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2 years ago Dear wthomas14,
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All the best,
On Tue, Nov 23, 2021 at 2:27 PM 'wthomas14' via UCSC Genome Browser Confidential Support @.***> wrote:
Sorry for posting for what might be a relatively easy path issue that I have yet to be able to fix. I have been running through the example here http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl#PATH_setup , to make sure everything is working before using my genomes of interest.
All the steps preceding running the actual script work, except that I am running this on my university HPCC, so all of my scripts, bins, and genomes are in a local directory, not the root directory.
When I run doBlastzChainNet.pl DEF -verbose=10 -noDbNameCheck -workhorse=localhost -bigClusterHub=localhost -skipDownload -dbHost=localhost -smallClusterHub=localhost -trackHub -fileServer=localhost -syntenicNet I get:
DEF looks OK! tDb=dm6 qDb=GCF_000005575.2_AgamP3 s1d=/gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/dm6.2bit isSelf= bash: hgsql: command not found bash: hgsql: command not found HgStepManager: executing from step 'partition' through step 'syntenicNet'. HgStepManager: executing step 'partition' Tue Nov 23 17:24:20 2021.
chmod a+x /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/trackData/GCF_000005575.2_AgamP3/run.blastz/doPartition.bash
ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' localhost nice /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/trackData/GCF_000005575.2_AgamP3/run.blastz/doPartition.bash
- cd /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/trackData/GCF_000005575.2_AgamP3/run.blastz
- /gpfs/scratch/withomas/project_noRoot_MGA/data/scripts/partitionSequence.pl 32100000 10000 /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/dm6.2bit /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/dm6.chrom.sizes -xdir xdir.sh -rawDir ../psl 18 -lstDir tParts lstDir tParts must be empty, but seems to have files (part062.lst ...) Command failed: ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' localhost nice /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/trackData/GCF_000005575.2_AgamP3/run.blastz/doPartition.bash
So my first question would be, why is my hgsql command not being found? I have the bin and scripts exported as a path in my bashrc export PATH=/usr/bin:/usr/sbin:/gpfs/scratch/withomas/project_noRoot_MGA/data/bin:/gpfs/scratch/withomas/project_noRoot_MGA/data/scripts:$PATH and I am able to use it outside of the script which hgsql /gpfs/scratch/withomas/project_noRoot_MGA/data/bin/hgsql and the path is set in my DEF file
dm6 vs GCF_000005575.2_AgamP3
PATH=/gpfs/scratch/withomas/project_noRoot_MGA/data/scripts:/gpfs/scratch/withomas/project_noRoot_MGA/data/bin BLASTZ=/gpfs/scratch/withomas/project_noRoot_MGA/data/bin/lastz-1.04.00 BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_Q=/gpfs/scratch/withomas/project_noRoot_MGA/data/lastz/HoxD55.q
TARGET: D. melanogaster dm6
SEQ1_DIR=/gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/dm6.2bit SEQ1_LEN=/gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/dm6.chrom.sizes SEQ1_CHUNK=32100000 SEQ1_LAP=10000 SEQ1_LIMIT=18
QUERY: GCF_000005575.2_AgamP3
SEQ2_DIR=/gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/trackData/GCF_000005575.2_AgamP3/GCF_000005575.2_AgamP3.2bit SEQ2_LEN=/gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/trackData/GCF_000005575.2_AgamP3/GCF_000005575.2_AgamP3.chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0
BASE=/gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/trackData/GCF_000005575.2_AgamP3 TMPDIR=/gpfs/scratch/withomas/project_noRoot_MGA/dev/shm
but still no luck.
I've attempted to play around with some of the function in doBlastzChainNet.pl such as loadDef and requirePath , but still haven't been able to figure it out. Any help would be greatly appreciated!
Noting: perhaps it isn't even a path issue, if HgStepManager seems to be working fine?
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AngieHinrichs
Sorry for posting for what might be a relatively easy path issue that I have yet to be able to fix. I have been running through the example here http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl#PATH_setup , to make sure everything is working before using my genomes of interest.
All the steps preceding running the actual script work, except that I am running this on my university HPCC, so all of my scripts, bins, and genomes are in a local directory, not the root directory.
When I run
doBlastzChainNet.pl DEF -verbose=10 -noDbNameCheck -workhorse=localhost -bigClusterHub=localhost -skipDownload -dbHost=localhost -smallClusterHub=localhost -trackHub -fileServer=localhost -syntenicNetI get:So my first question would be, why is my hgsql command not being found? I have the bin and scripts exported as a path in my bashrc
export PATH=/usr/bin:/usr/sbin:/gpfs/scratch/withomas/project_noRoot_MGA/data/bin:/gpfs/scratch/withomas/project_noRoot_MGA/data/scripts:$PATHand I am able to use it outside of the scriptwhich hgsql/gpfs/scratch/withomas/project_noRoot_MGA/data/bin/hgsqland the path is set in my DEF filebut still no luck.
I've attempted to play around with some of the function in doBlastzChainNet.pl such as loadDef and requirePath , but still haven't been able to figure it out. Any help would be greatly appreciated!
Noting: perhaps it isn't even a path issue, if HgStepManager seems to be working fine?