bam_readcount error: [bam_plp_destroy] memory leak: 1. Continue anyway.

Question

[jflucier]

Hello,

I used bam_readcount to analyse 6 of my samples. I get this error for 3/6 samples. Was wandering how i can solve this error.

I tried to set different quality parameters to prevent this error without success. I found that bam_readcount fails for the 3 of the biggest bam (3, 5, 6):

[jflucier@ip29-mp2 vl_samples]$ ll -h *.bam
-rw-rw-r-- 1 jflucier jacques 55M Jul 26 09:54 1.90.mka.bam
-rw-rw-r-- 1 jflucier jacques 77M Jul 26 09:58 2.90.mka.bam
-rw-rw-r-- 1 jflucier jacques 99M Jul 26 10:02 3.90.mka.bam
-rw-rw-r-- 1 jflucier jacques 76M Jul 26 10:05 4.90.mka.bam
-rw-rw-r-- 1 jflucier jacques 89M Jul 26 10:09 5.90.mka.bam
-rw-rw-r-- 1 jflucier jacques 90M Jul 26 10:13 6.90.mka.bam

Here are the command I am running:

[jflucier@ip29-mp2 vl_samples]$ ./programs/bam-readcount/bin/bam-readcount -f vl_ref.fa .3.90.mka.bam  > 3.90.mka.bam_readcount.tsv
Minimum mapping quality is set to 0
[bam_pileup_core] the input is not sorted (reads out of order)
[bam_plp_destroy] memory leak: 1. Continue anyway.
[jflucier@ip29-mp2 vl_samples]$ ./programs/bam-readcount/bin/bam-readcount -w 1 -b 30 -f vl_ref.fa 3.90.mka.bam  > 3.90.mka.bam_readcount.b30.tsv
Minimum mapping quality is set to 0
[bam_pileup_core] the input is not sorted (reads out of order)
[bam_plp_destroy] memory leak: 1. Continue anyway.

Nothing is outputted in tsv files when this error occurs.

thank for your help,

JF

[jflucier]

for those who face the same problem, i found that if your sort bam using samtools, I dont get this error anymore.

[GenoMax]

@Devon gave you that answer.

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Answer 1

[Devon Ryan]

Make sure your BAM files are sorted (samtools sort).