path issue doBlastzChainNet.pl
William Thomas
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 rundoBlastzChainNet.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 bashrcexport 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 scriptwhich 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?
Stony Brook University
Stony Brook, NY 11794 USA
Jairo Navarro Gonzalez
Hello,
Thank you for using the UCSC Genome Browser and sending your inquiry.
One of our engineers suggests that the hgsql PATH may not be the real issue with why the script
is failing. The problem appears to be stated in the following lines:
So the doPartition.bash command is failing because tParts seems to have files in it already but it
should be empty. If you remove the files in the tParts directory and rerun the script, the problem
should disappear.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
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