plotFingerprint [bwHdrRead] error

[tesa.s...@gmail.com]

Hi deepTools folks,
Yesterday I though I had successfully installed deeptools using conda.
All the tools I've tried to use so far have worked great. Then I tried using plotFingerprint like this:

 plotFingerprint -b *.bam --labels file.2 input.2 --minMappingQuality 20 --skipZeros  --plotFile fingerprints_2.png --outRawCounts fingerprints_2.tab


and got this error:


[bwHdrRead] There was an error while reading in the header!
Traceback (most recent call last):
  File "/home/NFS/users/t.severson/miniconda2/bin/plotFingerprint", line 11, in <module>
    main(args)
  File "/home/NFS/users/t.severson/miniconda2/lib/python2.7/site-packages/deeptools/plotFingerprint.py", line 362, in main
    num_reads_per_bin = cr.run()
  File "/home/NFS/users/t.severson/miniconda2/lib/python2.7/site-packages/deeptools/countReadsPerBin.py", line 244, in run
    y = pyBigWig.open(x)
RuntimeError: Received an error during file opening!

My bam files have worked for previous tools so I don't think there is a problem with them.
Any clues what is going on?
Thanks,
Tesa

[Devon Ryan]

Hi Tesa,

This will only happen if, for some reason, a BAM file can't be opened
(it falls back to assuming it's a bigWig file). Please ensure that the
files are indexed, since lacking an index is the most likely cause of
this.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

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[tesa.s...@gmail.com]

Thanks Devon, that was it. My files were indexed, but I re-indexed two and tested on them and it works fine.

Don't know what the index problem was but it's an easy fix.
Cheers,
Tesa

[maryamfo...@gmail.com]

Hi
I got the same error! How did you fix it? How can I find that my bam files are indexed?
Thanks
Maryam

[Devon Ryan]

If you don't see a .bai file with the same name as the BAM file(s) then
the file isn't indexed (use "samtools index" then).

Devon

--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dpry...@gmail.com

[maryamfo...@gmail.com]

thanks a lot for your quick response. I got my bam files from bed file ( using bedtobam software). it did not give me bai files.Is there any software that i got the bai file from bam file?

[Devon Ryan]

"samtools index", though I have to wonder what you're trying to achieve
starting with BED files, which normally contain things like where there
are peaks.

On 01/04/2017 10:19 PM, maryamfo...@gmail.com wrote:
> thanks a lot for your quick response. I got my bam files from bed file ( using bedtobam software). it did not give me bai files.Is there any software that i got the bai file from bam file?
>
>

[maryamfo...@gmail.com]

I have three set of peaks from three replicates. I did bedtoolsintersect to get the overlap between them. Then I tried to find the corelation between these three peak set file in the intersection region. So I had one bed file from intersect and three bed files from replicates.
After I got the error , I am thinking about using the bam file of each replicates instead of the peak calling files.
Thanks again for your help
Maryam

[maryamfo...@gmail.com]

Now I got another error : the software could not recognize my bed file type.
raise RuntimeError('{0} does not seem to be a recognized file type!'.format(self.filename))
RuntimeError: output_intersect_C_3rep_wa_wb.bed does not seem to be a recognized file type!

[Devon Ryan]

Your BED file has too few columns.