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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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Error with ChIP-seq histoneHMM bam headers #809

Closed davidsanin closed 2 years ago

davidsanin commented 2 years ago

Hey all! I was running the ChIP-seq pipe with the broad mark setting for some 5hmC ChIP samples generated with RELACs. Both this and the DNA-mapping pipelines ran smoothly all the way to the histoneHMM step which crashed. The log file for it shows first R loading a bunch of tools then getting to this error:

Error in .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file),  : 
  seqlevels(param) not in BAM header:
    seqlevels: ‘chr1’, ‘chr2’, ‘chr3’, ‘chr4’, ‘chr5’, ‘chr6’, ‘chr7’, ‘chr8’, ‘chr9’, ‘chr10’, ‘chr11’, ‘chr12’, ‘chr13’, ‘chr14’, ‘chr15’, ‘chr16’, ‘chr17’, ‘chr18’, ‘chr19’, ‘chrX’, ‘chrY’, ‘chrM’
    file: filtered_bam/OPA1_1_5hmC.filtered.bam

I did a quick samtools view -H to check the header of the filtered.bam file and the chromosome names were indeed formatted as "1", "2", etc... instead of "chr1", "chr2", etc... Bit confused by this as the whole thing is part of the same pipe, so I would guess this should be smoothed out somewhere.

There might be something wrong with my installation? I am running the pipe locally and I had a previous issue with dependencies. I got around it by symlinking the openblas library to the conda environment handling the histoneHMM step, as it was failing to load the library. Not sure if that is related. Happy to provide sessionInfo if that is useful.

Thanks in advance!

davidsanin commented 2 years ago

Found my error! My genome annotation had a bug! Thanks!