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Question: seqlevels(param) not in BAM header
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gravatar for james.dalgleish
4 months ago by
james.dalgleish30 wrote:

------------------------------------------------------------
Info: setting summary
------------------------------------------------------------
Name of aligned read file: SRR3105506.sorted.filtered.bam
Aligned read file format: BAM
Directory of processed bin-level files: ./jmosaics/
Construct bin-level files by chromosome? N
Is file for chromosome info provided? Y
Name of file for chromosome info:  hg19.chrom.sizes
Data type: Single-end tag (SET)
Average fragment length: 200
Bin size: 200
------------------------------------------------------------
Use the provided BAM index file.
Use the chromosome information provided in 'chrfile'.
Info: reading the aligned read file and processing it into bin-level files...
Info: reading the aligned read file and processing it into bin-level files...
Error in { : task 1 failed - "seqlevels(param) not in BAM header:
    seqlevels: ‘chr1_gl000191_random’

Is there a way to automatically exclude random chromosomes from analysis in jmosaics or some way to subset the bam files such that no random chromosomes are found in the files? I've used samtools with the following syntax, but it doesn't seem to be able to help things:

samtools view -@ 63 -b SRR3105504.sorted.bam chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY chrM > SRR3105504.sorted.filtered.bam

samtools index -@ 63 SRR3105504.sorted.filtered.bam

The error, unfortunately, still persists.

 

 

ADD COMMENTlink written 4 months ago by james.dalgleish30

I can't tell what package/command you are using.  It seems to me you need to look carefully at the 'param' in use.

ADD REPLYlink written 4 months ago by Vincent J. Carey, Jr.6.2k
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