Open GoogleCodeExporter opened 9 years ago
Hi there,
In phase 1, MosaikSort partially sorts alignments and store them in several
temporary files, while in phase 2, MosaikSort opens all temporary files,
globally sorts them, and out them in the archive,
fil.fq_a.no2L.375.extra.hs15.mks.
In this case, I guess MosaikSort cannot find those temporary files which should
be in MOSAIK_TMP.
Could you please check the directory for MOSAIK_TMP?
ps. the command line to change MOSAIK_TMP
> export MOSAIK_TMP=<temp directory>
Original comment by WanPing....@gmail.com
on 16 Nov 2010 at 5:28
Thanks so much for the helpful comment about setting the MOSAIK_TMP variable.
I had a similar problem (using MosaikSort v. 1.1.0006), although rather than
triggering a segmentation fault, the program simply hung during the middle of
the "restitch serialized alignment" phase--it would progress to around 20%
complete, and then not go any further. When I tried using a newer version of
MosaikSort (MosaikSort 1.0.1388), I got a segmentation fault, like the user
above reported. Setting the MOSAIK_TMP environment variable as suggested fixed
the problem for me. I wonder if it would be helpful to other users to add a
note about this fix to the documentation?
Original comment by seal...@gmail.com
on 11 May 2011 at 5:12
Original issue reported on code.google.com by
mrp...@gmail.com
on 13 Nov 2010 at 9:07