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trouble with bamfilter #57
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Hi guyleonard, Thanks for this. Have been busy these days, will look into it tomorrow. cheers, dom |
Hi, Thanks! |
Hi both, is the BAM file sorted by readname (this is usually how it comes out of an aligner)? Because pairs have to be together in the BAM file ... a position sorted BAM file would cause an error... let me know if that helps, cheers, dom |
Hi @DRL , My bam file was sorted by read name, and pairs were gathered. Thanks! |
Hello (and thanks for blobtools :) ), I want to extract all reads mapping to some scaffolds, thus I grepped all scaffolds name and ran the following command on my .bam file:
My bam file is around 42 Gb but when I run the command, the threads go to dorment status, it runs overnight with 450 Gb RAM usage (still increasing) and it outputs a 0 bytes InIn.fq
I guess this is not expected behaviour ? Any ideas of what goes wrong here ? |
Hi I have two issues with running the bamfilter program.
Firstly, I have an -i include list called scaffolds_vs_nt_1e-10_eukaryota_test.txt:
I also have a sorted+indexed bam file that I created by indexing the scaffolds.fasta with bwa and then mapping my individual libraries with bwa mem, then merging those bams to one final bam with samtools. All v1.3. Then followed with samtools sort and index.
When I try the code below, it works fine.
samtools view -b scaffolds_mapped_all_reads_sorted.bam NODE_10002_length_2789_cov_4.69971 > test.bam
I get the reads mapped to that scaffolds, but when I try:
Well you can see the error message - none of the scaffold IDs match anything in the BAM - which can't be the case as the samtools command above works fine. Is there something obvious I have missed?
Secondly, almost incidentally - and this may be because blobtools uses samtools v1.5 (though there doesn't seem to be anything in the release notes to suggest this behaviour) but if I repeat the same command above but with "--sort" on my unsorted BAM file, instead of the 5.5GB file I expect it comes out as 13GB and then working with that file is impossible.
Any help is much appreciated! :)
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