from trackDb' ++ hgLoadSqlTab -notOnServer knownGeneV39 knownGene /cluster/home/braney/kent/src/hg/lib/knownGene.sql knownGene.gp +Scanning through 1 files ++ hgLoadGenePred -genePredExt knownGeneV39 knownGeneExt knownGeneExt.gp ++ hgMapToGene -geneTableType=genePred -type=psl -all -tempDb=knownGeneV39 hg38 all_mrna knownGene knownToMrna ++ hgMapToGene -geneTableType=genePred -tempDb=knownGeneV39 hg38 refGene knownGene knownToRefSeq ++ hgMapToGene -geneTableType=genePred -type=psl -tempDb=knownGeneV39 hg38 all_mrna knownGene knownToMrnaSingle ++ makeGencodeKnownGene hg38 knownGeneV39 V39 txToAcc.tab ++ hgLoadSqlTab -notOnServer knownGeneV39 kgXref /cluster/home/braney/kent/src/hg/lib/kgXref.sql kgXref.tab +Scanning through 1 files ++ hgLoadSqlTab -notOnServer knownGeneV39 knownCanonical /cluster/home/braney/kent/src/hg/lib/knownCanonical.sql knownCanonical.tab +Scanning through 1 files ++ sort knownIsoforms.tab ++ uniq ++ hgLoadSqlTab -notOnServer knownGeneV39 knownIsoforms /cluster/home/braney/kent/src/hg/lib/knownIsoforms.sql stdin +Scanning through 1 files ++ cat ++ tawk '{print $5,$13}' ++ hgsql hg38 -Ne 'select * from wgEncodeGencodeAttrsV39' ++ sed -f colors.sed ++ hgLoadSqlTab -notOnServer knownGeneV39 kgColor /cluster/home/braney/kent/src/hg/lib/kgColor.sql colors.txt +Scanning through 1 files ++ genePredToProt knownGeneExt.gp /cluster/data/hg38/hg38.2bit tmp.faa ++ faFilter -uniq tmp.faa ucscGenes.faa ++ hgPepPred knownGeneV39 generic knownGenePep ucscGenes.faa +Processing ucscGenes.faa ++ twoBitToFa -noMask /cluster/data/hg38/hg38.2bit -bed=ucscGenes.bed stdout ++ faFilter -uniq stdin ucscGenes.fa ++ hgPepPred knownGeneV39 generic knownGeneMrna ucscGenes.fa +Processing ucscGenes.fa ++ hgsql -e 'select * from wgEncodeGencodeCompV39' --skip-column-names hg38 ++ cut -f 2-16 ++ tawk '{print $1,$13,$14,$8,$15}' ++ sort ++ uniq ++ hgLoadSqlTab -notOnServer knownGeneV39 knownCds /cluster/home/braney/kent/src/hg/lib/knownCds.sql knownCds.tab +Scanning through 1 files ++ hgsql -e 'select * from wgEncodeGencodeTagV39' --skip-column-names hg38 ++ sort ++ uniq ++ hgLoadSqlTab -notOnServer knownGeneV39 knownToTag /cluster/home/braney/kent/src/hg/lib/knownTo.sql knownToTag.tab +Scanning through 1 files ++ sort ++ hgsql knownGeneV39 -Ne 'select k.name, g.geneId, g.geneStatus, g.geneType,g.transcriptName,g.transcriptType,g.transcriptStatus, g.havanaGeneId, g.ccdsId, g.level, g.transcriptClass from knownGene k, hg38.wgEncodeGencodeAttrsV39 g where k.name=g.transcriptId' ++ uniq ++ hgLoadSqlTab -notOnServer knownGeneV39 knownAttrs /cluster/home/braney/kent/src/hg/lib/knownAttrs.sql knownAttrs.tab +Scanning through 1 files ++ hgsql knownGeneV39 -e 'select * from knownToMrna' ++ tail -n +2 ++ tawk '{if ($1 != last) {print last, count, buffer; count=1; buffer=$2} else {count++;buffer=$2","buffer} last=$1}' ++ tail -n +2 ++ sort ++ hgsql knownGeneV39 -e 'select * from knownToMrnaSingle' ++ tail -n +2 ++ sort ++ join tmp2 tmp1 ++ txGeneAlias hg38 sp180404 kgXref.tab knownGene.ev oldToNew.tab foo.alias foo.protAlias ++ tawk '{split($2,a,"."); for(ii = 1; ii <= a[2]; ii++) print $1,a[1] "." ii }' txToAcc.tab ++ tawk '{split($1,a,"."); for(ii = 1; ii <= a[2] - 1; ii++) print $1,a[1] "." ii }' txToAcc.tab ++ sort foo.alias ++ uniq ++ sort foo.protAlias ++ uniq ++ rm foo.alias foo.protAlias ++ hgLoadSqlTab -notOnServer knownGeneV39 kgAlias /cluster/home/braney/kent/src/hg/lib/kgAlias.sql ucscGenes.alias +Scanning through 1 files ++ hgLoadSqlTab -notOnServer knownGeneV39 kgProtAlias /cluster/home/braney/kent/src/hg/lib/kgProtAlias.sql ucscGenes.protAlias +Scanning through 1 files ++ hgsql knownGeneV39 -N -e 'select kgXref.kgID, spID, alias from kgXref, kgAlias where kgXref.kgID=kgAlias.kgID' ++ hgsql knownGeneV39 -N -e 'select kgXref.kgID, spID, alias from kgXref, kgProtAlias where kgXref.kgID=kgProtAlias.kgID' ++ cat kgSpAlias_0.tmp ++ sort -u ++ rm kgSpAlias_0.tmp ++ hgLoadSqlTab -notOnServer knownGeneV39 kgSpAlias /cluster/home/braney/kent/src/hg/lib/kgSpAlias.sql kgSpAlias.tab +Scanning through 1 files ++ txBedToGraph ucscGenes.bed ucscGenes ucscGenes.txg ++ txgAnalyze ucscGenes.txg /hive/data/genomes/hg38/hg38.2bit stdout ++ sort ++ uniq ++ bedClip stdin /cluster/data/hg38/chrom.sizes ucscSplice.bed ++ hgLoadBed knownGeneV39 knownAlt ucscSplice.bed +Reading ucscSplice.bed +Read 308278 elements of size 6 from ucscSplice.bed +Sorted +Creating table definition for knownAlt, bedSize: 6 +Saving bed.tab +Loading knownGeneV39 ++ txGeneExplainUpdate2 /cluster/data/hg38/bed/gencodeV38/build/ucscGenes.bed ucscGenes.bed kgOldToNew.tab ++ hgLoadSqlTab -notOnServer knownGeneV39 kgV38ToKgV39 /cluster/home/braney/kent/src/hg/lib/kg1ToKg2.sql kgOldToNew.tab +Scanning through 1 files ++ hgsql knownGeneV39 -Ne 'select kgId, geneSymbol, spID from kgXref' ++ genePredToBigGenePred -colors=colors.txt -geneNames=geneNames.txt -known -cds=knownCds.tab knownGene.gp stdout ++ sort -k1,1 -k2,2n ++ tawk '{print $4,$0}' gencodeAnnotV39.bgpInput ++ sort ++ hgsql hg38 -Ne 'select transcriptId, transcriptClass from wgEncodeGencodeAttrsV39' ++ sed s/problem/nonCoding/ ++ sort ++ join -t ' ' join1 attrs.txt ++ hgsql hg38 -Ne 'select transcriptId, source from wgEncodeGencodeTranscriptSourceV39' ++ sort ++ join -t ' ' join2 source.txt ++ hgsql hg38 -Ne 'select transcriptId, transcriptType from wgEncodeGencodeAttrsV39' ++ sort ++ join -t ' ' join3 biotype.txt ++ hgsql hg38 -Ne 'select transcriptId, tag from wgEncodeGencodeTagV39' ++ sort ++ tawk '{if ($1 != last) {print last,buff; buff=$2}else {buff=buff "," $2} last=$1} END {print last,buff}' ++ tail -n +2 ++ join -t ' ' -a 1 -enone -o auto join4 tags.txt ++ hgsql hg38 -Ne 'select transcriptId, level from wgEncodeGencodeAttrsV39' ++ sort ++ join -t ' ' join5 level.txt ++ grep basic tags.txt ++ tawk '{print $1, 1, "basic"}' ++ tawk '{print $5,0,"canonical"}' knownCanonical.tab ++ sort ++ tawk '{print $4,2,"all"}' gencodeAnnotV39.bgpInput ++ sort ++ sort -k1,1 -k2,2n basic.txt canonical.txt all.txt ++ tawk '{if ($1 != last) {print last,buff; buff=$3}else {buff=buff "," $3} last=$1} END {print last,buff}' ++ tail -n +2 ++ join -t ' ' join6 tier.txt ++ cut -f 2- -d ' ' join7 ++ sort -k1,1 -k2,2n ++ bedToBigBed -extraIndex=name -type=bed12+16 -tab -as=/cluster/home/braney/kent/src/hg/lib/gencodeBGP.as bgpInput.txt /cluster/data/hg38/chrom.sizes hg38.gencodeV39.bb +pass1 - making usageList (439 chroms): 196 millis +pass2 - checking and writing primary data (266064 records, 26 fields): 3729 millis +Sorting and writing extra index 0: 131 millis ++ rm -f /gbdb/hg38/gencode/gencodeV39.bb +++ pwd ++ ln -s /hive/data/genomes/hg38/bed/gencodeV39/build/hg38.gencodeV39.bb /gbdb/hg38/gencode/gencodeV39.bb ++ hgKgGetText knownGeneV39 stdout ++ sort +171018 hgFixed.refSeqSummary elements +Read in 265891 known genes from knownGeneV39 ++ tawk '{split($2,a,"."); printf "%s\t", $1;for(ii = 1; ii <= a[2]; ii++) printf "%s ",a[1] "." ii; printf "\n" }' txToAcc.tab ++ sort ++ join tempSearch2.txt tempSearch3.txt ++ sort ++ rm tempSearch2.txt tempSearch3.txt ++ ixIxx knownGene.txt knownGeneV39.ix knownGeneV39.ixx +309 words were longer than limit 31 length and were ignored. Run with -verbose=2 to see them. +The longest failed word length was 63. ++ rm -rf /gbdb/hg38/knownGene.ix /gbdb/hg38/knownGene.ixx +++ pwd ++ ln -s /hive/data/genomes/hg38/bed/gencodeV39/build/knownGeneV39.ix /gbdb/hg38/knownGene.ix +++ pwd ++ ln -s /hive/data/genomes/hg38/bed/gencodeV39/build/knownGeneV39.ixx /gbdb/hg38/knownGene.ixx ++ tawk '{print $5}' knownCanonical.tab ++ sort ++ tawk '$11 == "pseudo" {print $1}' knownAttrs.tab ++ sort ++ join knownCanonicalId.txt knownGene.txt ++ join -v 1 /dev/stdin pseudo.txt ++ ixIxx knownGeneFast.txt knownGeneFastV39.ix knownGeneFastV39.ixx +292 words were longer than limit 31 length and were ignored. Run with -verbose=2 to see them. +The longest failed word length was 63. ++ rm -rf /gbdb/hg38/knownGeneFastV39.ix /gbdb/hg38/knownGeneFastV39.ixx ++ ln -s /hive/data/genomes/hg38/bed/gencodeV39/build/knownGeneFastV39.ix /gbdb/hg38/knownGeneFastV39.ix ++ ln -s /hive/data/genomes/hg38/bed/gencodeV39/build/knownGeneFastV39.ixx /gbdb/hg38/knownGeneFastV39.ixx ++ bedToPsl /cluster/data/hg38/chrom.sizes ucscGenes.bed ucscGenes.psl ++ pslRecalcMatch ucscGenes.psl /cluster/data/hg38/hg38.2bit ucscGenes.fa kgTargetAli.psl ++ hgLoadPsl knownGeneV39 kgTargetAli.psl +Processing kgTargetAli.psl ++ hgsql knownGeneV39 -N -e 'select spDisplayID,kgID from kgXref where spDisplayID != '\'''\''' ++ hgLoadSqlTab knownGeneV39 spMrna /cluster/home/braney/kent/src/hg/lib/spMrna.sql spMrna.tab +Scanning through 1 files ++ hgsql knownGeneV39 -N -e 'select kgId,geneSymbol from kgXref' ++ perl -wpe 's/^(\S+)\t(\S+)/$1\t${1}__$2/ || die;' ++ sort -u ++ awk '{if (!found[$4]) print; found[$4]=1 }' ucscGenes.bed ++ subColumn 4 nodups.bed idSub.txt ucscGenesIdSubbed.bed ++ sequenceForBed -keepName -db=hg38 -bedIn=ucscGenesIdSubbed.bed -fastaOut=stdout ++ faToTwoBit stdin hg38KgSeqV39.2bit +Reading beds. +Writing sequences. +................... +Done. + ++ mkdir -p /gbdb/hg38/targetDb/ ++ rm -f /gbdb/hg38/targetDb/hg38KgSeqV39.2bit ++ ln -s /hive/data/genomes/hg38/bed/gencodeV39/build/hg38KgSeqV39.2bit /gbdb/hg38/targetDb/ ++ echo 'BuildCore successfully finished' +BuildCore successfully finished ++ buildBlast.sh ++ buildBioCyc.sh ++ buildFoldUtr.sh ++ wait ++ buildPfamScop.sh ++ buildTo.sh ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build ++ hgsql knownGeneV39 -Ne 'drop