Samtools (v1.2) merge doesn’t output any file of my two bam file and no message throwing out. It just hang there and reserved ~2.0g memory. However, 0.1.18 version finish the merging in ~2 mins.
The two sorted bam files are 449M and 448M in size. v1.2 samtools merge out.bam tmp/tmp.0000.bam tmp/tmp.0001.bam Version: 0.1.18 samtools merge out.bam tmp/tmp.0000.bam tmp/tmp.0001.bam real 2m26.713s user 2m20.100s sys 0m6.530s Any insight or similar issue with error message from community? Thanks, Chienchi From: Giuseppe Aprea <giuseppe.ap...@gmail.com<mailto:giuseppe.ap...@gmail.com>> Date: Friday, February 6, 2015 at 10:13 AM To: "samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>" <samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>> Subject: [Samtools-help] samtools merge Hi all. Is there any known limitation for bam merging? I am trying to merge 4 sorted bam files with samtools (v 1.2) but I get the following error: 39656 Segmentation fault (core dumped) samtools merge merging.bam *.sorted.realigned.nodup.sorted.bam *.sorted.realigned.nodup.sorted.bam are 4 files with sizes: 6.1G, 6.2G, 3.9G and 4.0G Any suggestion, please? Thanks in advance, Giuseppe
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