73cafbd4cad4da09db8158671513f36b753ae686 hiram Mon Mar 30 10:50:51 2020 -0700 completed all the vertebrate genbank assembly idKeys, now comparing all with all refs #24547 diff --git src/hg/makeDb/doc/assemblyEquivalence/README.txt src/hg/makeDb/doc/assemblyEquivalence/README.txt index 457df39..1e40628 100644 --- src/hg/makeDb/doc/assemblyEquivalence/README.txt +++ src/hg/makeDb/doc/assemblyEquivalence/README.txt @@ -1,331 +1,373 @@ ############################################################################# Procedure to determine equivalence between assemblies The process is to compare md5sums of each assembly to determine exact matches. When there isn't an exact match, them compare the md5sums of each sequence to determine how many match with each other. With enough matches, a partial equivalence can be established. There are sometimes small differences due to: 1. different or non-existing chrM/MT sequence between assemblies 2. duplicated sequences are usually eliminated in UCSC assemblies 3. elimination of sequences under a size limit, for example, do not use any sequences under 100 bases in length The md5sums are calculated with the automatic script: doIdKeys.pl which only needs a 2bit file to perform the calculation. There are two files created by this process: 1. <assemblyName>.idKeys.txt - individual md5sum of each sequence 2. <assemblyName>.keySignature.txt - md5sum of all the individual idKeys sums This is a single md5sum for the whole assembly There are five different sources of sequence that will be compared: 1. UCSC database browser genomes 2. NCBI RefSeq assemblies 3. NCBI Genbank assemblies 4. Ensembl assemblies -XXX 5. UCSC assembly hub genomes - maybe, this is the same ID as RefSeq/Genbank +XXX 5. UCSC assembly hub genomes - maybe Priority will go to exact matches. If there is an exact match, the partial matches will not be checked. When there is no exact match, the closest partial match will be used. ############################################################################# Working directory: /hive/data/inside/assemblyEquivalence/ ############################################################################# Ensembl version 99 sequences were downloaded to: /hive/data/outside/ensembl/genomes/release-99/fasta/ The 'idKeys' signatures for these sequences were calculated in: /hive/data/outside/ensembl/genomes/release-99/idKeys/ A typical run of idKeys in one of those directories, for example: cat /hive/data/outside/ensembl/genomes/release-99/idKeys/Vicugna_pacos/run.sh set -beEu -o pipefail cd /hive/data/outside/ensembl/genomes/release-99/idKeys/Vicugna_pacos doIdKeys.pl -buildDir=`pwd` -twoBit=`pwd`/Vicugna_pacos.vicPac1.2bit "Vicugna_pacos.vicPac1" All of these were set up with scripts to run them in parallel, the 2bit files was constructed from the fasta, then this doIdKeys.pl procedure was run which creates the two files of interest: # -rw-rw-r-- 1 14164089 Jan 21 21:58 Vicugna_pacos.vicPac1.idKeys.txt # -rw-rw-r-- 1 33 Jan 21 21:58 Vicugna_pacos.vicPac1.keySignature.txt The keySignature.txt is a single md5sum of all the individual sequence md5sums in the idKeys.txt file. For example: cat Vicugna_pacos.vicPac1.keySignature.txt 84f72c82109632aa712d85fe9d94d237 head Vicugna_pacos.vicPac1.idKeys.txt 000052eec7a560c419098fe75ce59ccd scaffold_62780 00008c4565756b4429fabffa2e374b2c scaffold_15650 00012aaa1678d5651863671f53c66e3e scaffold_138339 00014ee45a4daceca84ba8d39c05fa93 scaffold_24830 00016bdfe2b6c9cd9d3145bc59057443 scaffold_195552 ... etc ... ##### Gather the Ensembl keySignatures #################################### mkdir /hive/data/inside/assemblyEquivalence/ensembl cd /hive/data/inside/assemblyEquivalence/ensembl # There is a single file with all the name correspondences that will be useful: time rsync -av --stats rsync://ftp.ensembl.org/ensembl/pub/release-99/species_EnsemblVertebrates.txt ./ real 0m1.644s find /hive/data/outside/ensembl/genomes/release-99/idKeys -type f \ | grep keySignature.txt | while read K do idKeysDir=`dirname "${K}"` id=`basename "${K}" | sed -e 's/.keySignature.txt//;'` idKeys="$idKeysDir/$id.idKeys.txt" fullCount=`cat $idKeys | wc -l` uniqueCount=`cut -f1 $idKeys | sort -u | wc -l` keySig=`cat "${K}"` printf "%s\t%s\t%d\t%d\n" "${keySig}" "${id}" "${fullCount}" "${uniqueCount}" done | sort -k1,1 > ensembl.keySignatures.txt ##### Gather the UCSC database genomes keySignatures ###################### mkdir /hive/data/inside/assemblyEquivalence/ucscDb cd /hive/data/inside/assemblyEquivalence/ucscDb ### Avoiding an expensive 'find' operation on the hive directories, just ### check for specific named files: ls -d /hive/data/genomes/* | while read dbDir do db=`basename "${dbDir}"` keySig="${dbDir}/bed/idKeys/${db}.keySignature.txt" idKeysDir=`dirname "${keySig}"` if [ -s "${keySig}" ]; then idKeys="$idKeysDir/$db.idKeys.txt" fullCount=`cat $idKeys | wc -l` uniqueCount=`cut -f1 $idKeys | sort -u | wc -l` keySig=`cat "${keySig}"` printf "%s\t%s\t%d\t%d\n" "${keySig}" "${db}" "${fullCount}" "${uniqueCount}" fi done | sort -k1,1 > ucscDb.keySignatures.txt ##### Gather the NCBI Refseq keySignatures ###################### ##### There are two types of 'idKeys' in the NCBI assemblies ##### one at the top level: GCx/012/345/678/accessionId/idKeys/ ##### one at the build level: GCx/012/345/678/accessionId/trackData/idKeys/ ##### the top level one is for the 'original' assembly from NCBI, ##### the build level one is for the assembly hub which has duplicate ##### contigs removed. These are different key signatures when ##### duplicates have been removed. mkdir /hive/data/inside/assemblyEquivalence/refseq cd /hive/data/inside/assemblyEquivalence/refseq ### the maxdepth and mindepth seems to help speed up the find a lot, rather ### then letting run it without any limits: find /hive/data/genomes/asmHubs/refseqBuild/GCF \ -maxdepth 4 -mindepth 4 -type d | while read buildDir do asmId=`basename "${buildDir}"` keySig="${buildDir}/idKeys/${asmId}.keySignature.txt" idKeysDir=`dirname "${keySig}"` if [ -s "${keySig}" ]; then idKeys="$idKeysDir/$asmId.idKeys.txt" fullCount=`cat $idKeys | wc -l` uniqueCount=`cut -f1 $idKeys | sort -u | wc -l` keySig=`cat "${keySig}"` printf "%s\t%s\t%d\t%d\n" "${keySig}" "${asmId}" "${fullCount}" "${uniqueCount}" fi done | sort -k1,1 > refseq.keySignatures.txt ##### Gather the NCBI genbank keySignatures ###################### mkdir /hive/data/inside/assemblyEquivalence/genbank cd /hive/data/inside/assemblyEquivalence/genbank find /hive/data/genomes/asmHubs/genbankBuild/GCA \ -maxdepth 4 -mindepth 4 -type d | while read buildDir do asmId=`basename "${buildDir}"` keySig="${buildDir}/idKeys/${asmId}.keySignature.txt" idKeysDir=`dirname "${keySig}"` if [ -s "${keySig}" ]; then idKeys="$idKeysDir/$asmId.idKeys.txt" fullCount=`cat $idKeys | wc -l` uniqueCount=`cut -f1 $idKeys | sort -u | wc -l` keySig=`cat "${keySig}"` printf "%s\t%s\t%d\t%d\n" "${keySig}" "${asmId}" "${fullCount}" "${uniqueCount}" fi done | sort -k1,1 > genbank.keySignatures.txt ######################################################################## ### construct exact matches ######################################################################## cd /hive/data/inside/assemblyEquivalence ~/kent/src/hg/makeDb/doc/assemblyEquivalence/exact.sh ## this exact.sh script constructs the files: ## ensembl.genbank.exact.txt genbank.refseq.exact.txt refseq.ucsc.exact.txt ## ensembl.refseq.exact.txt genbank.ucsc.exact.txt ucsc.ensembl.exact.txt ## ensembl.ucsc.exact.txt refseq.ensembl.exact.txt ucsc.genbank.exact.txt ## genbank.ensembl.exact.txt refseq.genbank.exact.txt ucsc.refseq.exact.txt ~/kent/src/hg/makeDb/doc/assemblyEquivalence/exactTableTsv.pl \ | sort > table.2020-03-20.tsv # for a first peek at the functioning of this table, load these # exact matches: hgLoadSqlTab hgFixed asmEquivalent \ ~/kent/src/hg/lib/asmEquivalent.sql table.2020-03-20.tsv # what does this look like: hgsql -e 'desc asmEquivalent' hgFixed # Field Type Null Key Default Extra # source varchar(255) NO MUL NULL # destination varchar(255) NO MUL NULL # sourceAuthority enum('ensembl','ucsc','genbank','refseq') NO NULL # destinationAuthority enum('ensembl','ucsc','genbank','refseq') NO NULL # matchCount int(10) unsigned NO NULL # sourceCount int(10) unsigned NO NULL # destinationCount int(10) unsigned NO NULL hgsql -e 'select count(*) from asmEquivalent' hgFixed # +----------+ # | count(*) | # +----------+ # | 858 | # +----------+ hgsql -e 'show indexes from asmEquivalent' hgFixed # list of UCSC databases exactly equivalent to RefSeq assemblies hgsql -e 'select destination from asmEquivalent where sourceAuthority="refseq" and destinationAuthority="ucsc";' hgFixed ######################################################################## ### construct