view trackDb' ++ hgsql knownGeneV39 -Ne 'drop view chromInfo' ++ echo 'BuildKnown successfully finished' +BuildKnown successfully finished +==== doKnownTo.log ==== ++ . ./buildEnv.sh +++ export db=hg38 +++ db=hg38 +++ export GENCODE_VERSION=V39 +++ GENCODE_VERSION=V39 +++ export PREV_GENCODE_VERSION=V38 +++ PREV_GENCODE_VERSION=V38 +++ export dir=/hive/data/genomes/hg38/bed/gencodeV39/build +++ dir=/hive/data/genomes/hg38/bed/gencodeV39/build +++ export genomes=/hive/data/genomes +++ genomes=/hive/data/genomes +++ export tempDb=knownGeneV39 +++ tempDb=knownGeneV39 +++ export oldKnownDb=knownGeneV38 +++ oldKnownDb=knownGeneV38 +++ export oldDb=hg38 +++ oldDb=hg38 +++ export kent=/cluster/home/braney/kent +++ kent=/cluster/home/braney/kent +++ export spDb=sp180404 +++ spDb=sp180404 +++ export cpuFarm=ku +++ cpuFarm=ku +++ export oldGeneDir=/cluster/data/hg38/bed/gencodeV38/build +++ oldGeneDir=/cluster/data/hg38/bed/gencodeV38/build +++ export oldGeneBed=/cluster/data/hg38/bed/gencodeV38/build/ucscGenes.bed +++ oldGeneBed=/cluster/data/hg38/bed/gencodeV38/build/ucscGenes.bed +++ export Db=Hg38 +++ Db=Hg38 +++ export xdb=mm39 +++ xdb=mm39 +++ export Xdb=Mm39 +++ Xdb=Mm39 +++ export ydb=canFam4 +++ ydb=canFam4 +++ export zdb=rheMac8 +++ zdb=rheMac8 +++ export ratDb=rn6 +++ ratDb=rn6 +++ export RatDb=Rn6 +++ RatDb=Rn6 +++ export fishDb=danRer11 +++ fishDb=danRer11 +++ export flyDb=dm6 +++ flyDb=dm6 +++ export wormDb=ce11 +++ wormDb=ce11 +++ export yeastDb=sacCer3 +++ yeastDb=sacCer3 +++ export tempFa=/hive/data/genomes/hg38/bed/gencodeV39/build/ucscGenes.faa +++ tempFa=/hive/data/genomes/hg38/bed/gencodeV39/build/ucscGenes.faa +++ export genomes=/hive/data/genomes +++ genomes=/hive/data/genomes +++ export xdbFa=/hive/data/genomes/mm39/bed/gencodeVM27/build/ucscGenes.faa +++ xdbFa=/hive/data/genomes/mm39/bed/gencodeVM27/build/ucscGenes.faa +++ export ratFa=/hive/data/genomes/rn6/bed/ensGene.95/ensembl.faa +++ ratFa=/hive/data/genomes/rn6/bed/ensGene.95/ensembl.faa +++ export fishFa=/hive/data/genomes/danRer11/bed/ensGene.95/ensembl.faa +++ fishFa=/hive/data/genomes/danRer11/bed/ensGene.95/ensembl.faa +++ export flyFa=/hive/data/genomes/dm6/bed/ensGene.95/ensembl.faa +++ flyFa=/hive/data/genomes/dm6/bed/ensGene.95/ensembl.faa +++ export wormFa=/hive/data/genomes/ce11/bed/ws245Genes/ws245Pep.faa +++ wormFa=/hive/data/genomes/ce11/bed/ws245Genes/ws245Pep.faa +++ export yeastFa=/hive/data/genomes/sacCer3/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa +++ yeastFa=/hive/data/genomes/sacCer3/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa +++ export scratchDir=/hive/users/braney/scratch +++ scratchDir=/hive/users/braney/scratch +++ export blastTab=hgBlastTab +++ blastTab=hgBlastTab +++ export xBlastTab=mmBlastTab +++ xBlastTab=mmBlastTab +++ export rnBlastTab=rnBlastTab +++ rnBlastTab=rnBlastTab +++ export dbHost=hgwdev +++ dbHost=hgwdev +++ export ramFarm=ku +++ ramFarm=ku +++ export cpuFarm=ku +++ cpuFarm=ku +++ export bioCycDir=/hive/data/outside/bioCyc/210823/humancyc/23.0/data +++ bioCycDir=/hive/data/outside/bioCyc/210823/humancyc/23.0/data +++ export multizDir=/cluster/data/hg38/bed/multiz100way +++ multizDir=/cluster/data/hg38/bed/multiz100way +++ export mz=multiz100way +++ mz=multiz100way +++ export gnfU133TableLookup=knownToU133 +++ gnfU133TableLookup=knownToU133 +++ export 'gnfU95TablesFixed=hgFixed.gnfHumanU95MedianRatio hgFixed.gnfHumanU95Exps' +++ gnfU95TablesFixed='hgFixed.gnfHumanU95MedianRatio hgFixed.gnfHumanU95Exps' +++ export gnfU95TableLookup=knownToU95 +++ gnfU95TableLookup=knownToU95 +++ export 'gnfAtlasTablesFixed=hgFixed.gnfHumanAtlas2MedianRatio hgFixed.gnfHumanAtlas2MedianExps' +++ gnfAtlasTablesFixed='hgFixed.gnfHumanAtlas2MedianRatio hgFixed.gnfHumanAtlas2MedianExps' +++ export gnfAtlasTableLookup=knownToGnfAtlas2 +++ gnfAtlasTableLookup=knownToGnfAtlas2 +++ export hprd_website=http://www.hprd.org/edownload/ +++ hprd_website=http://www.hprd.org/edownload/ +++ export hprd_tar=HPRD_FLAT_FILES_041310 +++ hprd_tar=HPRD_FLAT_FILES_041310 +++ export hprd_file=FLAT_FILES_072010/HPRD_ID_MAPPINGS.txt +++ hprd_file=FLAT_FILES_072010/HPRD_ID_MAPPINGS.txt ++ hgsql --skip-column-names -e 'select mrnaAcc,locusLinkId from ncbiRefSeqLink where mrnaAcc != '\'''\''' hg38 ++ hgMapToGene -geneTableType=genePred -tempDb=knownGeneV39 hg38 ncbiRefSeq knownGene knownToLocusLink -lookup=refToLl.txt ++ rm refToLl.txt ++ test '' '!=' '' ++ awk '{OFS="\t"} {print $4,$4}' ucscGenes.bed ++ sort ++ uniq ++ cp knownToEnsembl.tab knownToGencodeV39.tab ++ hgLoadSqlTab -notOnServer knownGeneV39 knownToEnsembl /cluster/home/braney/kent/src/hg/lib/knownTo.sql knownToEnsembl.tab +Scanning through 1 files ++ hgLoadSqlTab -notOnServer knownGeneV39 knownToGencodeV39 /cluster/home/braney/kent/src/hg/lib/knownTo.sql knownToGencodeV39.tab +Scanning through 1 files ++ test '' '!=' '' ++ knownToVisiGene knownGeneV39 -probesDb=hg38 ++ hgsql knownGeneV39 -e 'select geneSymbol,name from knownGene g, kgXref x where g.name=x.kgId ' ++ sort ++ join -t ' ' /hive/groups/browser/wikipediaScrape/symbolToPage.txt knownGeneV39.symbolToId.txt ++ tawk '{print $3,$2}' ++ sort ++ uniq ++ hgLoadSqlTab knownGeneV39 knownToWikipedia /cluster/home/braney/kent/src/hg/lib/knownTo.sql knownGeneV39.idToPage.txt +Scanning through 1 files ++ test knownToU133 '!=' '' ++ hgMapToGene -geneTableType=genePred -tempDb=knownGeneV39 hg38 affyU133 knownGene knownToU133 ++ test knownToGnfAtlas2 '!=' '' ++ hgMapToGene -geneTableType=genePred -tempDb=knownGeneV39 hg38 gnfAtlas2 knownGene knownToGnfAtlas2 '-type=bed 12' ++ test 'hgFixed.gnfHumanAtlas2MedianRatio hgFixed.gnfHumanAtlas2MedianExps' '!=' '' ++ hgExpDistance knownGeneV39 hgFixed.gnfHumanAtlas2MedianRatio hgFixed.gnfHumanAtlas2MedianExps gnfAtlas2Distance -lookup=knownToGnfAtlas2 +Have 44696 elements in hgFixed.gnfHumanAtlas2MedianRatio +Got 139864 unique elements in hgFixed.gnfHumanAtlas2MedianRatio +Made gnfAtlas2Distance.tab +Loaded gnfAtlas2Distance +Made query index + +real 145m47.280s +user 125m26.114s +sys 0m48.432s ++ test knownToU95 '!=' '' ++ hgMapToGene -geneTableType=genePred -tempDb=knownGeneV39 hg38 affyU95 knownGene knownToU95 ++ test 'hgFixed.gnfHumanU95MedianRatio hgFixed.gnfHumanU95Exps' '!