segmentation fault for speedseq sv

[crazyhottommy]

Hi Colby,

I want to let you know that I am having speedseq running OK for all my samples except this one which gives me segmentation fault.

I am not sure why this particular one gives me trouble. I have 50 others finished without error. Also let you know that the new svtyper now gives me correct genotypes.

/risapps/rhel6/speedseq/0.1.0//bin/lumpyexpress: line 411: 31825 Segmentation fault      (core dumped) $LUMPY $PROB_CURVE -t ${TEMP_DIR}/${OUTBASE} -msw $MIN_SAMPLE_WEIGHT -tt $TRIM_THRES $EXCLUDE_BED_FMT $LUMPY_DISC_STRING $LUMPY_SPL_STRING > $OUTPUT

Thanks, Ming

[cc2qe]

good to hear. Regarding the seg fault, I know that Ryan made a modification to LUMPY recently (https://github.com/arq5x/lumpy-sv/commit/d4e15812566b0cc0cac34f478f04a6ff54d0bfce) to address some of these issues. I incorporated it into speedseq (https://github.com/hall-lab/speedseq/commit/be664483a2533b21ffd373ffe8137c2a069b105b) but it was only about a month ago, so that may solve it

[crazyhottommy]

Thanks, so I will only need to update my speedseq.

Ming

[cc2qe]

if you have the error log (run with -v) could you also post it? can't e certain that that is the problem, but it's my best guess at the moment

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Sent from mobile.

On Oct 5, 2015, at 17:33, Ming Tang [email protected] wrote:

Thanks, so I will only need to update my speedseq.

Ming

— Reply to this email directly or view it on GitHub https://github.com/hall-lab/speedseq/issues/50#issuecomment-145674740.