hello,
i'm having trouble running samtools mpileup with about 90 bam files as input.
the command is
samtools mpileup -ugf bam1 bam2 bam3 ... > pleasework.bcf
but these lines are printed on the screen:
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[mpileup] 37 samples in 98 input files
[bam_plp_destroy] memory leak: 19. Continue anyway.
[bam_plp_destroy] memory leak: 113. Continue anyway.
[bam_plp_destroy] memory leak: 5. Continue anyway.
[bam_plp_destroy] memory leak: 74. Continue anyway.
[bam_plp_destroy] memory leak: 4. Continue anyway.
...... memory leak alert for every input file
then the process comes to an end in about a second.
A bcf file is made indeed, but it's empty with just the header and no variant called whatsoever.
The bam files are sorted, and the weird thing is the mpileup works fine with just one or two inputs.
It just shuts down on me when 98 are shoved in and I can't figure out why..
would be great if I can!
thank you.
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