=' '' ++ hgExpDistance knownGeneV39 hgFixed.gnfHumanU95MedianRatio hgFixed.gnfHumanU95Exps gnfU95Distance -lookup=knownToU95 +Have 11545 elements in hgFixed.gnfHumanU95MedianRatio +Got 85826 unique elements in hgFixed.gnfHumanU95MedianRatio +Made gnfU95Distance.tab +Loaded gnfU95Distance +Made query index + +real 39m26.841s +user 29m13.175s +sys 0m16.425s ++ test FLAT_FILES_072010/HPRD_ID_MAPPINGS.txt '!=' '' ++ wget http://www.hprd.org/edownload//HPRD_FLAT_FILES_041310 +--2022-01-18 12:08:06-- http://www.hprd.org/edownload//HPRD_FLAT_FILES_041310 +Resolving www.hprd.org... 54.196.163.61 +Connecting to www.hprd.org|54.196.163.61|:80... connected. +HTTP request sent, awaiting response... 302 Moved Temporarily +Location: /RELEASE9/HPRD_FLAT_FILES_041310.tar.gz [following] +--2022-01-18 12:08:07-- http://www.hprd.org/RELEASE9/HPRD_FLAT_FILES_041310.tar.gz +Reusing existing connection to www.hprd.org:80. +HTTP request sent, awaiting response... 500 Internal Server Error +2022-01-18 12:08:07 ERROR 500: Internal Server Error. + +==== doPfamScop.log ==== ++ mkdir -p /hive/data/genomes/hg38/bed/gencodeV39/build/pfam ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build/pfam ++ rm -rf splitProt ++ mkdir splitProt ++ faSplit sequence /hive/data/genomes/hg38/bed/gencodeV39/build/ucscGenes.faa 10000 splitProt/ ++ mkdir -p result ++ ls -1 splitProt ++ cat ++ chmod +x doPfam ++ cat ++ gensub2 prot.list single template jobList ++ ssh ku 'cd /hive/data/genomes/hg38/bed/gencodeV39/build/pfam; para make jobList' +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +Checking input files +9437 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/pfam/batch +9437 jobs in batch +0 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 9437 +================ +Checking job status 0 minutes after launch +9437 jobs in batch +10381 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +9437 jobs in batch +20088 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +9437 jobs in batch +20088 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +9437 jobs in batch +19600 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +9437 jobs in batch +18933 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +9437 jobs in batch +18484 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 7 minutes after launch +9437 jobs in batch +17837 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 9 minutes after launch +9437 jobs in batch +17022 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 11 minutes after launch +9437 jobs in batch +16078 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 14 minutes after launch +9437 jobs in batch +15018 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 17 minutes after launch +9437 jobs in batch +13852 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 20 minutes after launch +9437 jobs in batch +12538 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 23 minutes after launch +9437 jobs in batch +11102 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 27 minutes after launch +9437 jobs in batch +10559 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 31 minutes after launch +9437 jobs in batch +8867 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 35 minutes after launch +9437 jobs in batch +6907 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 39 minutes after launch +9437 jobs in batch +5778 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 44 minutes after launch +9437 jobs in batch +3701 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! ++ ssh ku 'cd /hive/data/genomes/hg38/bed/gencodeV39/build/pfam; para time > run.time' +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +9437 jobs in batch +3675 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs ++ cat run.time +Completed: 9437 of 9437 jobs +CPU time in finished jobs: 811040s 13517.33m 225.29h 9.39d 0.026 y +IO & Wait Time: 140769s 2346.15m 39.10h 1.63d 0.004 y +Average job time: 101s 1.68m 0.03h 0.00d +Longest finished job: 171s 2.85m 0.05h 0.00d +Submission to last job: 2544s 42.40m 0.71h 0.03d +Estimated complete: 0s 0.00m 0.00h 0.00d ++ cat ++ awk -f makePfamRa.awk /hive/data/outside/pfam/Pfam34.0/Pfam-A.hmm ++ raToTab -cols=ACC,NAME,DESC,TC pfamDesc.ra stdout ++ awk -F '\t' '{printf("%s\t%s\t%s\t%g\n", $1, $2, $3, $4);}' ++ sort ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build/pfam ++ catDir result ++ sed '/^#/d' ++ awk 'BEGIN {OFS="\t"} { print $5,$1,$18-1,$19,$4,$14}' allResults.tab ++ sort ++ join -t ' ' -j 1 allUcscPfam.tab pfamDesc.tab ++ tawk '{if ($6 > $9) print $2, $3, $4, $5, $6, $1}' ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build ++ tawk '{print $1, gensub(/\.[0-9]+/, "", "g", $6)}' pfam/ucscPfam.tab ++ sort -u ++ hgLoadSqlTab -notOnServer knownGeneV39 knownToPfam /cluster/home/braney/kent/src/hg/lib/knownTo.sql knownToPfam.tab +Scanning through 1 files ++ tawk '{print gensub(/\.[0-9]+/, "", "g", $1), $2, $3}' pfam/pfamDesc.tab ++ hgLoadSqlTab -notOnServer knownGeneV39 pfamDesc /cluster/home/braney/kent/src/hg/lib/pfamDesc.sql stdin +Scanning through 1 files ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build/pfam ++ genePredToFakePsl knownGeneV39 knownGene knownGene.psl cdsOut.tab ++ sort cdsOut.tab ++ sed 's/\.\./ /' ++ sort ucscPfam.tab ++ awk '{print $10, $11}' knownGene.psl ++ join sortCdsOut.tab sortPfam.tab ++ awk '{print $1, $2 - 1 + 3 * $4, $2 - 1 + 3 * $5, $6}' ++ bedToPsl gene.sizes stdin domainToGene.psl ++ pslMap domainToGene.psl knownGene.psl stdout ++ pslToBed stdin stdout ++ bedOrBlocks -useName stdin domainToGenome.bed ++ hgLoadBed knownGeneV39 ucscGenePfam domainToGenome.bed +Reading domainToGenome.bed +Read 70077 elements of size 12 from domainToGenome.bed +Sorted +Creating table definition for ucscGenePfam, bedSize: 12 +Saving bed.tab +Loading knownGeneV39 ++ mkdir -p /hive/data/genomes/hg38/bed/gencodeV39/build/scop ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build/scop ++ rm -rf result ++ mkdir result ++ ls -1 ../pfam/splitProt ++ cat ++ chmod +x doScop ++ cat ++ gensub2 prot.list single template jobList ++ ssh ku 'cd /hive/data/genomes/hg38/bed/gencodeV39/build/scop; para make jobList' +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +Checking input files +9437 jobs written to /hive/data/genomes/hg38/bed/gencodeV39/build/scop/batch +9437 jobs in batch +2835 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Pushed Jobs: 9437 +================ +Checking job status 0 minutes after launch +9437 jobs in batch +12150 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 1 minutes after launch +9437 jobs in batch +11976 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 2 minutes after launch +9437 jobs in batch +11689 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 3 minutes after launch +9437 jobs in batch +11168 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 4 minutes after launch +9437 jobs in batch +11556 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 5 minutes after launch +9437 jobs in batch +10734 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 7 minutes after launch +9437 jobs in batch +9703 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 9 minutes after launch +9437 jobs in batch +8792 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 12 minutes after launch +9437 jobs in batch +7676 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 14 minutes after launch +9437 jobs in batch +7388 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 17 minutes after launch +9437 jobs in batch +5815 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 20 minutes after launch +9437 jobs in batch +5370 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 23 minutes after launch +9437 jobs in batch +3648 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 27 minutes after launch +9437 jobs in batch +1396 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 31 minutes after launch +9437 jobs in batch +1004 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +================ +Checking job status 35 minutes after launch +9437 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs +updated job database on disk +Successful batch! ++ ssh ku 'cd /hive/data/genomes/hg38/bed/gencodeV39/build/scop; para time > run.time' +.bashrc.braney machine not recognized in case statement: 'ku.gi.ucsc.edu' +9437 jobs in batch +32 jobs (including everybody's) in Parasol queue or running. +Checking finished jobs ++ cat run.time +Completed: 9437 of 9437 jobs +CPU time in finished jobs: 704207s 11736.78m 195.61h 8.15d 0.022 y +IO & Wait Time: 121258s 2020.97m 33.68h 1.40d 0.004 y +Average job time: 87s 1.46m 0.02h 0.00d +Longest finished job: 336s 5.60m 0.09h 0.00d +Submission to last job: 1857s 30.95m 0.52h 0.02d +Estimated complete: 0s 0.00m 0.00h 0.00d ++ cd /hive/data/genomes/hg38/bed/gencodeV39/build ++ catDir scop/result ++ sed '/^#/d' ++ awk 'BEGIN {OFS="\t"} {if ($7 <= 0.0001) print $1,$18-1,$19,$4, $7,$8}' ++ sort ++ sort -k 2 /hive/data/outside/scop/1.75/model.tab ++ scopCollapse scopPlusScore.tab scop.model.tab ucscScop.tab scopDesc.tab knownToSuper.tab ++ hgLoadSqlTab -notOnServer knownGeneV39 scopDesc /cluster/home/braney/kent/src/hg/lib/scopDesc.sql scopDesc.tab +Scanning through 1 files ++ hgLoadSqlTab knownGeneV39 knownToSuper /cluster/home/braney/kent/src/hg/lib/knownToSuper.sql knownToSuper.tab +Scanning through 1 files ++ hgLoadSqlTab knownGeneV39 ucscScop /cluster/home/braney/kent/src/hg/lib/ucscScop.sql ucscScop.tab +Scanning through 1 files ++ echo 'BuildPfamScop successfully finished' +BuildPfamScop successfully finished