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TrinityCTAT / CTAT-VirusIntegrationFinder

BSD 3-Clause "New" or "Revised" License
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Issue with bamsifter #31

Closed rpauly closed 2 years ago

rpauly commented 3 years ago

Hi, It is looking for bamsifter within the folder "/util/bamsifter/", butr it does not exist. Should it? This is the command I ran: ctat-VIF.py \ --genome_lib_dir ctat_genome_lib_build_dir/ \ --left_fq ${1}_R1.fastq.gz \ --right_fq ${1}_R2.fastq.gz \ --viral_db_fasta ebv.fa \ --viral_db_gtf ebv.custom.gtf \ -O ${1}_VIF

This is the partial error: bash -c 'set -eou pipefail && samtools view -h VIF_starChim_init/Aligned.sortedByCoord.out.bam EBV | samtools depth - > EBV.depth.tsv ' /bin/sh: /data/MoCha/paulyr/CTAT-VirusIntegrationFinder/util/bamsifter/bamsifter: No such file or directory Traceback (most recent call last): File "/data/MoCha/paulyr/CTAT-VirusIntegrationFinder/ctat-VIF.py", line 678, in main() File "/data/MoCha/paulyr/CTAT-VirusIntegrationFinder/ctat-VIF.py", line 301, in main pipeliner.run() File "/gpfs/gsfs6/users/MoCha/paulyr/CTAT-VirusIntegrationFinder/PyLib/Pipeliner.py", line 75, in run cmd.run(checkpoint_dir) File "/gpfs/gsfs6/users/MoCha/paulyr/CTAT-VirusIntegrationFinder/PyLib/Pipeliner.py", line 136, in run raise RuntimeError(errmsg

Thanks!

brianjohnhaas commented 3 years ago

Hi,

It looks like an installation issue. Were you able to run 'make' in the base directory? This should build everything. Note, be sure to pull the full release code from our downloads section on github. If you, instead, cloned the code from github, you'd need to do so recursively to retain the bamsifter submodule.

best,

~b

On Fri, Jul 2, 2021 at 10:47 AM rpauly @.***> wrote:

Hi, It is looking for bamsifter within the folder "/util/bamsifter/", butr it does not exist. Should it? This is the command I ran: ctat-VIF.py --genome_lib_dir ctat_genome_lib_build_dir/ --left_fq ${1}_R1.fastq.gz --right_fq ${1}_R2.fastq.gz --viral_db_fasta ebv.fa --viral_db_gtf ebv.custom.gtf -O ${1}_VIF

This is the partial error: bash -c 'set -eou pipefail && samtools view -h VIF_starChim_init/Aligned.sortedByCoord.out.bam EBV | samtools depth - > EBV.depth.tsv ' /bin/sh: /data/MoCha/paulyr/CTAT-VirusIntegrationFinder/util/bamsifter/bamsifter: No such file or directory Traceback (most recent call last): File "/data/MoCha/paulyr/CTAT-VirusIntegrationFinder/ctat-VIF.py", line 678, in main() File "/data/MoCha/paulyr/CTAT-VirusIntegrationFinder/ctat-VIF.py", line 301, in main pipeliner.run() File "/gpfs/gsfs6/users/MoCha/paulyr/CTAT-VirusIntegrationFinder/PyLib/Pipeliner.py", line 75, in run cmd.run(checkpoint_dir) File "/gpfs/gsfs6/users/MoCha/paulyr/CTAT-VirusIntegrationFinder/PyLib/Pipeliner.py", line 136, in run raise RuntimeError(errmsg

Thanks!

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas