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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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parallel: Error #330

Open huihuigogo opened 4 months ago

huihuigogo commented 4 months ago

Hello, when I use the 4.3.0 version of tb-profiler to run the ERR2184272 sample, The command is as follows: tb-profiler profile -1 ERR2184272_1.fastq.gz -2 ERR2184272_2.fastq.gz -t 2 -p ERR2184272 --csv

The following error is encountered: _```

Traceback:

  File "/public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/bin/tb-profiler", line 619, in <module>
    args.func(args)
  File "/public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/bin/tb-profiler", line 150, in main_profile
    results.update(pp.run_profiler(args))
  File "/public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/lib/python3.9/site-packages/pathogenprofiler/cli.py", line 37, in run_profiler
    results = bam_profiler(
  File "/public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/lib/python3.9/site-packages/pathogenprofiler/profiler.py", line 28, in bam_profiler
    vcf_obj = bam_obj.call_variants(conf["ref"], caller=caller, bed_file=conf["bed"], threads=threads, calling_params=calling_params, samclip = samclip, min_dp=min_depth)
  File "/public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/lib/python3.9/site-packages/pathogenprofiler/bam.py", line 78, in call_variants
    run_cmd('%(windows_cmd)s | parallel -j %(threads)s --col-sep " " "%(calling_cmd)s"' % vars(self))
  File "/public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/lib/python3.9/site-packages/pathogenprofiler/utils.py", line 397, in run_cmd
    raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,stderr.decode()))

Value:


Command Failed:
set -u pipefail; cat /public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/share/tbprofiler//tbdb.bed | awk '{print $1":"$2"-"$3" "$1"_"$2"_"$3}' | parallel -j 2 --col-sep " " "samtools view -T /public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/share/tbprofiler//tbdb.fasta -h ./aabc9515-2bb0-4d25-86b6-c4079725a2c1.bam {1} | samclip --ref /public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/share/tbprofiler//tbdb.fasta | samtools view -b > ./aabc9515-2bb0-4d25-86b6-c4079725a2c1.{2}.tmp.bam && samtools index ./aabc9515-2bb0-4d25-86b6-c4079725a2c1.{2}.tmp.bam && freebayes -f /public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/share/tbprofiler//tbdb.fasta -r {1} --haplotype-length -1  ./aabc9515-2bb0-4d25-86b6-c4079725a2c1.{2}.tmp.bam | bcftools view -c 1 | bcftools norm -f /public/home/bdpstu/cenhui2018/miniconda3/envs/TBprofiler_4.3.0/share/tbprofiler//tbdb.fasta | bcftools filter -t {1} -e 'FMT/DP<10' -S . -Oz -o ./aabc9515-2bb0-4d25-86b6-c4079725a2c1.{2}.vcf.gz"
stderr:
parallel: Error: Output is incomplete.
parallel: Error: Cannot append to buffer file in /tmp.
parallel: Error: Is the disk full?
parallel: Error: Change $TMPDIR with --tmpdir or use --compress.
```_

I don't know how to solve this problem and I'm really looking forward to your answer!
jodyphelan commented 2 months ago

Hi @huihuigogo ,

Looks like this might be an issue with your system disk being full. Can you confirm if this is still an issue for you?