Skip to content

Error while running docker image #1

@zyxNo1

Description

@zyxNo1

I download hg38 docker image and tried to run the pipeline using test data. The command is:
python3 scripts/DNAscan.py -format fastq -in data/test_data.1.fq.gz -in2 data/test_data.2.fq.gz -reference hg38 -alignment -variantcalling -annotation -iobio -out outdir/
But got errors:

Error reading _rstarts[] array: 14512, 19788
Error: Encountered internal HISAT2 exception (#1)
Command: /DNAscanv2/local/Miniconda3/bin/hisat2-align-s --wrapper basic-0 --no-spliced-alignment -p 4 -x //DNAscanv2//hg38/hg38 --read-lengths 222,221,220,219,217,216,213,210,209,207,206,194,189,176 -1 /tmp/231.inpipe1 -2 /tmp/231.inpipe2
(ERR): hisat2-align exited with value 1
samblaster: Input file is empty. Exiting.
samblaster: Premature exit (return code 1).

gzip: stdout: Broken pipe

gzip: stdout: Broken pipe
Traceback (most recent call last):
  File "scripts/DNAscan.py", line 422, in <module>
    is_variant_file_OK(bam_file, "bam", "alignment")
  File "scripts/DNAscan.py", line 188, in is_variant_file_OK
    with pysam.AlignmentFile(file, 'rb') as f:
  File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 991, in pysam.libcalignmentfile.AlignmentFile._open
ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False

What's wrong with that? Can you tell me what I should do to run the pipeline smoothly?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions