SAM output stdout fail and cannot convert to bam about chromap HOT 13 CLOSED

The --hic option implicitly uses --low-mem option, which needs to generate temporary files using the prefix of the -o option. I don't think you can create a file in the folder /dev/ folder so Chromap could not generate the temporary files. In this case, you can either generate sam->bam as you already did, or run Chromap with the option "-o /dev/stdout --split-alignment --pairs" instead of "--hic". Your data is not very large, so the memory usage should not increase much.

We will find a better solution in the future. Thanks.

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But when I use the the sam->bam, the samtools throw the error

[E::sam_parse1] CIGAR and query sequence are of different length
[W::sam_read1] Parse error at line 20315
[main_samview] truncated file.

from chromap.

I run into the same error too

from chromap.

Which Chromap version did you use?

It seems that in your example the cigar length is 104 and the sequence length is 150, which is the full read length. I thought this was fixed in #29, where we forgot to trim the sequence before we output it. But it seems the problem is still there with your example. I will double check and fix this problem if it is still there in next release.

from chromap.

chromap (0.1.3) installed from the conda. I can try the latest 0.1.4 for small test data. Stay tuned.

from chromap.

chromap (0.1.3) installed from the conda. I can try the latest 0.1.4 for small test data. Stay tuned.

Hi,

No need to try that. I just located the problem. It is a bug with the SAM output and the sequence is not trimmed properly in the SAM output. I will generate a fix tomorrow. It would be great if you can try that later.

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from chromap.

Could you try the new branch trim-hic-sam (#57) and see if the issue is fixed? I tried on my Hi-C data and I could then run SAMtools to convert the SAM output by Chromap to BAM without errors. Please let know if the problem is resolved so that I will tag a new release.

from chromap.

My test results on other benchmark data look fine. So I merged this into the master branch. You can now try master branch. I will tag a new release soon.

from chromap.

Sorry, I have met a install issue with make on master branch, I can try it with the updated conda version.

from chromap.

Sorry, I have met a install issue with make on master branch, I can try it with the updated conda version.

It is now updated on bioconda with new release v0.1.5.

from chromap.

Sorry for the delay in testing, but the this seems to have solved the issue, I can now convert SAM to BAM with samtools

Thank you!

from chromap.

Sorry for the delay in testing, but the this seems to have solved the issue, I can now convert SAM to BAM with samtools

Thank you!

Good to know. Close this issue.

from chromap.