path issue for doBlastzChainNet.pl #63
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Dear wthomas14,
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doBlastzChainNet.pl
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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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@wthomas14 it looks like github helpfully sanitized the email addresses out of my colleague's reply there. That should read: This question is likely best sent to our mailing list at genome@soe.ucsc.edu, |
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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 script
which hgsql/gpfs/scratch/withomas/project_noRoot_MGA/data/bin/hgsqland the path is set in my DEF file
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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