header error with pacbio data

[nbx0]

Hey Chienchi!

I hadn't realized it before but apparently amplicov is failing on our pacbio data due to header:

Error:

Traceback (most recent call last):
  File "/scicomp/groups-pure/sars2seq/miniconda/envs/snakemake/bin/amplicov", line 534, in <module>
    run(argvs)
  File "/scicomp/groups-pure/sars2seq/miniconda/envs/snakemake/bin/amplicov", line 501, in run
    cov_array = parse_bam_file(argvs.bam,argvs.pp, argvs.outdir, argvs.refID)
  File "/scicomp/groups-pure/sars2seq/miniconda/envs/snakemake/bin/amplicov", line 214, in parse_bam_file
    for line in pysam.samtools.depth("-aa","-d0", bam_input ,split_lines=True):
  File "/scicomp/groups-pure/sars2seq/miniconda/envs/snakemake/lib/python3.8/site-packages/pysam/utils.py", line 69, in __call__
    raise SamtoolsError(
pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=[], stderr=[\'samtools depth: Couldn\\\'t read header for "IRMA/3003752441_N8KHGVQF_SARS-CoV-2_sorted.bam": Broken pipe\']'

And the header in reference:

@SQ	SN:SARS-CoV-2	LN:29903
@PG	ID:minimap2	PN:minimap2	VN:2.9-r720	CL:minimap2 -a --secondary=no -t 1 -A 2 -B 5 -O 10 -E 1 /tmp/clarity/IRMAv1.0.4/_3003752441_N8KHGVQF-WZvI4XhBkKrFdQ1DIEgyyQfW0gSCi7Qu/ASSEMBLY/F1-SARS-CoV-2.ref /tmp/clarity/IRMAv1.0.4/_3003752441_N8KHGVQF-WZvI4XhBkKrFdQ1DIEgyyQfW0gSCi7Qu/ASSEMBLY/SARS-CoV-2_0001.fastq
@PG	ID:samtools	PN:samtools	PP:minimap2	VN:1.14	CL:/scicomp/groups-pure/sars2seq/prod/irma/IRMA_RES/scripts/samtools_Linux view -bS /tmp/clarity/IRMAv1.0.4/_3003752441_N8KHGVQF-WZvI4XhBkKrFdQ1DIEgyyQfW0gSCi7Qu/ASSEMBLY/F1-SARS-CoV-2.sam

Have you seen this error before and have any thoughts on fixing?

Thanks!
Ben