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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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markdup - segmentation fault #483

Closed BioinfoRDX closed 2 years ago

BioinfoRDX commented 2 years ago

Hi,

I try to run a WES bam of 3Gb, SO:coordinate. I'm running on a single ubuntu-server 21.10 node, Intel(R) Xeon(R) Gold 6230 CPU @ 2.10GHz

INSTALLATION

apt install sambamba

VERSION

sambamba 0.8.0
 by Artem Tarasov and Pjotr Prins (C) 2012-2020
    LDC 1.24.0 / DMD v2.094.1 / LLVM11.0.0 / bootstrap LDC - the LLVM D compiler (1.24.0)

CODE

sambamba markdup \
"sorted.bam" \
"sorted.mark.bam" \
--show-progress \
--nthreads=15 \
--tmpdir=/tmp

LOGS

finding positions of the duplicate reads in the file...
[==============================================================================]
  sorted 29226666 end pairs
     and 14778 single ends (among them 0 unmatched pairs)
  collecting indices of duplicate reads...   done in 3812 ms
  found 3551068 duplicates
collected list of positions in 1 min 40 sec
marking duplicates...
[                                                                              ]Segmentation fault (core dumped)

If you need more information let me know.

sambamba sort is OK.

Best

pjotrp commented 2 years ago

If you can share the file I can take a look. Did you try the static binaries provided on github?