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Description
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?
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