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cauyrd / transIndel

Indel caller for DNA-seq or RNA-seq
GNU General Public License v3.0
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Struggling to run transIndel_build_RNA.py #5

Open yesitsjess opened 5 years ago

yesitsjess commented 5 years ago

Hello,

I'm getting an error when try to run transIndel_build_RNA.py like this: python transIndel/transIndel_build_RNA.py -i sam.sorted.bam -r hg38.fa -g Homo_sapiens.GRCh38.94.gtf -o sam.indels.bam

I'm using samtools_v1.4.1. The output I get is:

[bam_sort_core] merging from 10 files...
Traceback (most recent call last):
  File "transIndel/transIndel_build_RNA.py", line 304, in <module>
    main()
  File "transIndel/transIndel_build_RNA.py", line 296, in main
    softclipping_realignment(mapq_cutoff, max_del_len, input, output, ref_genome, gtf, splice_bin)
  File "transIndel/transIndel_build_RNA.py", line 206, in softclipping_realignment
    subprocess.check_call("samtools index {}".format(output), shell=True)
  File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'samtools index sam.indel.bam' returned non-zero exit sta
cauyrd commented 5 years ago

Could you send a test file so that we can check your problem, we have tested transindel in our end and have not found any problem.

On Mon, Nov 12, 2018 at 7:48 AM Jess notifications@github.com wrote:

Hello,

I'm getting an error when try to run transIndel_build_RNA.py like this: python transIndel_build_RNA.py -i sam.sorted.bam -r hg38.fa -g Homo_sapiens.GRCh38.94.gtf -o sam.indels.bam

I'm using samtools_v1.4.1. The output I get is:

[bam_sort_core] merging from 10 files... Traceback (most recent call last): File "transIndel/transIndel_build_RNA2.py", line 304, in main() File "transIndel/transIndel_build_RNA2.py", line 296, in main softclipping_realignment(mapq_cutoff, max_del_len, input, output, ref_genome, gtf, splice_bin) File "transIndel/transIndel_build_RNA2.py", line 206, in softclipping_realignment subprocess.check_call("/software/bioinf/samtools/bin/samtools index {}".format(output), shell=True) File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/software/bioinf/samtools/bin/samtools index SRR2135523.indel.bam' returned non-zero exit sta

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