close matches ######################################################################## mkdir /hive/data/inside/assemblyEquivalence/notExact cd /hive/data/inside/assemblyEquivalence/notExact ~/kent/src/hg/makeDb/doc/assemblyEquivalence/allByAll.sh ### the output of this script is summarized in ./results/ ### into two categories: match and notMatch. ### This allByAll.sh script eliminates all the 'exact' matches as found ### above. For those assemblies remaining in each category that do not ### have an exact match: ### ensembl refseq genbank ucsc ### and then pairs them up according to how many unique sequences they ### have, where 'unique' means without duplicate contigs. If the number of ### unique sequences are close within +- 10 to each other, it runs a ### comparison procedure that checks how many of the sequences in each assembly ### match to each other. If the match is within %10 of the number of sequences, ### it calls that a 'match', anything outside %10 in common are ### called 'notMatch' ### Finally, to get the lines that belong in the final asmEquivalent ### table in hgFixed: -sed -e 's/\tcount A .*//;' results/match.*.txt > notExact.table.2020-03-26.tsv +sed -e 's/\tcount A .*//;' results/match.*.txt > notExact.table.2020-03-30.tsv To load up both the exact and these notExact matches into the hgFixed table: -sort notExact.table.2020-03-26.tsv ../table.2020-03-26.tsv \ +sort notExact.table.2020-03-30.tsv ../table.2020-03-30.tsv \ | hgLoadSqlTab hgFixed asmEquivalent ~/kent/src/hg/lib/asmEquivalent.sql stdin hgsql -e 'select count(*) from asmEquivalent;' hgFixed +----------+ | count(*) | +----------+ -| 2036 | +| 2118 | +----------+ +### There shouldn't be any duplicate entries: + +hgsql -N -e 'select source,destination from asmEquivalent;' hgFixed \ + | sort | uniq -c | sort -rn | head + 1 zonAlb1 Zonotrichia_albicollis.Zonotrichia_albicollis-1.0.1 + 1 zonAlb1 GCF_000385455.1_Zonotrichia_albicollis-1.0.1 + 1 zonAlb1 GCA_000385455.1_Zonotrichia_albicollis-1.0.1 + 1 xipMac1 GCA_000241075.1_Xiphophorus_maculatus-4.4.2 + 1 xenTro9 Xenopus_tropicalis.Xenopus_tropicalis_v9.1 + 1 xenTro9 GCA_000004195.3_Xenopus_tropicalis_v9.1 + 1 xenLae2 GCF_001663975.1_Xenopus_laevis_v2 + 1 xenLae2 GCA_001663975.1_Xenopus_laevis_v2 + 1 wuhCor1 GCF_009858895.2_ASM985889v3 + 1 vicPac2 GCA_000164845.3_Vicugna_pacos-2.0.2 +hgsql -N -e 'select source,destination from asmEquivalent;' hgFixed \ + | sort | uniq -c | sort -rn | tail + + 1 Anabas_testudineus.fAnaTes1.1 GCF_900324465.1_fAnaTes1.1 + 1 Amphiprion_percula.Nemo_v1 GCA_003047355.1_Nemo_v1 + 1 Amphiprion_ocellaris.AmpOce1.0 GCF_002776465.1_AmpOce1.0 + 1 Amphiprion_ocellaris.AmpOce1.0 GCA_002776465.1_AmpOce1.0 + 1 Amphilophus_citrinellus.Midas_v5 GCA_000751415.1_Midas_v5 + 1 Ailuropoda_melanoleuca.ailMel1 ailMel1 + 1 Ailuropoda_melanoleuca.ailMel1 GCF_000004335.2_AilMel_1.0 + 1 Ailuropoda_melanoleuca.ailMel1 