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GenomeSTRiP installtest error
Hi, I just installed genomestrip version 2.00.1602. I tried to run the installation test. discovery.sh ran successfully, but genotyping.sh failed with error.
The following are the error messages:
INFO 13:51:53,638 FunctionEdge - Starting: samtools index test2/installtest.alt.bam
INFO 13:51:53,639 FunctionEdge - Output written to /data/endoxifen_wgs/bin/svtoolkit/installtest/test2/logs/SVAltAlign-7.out
INFO 13:51:53,801 QGraph - 0 Pend, 1 Run, 0 Fail, 6 Done
ERROR 13:52:23,617 FunctionEdge - Error: samtools index test2/installtest.alt.bam
ERROR 13:52:23,623 FunctionEdge - Contents of /data/endoxifen_wgs/bin/svtoolkit/installtest/test2/logs/SVAltAlign-7.out:
Segmentation fault (core dumped)
INFO 13:52:23,625 QGraph - Writing incremental jobs reports...
INFO 13:52:23,626 QGraph - 0 Pend, 0 Run, 1 Fail, 6 Done
INFO 13:52:23,629 QCommandLine - Writing final jobs report...
INFO 13:52:23,630 QCommandLine - Done with errors
INFO 13:52:23,633 QGraph - -------
INFO 13:52:23,633 QGraph - Failed: samtools index test2/installtest.alt.bam
INFO 13:52:23,658 QGraph - Log: /data/endoxifen_wgs/bin/svtoolkit/installtest/test2/logs/SVAltAlign-7.out
INFO 13:52:23,659 QCommandLine - Script failed: 0 Pend, 0 Run, 1 Fail, 6 Done
It seems like samtools failed to index the bam file. The content on SVAltAlign-7.out is 'Segmentation fault (core dumped)'.
Please help. Thanks.