Hi,
I am trying to run StrainPhlan but keep getting an error message: samtools view: error reading file “/workdir/mjc437/shotgun_bs3/consensus_markers/tmppg99h1r4/BS3_30_R1_kneaddata.fastq.sam”
I’m using Methphlan 3.0 (installed via Conda), and added bowtie2, muscle, and samtools (version 1.14) to PATH. I’m also using a remote server to run StrainPhlan. I’m relatively new to StrainPhlan, and any help would be appreciated. My code is below. Thanks!
(mpa) [mjc437@cbsujohnson shotgun_bs3]$ export PATH=/programs/bowtie2-2.4.3-linux-x86_64:$PATH
(mpa) [mjc437@cbsujohnson shotgun_bs3]$ export PATH=/programs/samtools-1.14/bin:$PATH
(mpa) [mjc437@cbsujohnson shotgun_bs3]$ export PATH=/programs/muscle:$PATH
(mpa) [mjc437@cbsujohnson shotgun_bs3]$ sample2markers.py -i sams/*.sam.bz2 -o consensus_markers --nproc 4
Thu Feb 10 11:02:04 2022: Start samples to markers execution
Thu Feb 10 11:02:04 2022: Decompressing samples…
bzip2: Compressed file ends unexpectedly;
perhaps it is corrupted? Possible reason follows.
bzip2: Success
Input file = sams/BS3_30_R1_kneaddata.fastq.sam.bz2, output file = (stdout)
It is possible that the compressed file(s) have become corrupted.
You can use the -tvv option to test integrity of such files.
You can use the `bzip2recover’ program to attempt to recover
data from undamaged sections of corrupted files.
Thu Feb 10 11:02:36 2022: Done.
Thu Feb 10 11:02:36 2022: Converting samples to BAM format…
[W::sam_read1_sam] Parse error at line 2985311
samtools view: error reading file “consensus_markers/tmpj6bvyh73/BS3_30_R1_kneaddata.fastq.sam”