samtools sam-to-bam conversion => bamfile RSeQC tool bam_stats.py cannot use. ValueError: file has no sequences defined (mode='rb')
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2.6 years ago
RNAseqer ▴ 160

Is there a known issue with samtools conversion of sam to bam files using this commandline:

$ samtools view testoutput2_paired_reads.sam > testoutput2_paired_reads.bam

RSeQC's bam_stat.py program works with the original samfile, but not the bam file I generated with samtools. Since I'd like an intact bam file going forward I was hoping to learn whats wrong with my bam file. Because when I go to use the most recent version of RSeQC on this bam file

$ bam_stat.py  -i testoutput2_paired_reads.bam

I get the following message:

Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/qcmodule/SAM.py", line 2311, in __init__
    self.samfile = pysam.Samfile(inputFile,'rb')
  File "pysam/libcalignmentfile.pyx", line 736, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 985, in pysam.libcalignmentfile.AlignmentFile._open
ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False

Is my sam to bam conversion commandline missing some option resulting in incomplete bam file output? Or is this a known conflict between samtool generated bam files and RSeQC. If it matters my .sam file was generated by HISAT2.

Here are the first few lines of that .bam file:

SRR350718.8385  16      16      69845176        60      103M    *       0       0       TTATTGTGGGAATGAACTGAGATGAGGCATGTCAGTCAGAGGGCCTTACACAACGGGAGCACTCGGTGGAAGTGGCAGTGGGTTTTCTTTGTATCTGGAGACT BEDB@EAC5362-,?<:=0C?8A>CBDC.>.EEGFFHHGCEGEHEHHFDDDDD8CEDDFG(FFHHHHHGHHHFBGGFFDHHGHEHGHHFHHFHGHHHHHHEHH AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:103        YT:Z:UU NH:i:1
SRR350718.8387  0       13      106491737       60      103M    *       0       0       CTGGGGGGAGGGGGATCTGACCTACCTTTTATAGATAAGGATTCTTTAATAACAACGATGATGATGGAATTACAGCCTGTTTGACCTTTGGCTTTTCAACTTT HHHHHHHHFHEHHHEFHEFHFHHHHFHHHHFEEHFHFHFFEEFEEEBDDBHFHHEHHHHFHHFEBDFEEFFEBEECDEEEE9<EDEDEE.?9=DDB@CC?==A AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:103        YT:Z:UU NH:i:1
SRR350718.8389  0       X       154443297       60      104M    *       0       0       GCCAAGCAGAAGGAGGTGGGAAAACGGACCCAAACCCCAGTGTGCCCTGCCCCATGCCTTTCCTTTAGTGGTGGGAAACCCTTATCTTGCAAAGTGAATGTGTC        HHHHHHHHHGHGHHHH@HHHGGHGFDHFHHGGHHFHHHFFEFBHCDHEFHGGIGGHHHHHHHHHHHHHHHG<GFH?GGCFFFFF8FHFBHEFA3BEBEB=CCB7        AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:104

Sorry for the eyesore of test and output, but can you spot whats wrong?

Grateful for any light you can shed on the matter!

samtools bam RSeQC bam_stats.py (mode='rb') • 1.3k views
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Which version of samtools are you using? Anyway, I believe you need samtools view -h to include the headers into the bam.

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That fixed it! Thanks!

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Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

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Thank you for that, I only just began using biostars three days ago so I missed that (silly oversight on my part) and will be sure to do this in the future!

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Is there no header in your SAM (and thus BAM) file?

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It turns out that was the case. view -h was what i needed.

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2.6 years ago

Try this:

samtools view testoutput2_paired_reads.sam -o testoutput2_paired_reads.bam
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