GCA_000004335.1_AilMel_1.0 + 1 Acanthochromis_polyacanthus.ASM210954v1 GCF_002109545.1_ASM210954v1 + 1 Acanthochromis_polyacanthus.ASM210954v1 GCA_002109545.1_ASM210954v1 + +# How many ensembl assemblies map to genbank or refseq assemblies: +hgsql -N -e 'select source,destination from asmEquivalent where + sourceAuthority="ensembl" AND (destinationAuthority="genbank" OR + destinationAuthority="refseq");' hgFixed | wc -l +# 354 + +# How many ucsc assemblies map to genbank or refseq assemblies: +hgsql -N -e 'select source,destination from asmEquivalent where + sourceAuthority="ucsc" AND (destinationAuthority="genbank" OR + destinationAuthority="refseq");' hgFixed | wc -l +# 350 + +# ucsc to only refseq: +hgsql -N -e 'select source,destination from asmEquivalent where + sourceAuthority="ucsc" AND destinationAuthority="refseq";' hgFixed | wc -l +# 146 + +# ucsc to only genbank +hgsql -N -e 'select source,destination from asmEquivalent where + sourceAuthority="ucsc" AND destinationAuthority="genbank";' hgFixed | wc -l +# 204 + +# How many ucsc assemblies map to ensembl assemblies: +hgsql -N -e 'select source,destination from asmEquivalent where + sourceAuthority="ucsc" AND destinationAuthority="ensembl";' hgFixed | wc -l +# 85 + +# These counts should always be symmetrical, e.g. ensembl to ucsc + hgsql -N -e 'select source,destination from asmEquivalent where + sourceAuthority="ensembl" AND destinationAuthority="ucsc";' hgFixed | wc -l +# 85 + # To see some of the highest differences, sort by column 1 and by column 2 # and check head or tail of such sorts, there shouldn't be any '0 0' columns # as that would be an 'exact' match and that has already been ruled # out: (this could be done with the loaded table too) -awk -F$'\t' '{printf "%4d %4d\t%s\t%s\n", $5-$7,$6-$7,$1,$2}' notExact.table.2020-03-26.tsv | sort -k1,1n | head --1473 0 GCA_000768395.1_Cpor_2.0 croPor0 --1473 0 croPor0 GCA_000768395.1_Cpor_2.0 --756 -2 GCA_000708225.1_ASM70822v1 nipNip0 --754 2 nipNip0 GCA_000708225.1_ASM70822v1 --454 -1 GCA_000231765.1_GadMor_May2010 gadMor1 --453 1 gadMor1 GCA_000231765.1_GadMor_May2010 --428 -1 GCA_003265705.1_ASM326570v1 GCF_003265705.1_ASM326570v1 --427 1 GCF_003265705.1_ASM326570v1 GCA_003265705.1_ASM326570v1 --412 -1 GCA_003584765.1_ASM358476v1 GCF_003584765.1_ASM358476v1 --411 1 GCF_003584765.1_ASM358476v1 GCA_003584765.1_ASM358476v1 - -awk -F$'\t' '{printf "%4d %4d\t%s\t%s\n", $5-$7,$6-$7,$1,$2}' notExact.table.2020-03-26.tsv | sort -k2,2n | head --141 -141 Otolemur_garnettii.OtoGar3 GCA_000181295.3_OtoGar3 --141 -141 Otolemur_garnettii.OtoGar3 GCF_000181295.1_OtoGar3 --141 -141 Otolemur_garnettii.OtoGar3 otoGar3 --115 -113 vicPac2 GCA_000164845.3_Vicugna_pacos-2.0.2 --109 -109 takFla1 GCA_000400755.1_version_1_of_Takifugu_flavidus_genome - -42 -42 Mustela_putorius_furo.MusPutFur1.0 GCF_000215625.1_MusPutFur1.0 - -42 -42 musFur1 GCF_000215625.1_MusPutFur1.0 - -41 -41 Mustela_putorius_furo.MusPutFur1.0 GCA_000215625.1_MusPutFur1.0 - -41 -41 musFur1 GCA_000215625.1_MusPutFur1.0 - -19 -19 gorGor4 GCA_000151905.3_gorGor4 - -awk -F$'\t' '{printf "%4d %4d\t%s\t%s\n", $5-$7,$6-$7,$1,$2}' notExact.table.2020-03-26.tsv | sort -k1,1n | tail - 0 16 Neolamprologus_brichardi.NeoBri1.0 neoBri1 - 0 19 GCA_000151905.3_gorGor4 gorGor4 - 0 41 GCA_000215625.1_MusPutFur1.0 Mustela_putorius_furo.MusPutFur1.0 - 0 41 GCA_000215625.1_MusPutFur1.0 musFur1 - 0 42 GCF_000215625.1_MusPutFur1.0 Mustela_putorius_furo.MusPutFur1.0 - 0 42 GCF_000215625.1_MusPutFur1.0 musFur1 - 0 109 GCA_000400755.1_version_1_of_Takifugu_flavidus_genome takFla1 - 0 141 GCA_000181295.3_OtoGar3 Otolemur_garnettii.OtoGar3 - 0 141 GCF_000181295.1_OtoGar3 Otolemur_garnettii.OtoGar3 - 0 141 otoGar3 Otolemur_garnettii.OtoGar3 - -awk -F$'\t' '{printf "%4d %4d\t%s\t%s\n", $5-$7,$6-$7,$1,$2}' notExact.table.2020-03-26.tsv | sort -k2,2n | tail - -1 19 Gorilla_gorilla.gorGor4 gorGor4 - 0 41 GCA_000215625.1_MusPutFur1.0 Mustela_putorius_furo.MusPutFur1.0 - 0 41 GCA_000215625.1_MusPutFur1.0 musFur1 - 0 42 GCF_000215625.1_MusPutFur1.0 Mustela_putorius_furo.MusPutFur1.0 - 0 42 GCF_000215625.1_MusPutFur1.0 musFur1 - 0 109 GCA_000400755.1_version_1_of_Takifugu_flavidus_genome takFla1 - -2 113 GCA_000164845.3_Vicugna_pacos-2.0.2 vicPac2 - 0 141 GCA_000181295.3_OtoGar3 Otolemur_garnettii.OtoGar3 - 0 141 GCF_000181295.1_OtoGar3 Otolemur_garnettii.OtoGar3 - 0 141 otoGar3 Otolemur_garnettii.OtoGar3 +awk -F$'\t' '{printf "%4d %4d\t%s\t%s\n", $6-$5,$7-$5,$1,$2}' \ + notExact.table.2020-03-30.tsv | sort -k1,1n -k3,3 | head + 0 1 Anabas_testudineus.fAnaTes1.1 GCF_900324465.1_fAnaTes1.1 + 0 1 Aotus_nancymaae.Anan_2.0 GCF_000952055.2_Anan_2.0 + 0 1 Aotus_nancymaae.Anan_2.0 aotNan1 + 0 1 Astatotilapia_calliptera.fAstCal1.2 GCF_900246225.1_fAstCal1.2 + 0 1 Astyanax_mexicanus_pachon.Astyanax_mexicanus-1.0.2 astMex1 + 0 1 Betta_splendens.fBetSpl5.2 GCF_900634795.2_fBetSpl5.2 + 0 1 Bos_indicus_hybrid.UOA_Brahman_1 GCA_003369695.2_UOA_Brahman_1 + 0 1 CHM1 GCA_000306695.2_CHM1_1.1 + 0 1 Canis_lupus_familiarisgreatdane.UMICH_Zoey_3.1 GCA_005444595.1_UMICH_Zoey_3.1 + 0 1 Cercocebus_atys.Caty_1.0 cerAty1 + +awk -F$'\t' '{printf "%4d %4d\t%s\t%s\n", $6-$5,$7-$5,$1,$2}' \ + notExact.table.2020-03-30.tsv | sort -k1,1n | tail + 453 454 GCA_000231765.1_GadMor_May2010 gadMor1 + 454 453 gadMor1 GCA_000231765.1_GadMor_May2010 + 754 756 GCA_000708225.1_ASM70822v1 nipNip0 + 756 754 nipNip0 GCA_000708225.1_ASM70822v1 +1233 1234 GCA_900497805.2_bare-nosed_wombat_genome_assembly GCF_900497805.2_bare-nosed_wombat_genome_assembly +1233 1234 GCA_900497805.2_bare-nosed_wombat_genome_assembly Vombatus_ursinus.bare-nosed_wombat_genome_assembly +1234 1233 GCF_900497805.2_bare-nosed_wombat_genome_assembly GCA_900497805.2_bare-nosed_wombat_genome_assembly +1234 1233 Vombatus_ursinus.bare-nosed_wombat_genome_assembly GCA_900497805.2_bare-nosed_wombat_genome_assembly +1473 1473 GCA_000768395.1_Cpor_2.0 croPor0 +1473 1473 croPor0 GCA_000768395.1_Cpor_2.0 # This could be done with the loaded table too: -hgsql -N -e 'select matchCount-sourceCount,matchCount-destinationCount,(matchCount-sourceCount)-(matchCount-destinationCount),source from asmEquivalent where matchCount-sourceCount!=0;' hgFixed | sort -k3,3n | tail --1 -3 2 enhLutKen1 --1 -3 2 manPen1 --1 -3 2 serCan1 --1 -3 2 serCan1 --754 -756 2 GCA_000708225.1_ASM70822v1 --1 -4 3 GCA_001541155.1_Algmis_Hirise_1.0 --1 -9 8 xipMac1 --1 -16 15 neoBri1 --1 -20 19 gorGor4 --2 -115 113 vicPac2 - -hgsql -N -e 'select matchCount-sourceCount,matchCount-destinationCount,(matchCount-sourceCount)-(matchCount-destinationCount),source from asmEquivalent where matchCount-sourceCount!=0;' hgFixed | sort -k3,3n | head --141 0 -141 GCA_000181295.3_OtoGar3 --141 0 -141 GCF_000181295.1_OtoGar3 --141 0 -141 otoGar3 --115 -2 -113 GCA_000164845.3_Vicugna_pacos-2.0.2 --109 0 -109 GCA_000400755.1_version_1_of_Takifugu_flavidus_genome --42 0 -42 GCF_000215625.1_MusPutFur1.0 --42 0 -42 GCF_000215625.1_MusPutFur1.0 --41 0 -41 GCA_000215625.1_MusPutFur1.0 --41 0 -41 GCA_000215625.1_MusPutFur1.0 --19 0 -19 GCA_000151905.3_gorGor4 +hgsql -N -e 'select sourceCount-matchCount,destinationCount-matchCount,source,destination from asmEquivalent where + matchCount!=sourceCount OR matchCount!=destinationCount;' hgFixed \ + | sort -k1,1n -k3,3 | head +0 1 Anabas_testudineus.fAnaTes1.1 GCF_900324465.1_fAnaTes1.1 +0 1 Aotus_nancymaae.Anan_2.0 GCF_000952055.2_Anan_2.0 +0 1 Aotus_nancymaae.Anan_2.0 aotNan1 +0 1 Astatotilapia_calliptera.fAstCal1.2 GCF_900246225.1_fAstCal1.2 +0 1 Astyanax_mexicanus_pachon.Astyanax_mexicanus-1.0.2 astMex1 +0 1 Betta_splendens.fBetSpl5.2 GCF_900634795.2_fBetSpl5.2 +0 1 Bos_indicus_hybrid.UOA_Brahman_1 GCA_003369695.2_UOA_Brahman_1 +0 1 CHM1 GCA_000306695.2_CHM1_1.1 +0 1 Canis_lupus_familiarisgreatdane.UMICH_Zoey_3.1 GCA_005444595.1_UMICH_Zoey_3.1 +0 1 Cercocebus_atys.Caty_1.0 cerAty1 + +hgsql -N -e 'select sourceCount-matchCount,destinationCount-matchCount,source,destination from asmEquivalent where + matchCount!=sourceCount OR matchCount!=destinationCount;' hgFixed \ + | sort -k1,1n -k3,3 | tail +453 454 GCA_000231765.1_GadMor_May2010 gadMor1 +454 453 gadMor1 GCA_000231765.1_GadMor_May2010 +754 756 GCA_000708225.1_ASM70822v1 nipNip0 +756 754 nipNip0 GCA_000708225.1_ASM70822v1 +1233 1234 GCA_900497805.2_bare-nosed_wombat_genome_assembly GCF_900497805.2_bare-nosed_wombat_genome_assembly +1233 1234 GCA_900497805.2_bare-nosed_wombat_genome_assembly Vombatus_ursinus.bare-nosed_wombat_genome_assembly +1234 1233 GCF_900497805.2_bare-nosed_wombat_genome_assembly GCA_900497805.2_bare-nosed_wombat_genome_assembly +1234 1233 Vombatus_ursinus.bare-nosed_wombat_genome_assembly GCA_900497805.2_bare-nosed_wombat_genome_assembly +1473 1473 GCA_000768395.1_Cpor_2.0 croPor0 +1473 1473 croPor0 GCA_000768395.1_Cpor_2.0