Error: Empty BAM file in DANPOS3
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10 months ago
sshibin • 0

Hi everyone, I am currently trying to run the command in DANPOS3 - which is a software to analyse nucleosome positions and call peaks. This is the command

$python3 danpos.py dpos <filename.bam> [optional parameters]

The bam file I am using was created using Galaxy. So the reads were aligned using Bowtie2 and then using "samtools view" I obtained only chromosome 5 reads. I validated this file for any errors using "Validatesamfiles" which assess SAM/BAM files, I was able to conclude that there are no errors.

However, after running the above the command, I get the following error

ERROR: empty BAM file

Is something wrong with the header file? It looks like this with the @SQ for all chromosomes

@HD VN:1.0 SO:coordinate @SQ SN:chr10 LN:129993255`
@PG ID:bowtie2 PN:bowtie2 VN:2.3.4.1 CL:"/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-5bee08a20f60a5597c4ecd54735d608dc6a44caf6f433cd52f23c80aa5a38d02/bin/bowtie2-align-s --wrapper basic-0 -p 10 -x /cvmfs/data.galaxyproject.org/byhand/mm9/mm9full/bowtie2_index/mm9full -U input_f.fastq.gz"`

If there is no error in the BAM file when I validate, why would I get empty BAM file when I run the first mentioned command?? I am so new to this analysis of nucleosome positions, any insights into this will help!!

Thanks in advance

sequence nucleosome danpos galaxy • 383 views
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Hey, this is juste a hypothesis, but coud it be that DANPOS is checking if there are reads assigned to every chromosome listed in the bam header ? When it finds 0 reads for chromosome1, then it gets confused and say that the bam file is empty ? Perhaps you could try to remove the @SQ line for the "empty" chrosome (keep only chr5) or try to feed DANPOS with the full bam.

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Given the horrible implementation of DANPOS I wouldn't be surprised if that was actually the case..

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I'd post DANPOS3 issues directly to the dev's github: https://github.com/sklasfeld/DANPOS3/issues. DANPOS3 is a Python3 port of DANPOS/2, but from a 3rd party dev. The port has/used to have some issues, maybe this is one of them.

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