Got 936 lifts in Macaca_fascicularis.Macaca_fascicularis_6.0.GCA_011100615.1_Macaca_fascicularis_6.0.lift
Lifting Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66579 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66580 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66581 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66582 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66583 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66584 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66585 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66586 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66587 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
MT isn't in liftSpec file line 66588 of Macaca_fascicularis.Macaca_fascicularis_6.0.103.gp.gz
checked: 66582 failed: 0
kept: 66582 dropped: 0
pass1 - making usageList (175 chroms): 45 millis
pass2 - checking and writing primary data (66582 records, 12 fields): 909 millis
Sorting and writing extra index 0: 28 millis

real	0m16.398s
user	0m21.542s
sys	0m1.653s
#### begin processing #### 1685135432 2023-05-26 14:10:32
# working /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/ensGene
/hive/data/outside/ensembl/rapid-release/bin/ensemblGff3ToBigEnsembl /hive/data/outside/ensembl/rapid-release/ /dev/stdout | cut -f1-21 > GCA_011100615.1_ensGene.bed
#### begin processing #### 1686179784 2023-06-07 16:16:24
# working /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/ensGene
/hive/data/outside/ensembl/rapid-release/bin/ensemblGff3ToBigEnsembl /hive/data/outside/ensembl/rapid-release/ /dev/stdout | cut -f1-21 > GCA_011100615.1_ensGene.bed
#### begin processing #### 1686182056 2023-06-07 16:54:16
# working /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/ensGene
/hive/data/outside/ensembl/rapid-release/bin/ensemblGff3ToBigEnsembl /hive/data/outside/ensembl/rapid-release/species/Macaca_fascicularis/GCA_011100615.1/ensembl/geneset/2020_08/Macaca_fascicularis-GCA_011100615.1-2020_08-genes.gff3.gz /dev/stdout | cut -f1-21 > GCA_011100615.1_ensGene.bed
liftUp -type=.bed stdout ens.lift warn GCA_011100615.1_ensGene.bed
Got 936 lifts in ens.lift
Lifting GCA_011100615.1_ensGene.bed
pass1 - making usageList (172 chroms): 61 millis
pass2 - checking and writing primary data (65343 records, 21 fields): 821 millis
Sorting and writing extra index 0: 23 millis
checking bbi/GCA_011100615.1_Macaca_fascicularis_6.0.ensGene.bb  fb.GCA_011100615.1_Macaca_fascicularis_6.0.ensGene.txt
checked: 65343 failed: 0
# ensGene itemCount: 65,343 basesCovered: 1,236,411,116
genePredToGtf -utr file ensGene.2020_08 stdout
checking GCA_011100615.1_ensGene.bed GCA_011100615.1_Macaca_fascicularis_6.0.ensGene.ix
working GCA_011100615.1_ensGene.bed GCA_011100615.1_Macaca_fascicularis_6.0.ensGene.ix
2020_08	Macaca_fascicularis-GCA_011100615.1-2020_08-genes.gff3.gz
+ cd /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0
+ export defaultName=GCA_011100615.1_Macaca_fascicularis_6.0
+ defaultName=GCA_011100615.1_Macaca_fascicularis_6.0
+ export asmId=GCA_011100615.1_Macaca_fascicularis_6.0
+ asmId=GCA_011100615.1_Macaca_fascicularis_6.0
+ export buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0
+ buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0
+ rm -f GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.txt
+ ln -s trackData/chromAlias/GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.txt .
+ '[' -s trackData/chromAlias/GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.bb ']'
+ rm -f GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.bb
+ ln -s trackData/chromAlias/GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.bb .
+ /cluster/home/hiram/kent/src/hg/utils/automation/asmHubTrackDb.sh GCA_011100615.1_Macaca_fascicularis_6.0 GCA_011100615.1_Macaca_fascicularis_6.0 /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0
composite chainNet
constructing synNet.bb links GCA_011100615.1_Macaca_fascicularis_6.0 hg38
constructing rbestNet.bb links GCA_011100615.1_Macaca_fascicularis_6.0 hg38
constructing synNet.bb links GCA_011100615.1_Macaca_fascicularis_6.0 mm39
constructing rbestNet.bb links GCA_011100615.1_Macaca_fascicularis_6.0 mm39
#### end processing #### 1686182079 2023-06-07 16:54:39
#### begin processing #### 1687027982 2023-06-17 11:53:02
# working /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/ensGene
liftUp -type=.bed stdout ens.lift warn GCA_011100615.1_ensGene.bed
Got 936 lifts in ens.lift
Lifting GCA_011100615.1_ensGene.bed
pass1 - making usageList (172 chroms): 64 millis
pass2 - checking and writing primary data (65343 records, 21 fields): 812 millis
Sorting and writing extra index 0: 40 millis
checking bbi/GCA_011100615.1_Macaca_fascicularis_6.0.ensGene.bb  fb.GCA_011100615.1_Macaca_fascicularis_6.0.ensGene.txt
checking GCA_011100615.1_ensGene.bed GCA_011100615.1_Macaca_fascicularis_6.0.ensGene.ix
2020_08	Macaca_fascicularis-GCA_011100615.1-2020_08-genes.gff3.gz
+ cd /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0
+ export defaultName=GCA_011100615.1_Macaca_fascicularis_6.0
+ defaultName=GCA_011100615.1_Macaca_fascicularis_6.0
+ export asmId=GCA_011100615.1_Macaca_fascicularis_6.0
+ asmId=GCA_011100615.1_Macaca_fascicularis_6.0
+ export buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0
+ buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0
+ rm -f GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.txt
+ ln -s trackData/chromAlias/GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.txt .
+ '[' -s trackData/chromAlias/GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.bb ']'
+ rm -f GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.bb
+ ln -s trackData/chromAlias/GCA_011100615.1_Macaca_fascicularis_6.0.chromAlias.bb .
+ /cluster/home/hiram/kent/src/hg/utils/automation/asmHubTrackDb.sh GCA_011100615.1_Macaca_fascicularis_6.0 GCA_011100615.1_Macaca_fascicularis_6.0 /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0
composite chainNet
constructing synNet.bb links GCA_011100615.1_Macaca_fascicularis_6.0 hg38
constructing rbestNet.bb links GCA_011100615.1_Macaca_fascicularis_6.0 hg38
constructing synNet.bb links GCA_011100615.1_Macaca_fascicularis_6.0 mm39
constructing rbestNet.bb links GCA_011100615.1_Macaca_fascicularis_6.0 mm39
#### end processing #### 1687027988 2023-06-17 11:53:08