Segmentation fault error in a subset of samples using LUMPY Express

[info-97]

Hello,

As pointed out in previous threads ----
#314
#129
I am having similar issues while running lumpyExpress---

The command used ----

/nfs/software/lumpy-sv/bin/lumpyexpress -B ${bam_path} -D ${DIR_SELECT}/${sample_name}/discordants/${sample_name}.disc.sort.bam -S ${DIR_SELECT}/${sample_name}/splitters/${sample_name}.splitters.sort.bam -o ${DIR_SELECT}/${sample_name}/lumpy/${sample_name}.vcf

The same error was reported in 2 separate runs ( one on cluster with maxvmem ~ 2.0G ), where 12 G was allocated.

A partial vcf file was generated with core dumped---

I am providing here tail of the log files for 1 sample ---

Alignment name:A00123:173:HGYYVDSXX:4:1503:21730:33082
Cannot determine BP type:side_l.start:63968263 side_l.end:63968330 side_r.start:63968396 side_r.end:63968547 query_l.qs_pos:0 query_r.qs_pos:0 side_l.strand:+ side_r.strand:-
Alignment name:A00123:173:HGYYVDSXX:1:2327:8061:18364
Cannot determine BP type:side_l.start:63982364 side_l.end:63982398 side_r.start:63982687 side_r.end:63982838 query_l.qs_pos:0 query_r.qs_pos:0 side_l.strand:+ side_r.strand:-
Alignment name:A00123:173:HGYYVDSXX:1:1329:15998:11162
ERROR IN BAM FILE. TYPE not detected (DELETION,DUPLICATION,INVERSION)
0,+ 0,+ 1,46539960,46539998 1,63999928,64000079
Error creating split read:
/nfs/software/lumpy-sv/bin/lumpyexpress: line 413: 22084 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

Please let me know if you have any suggestions to troubleshoot and also if you would need temporary files created while lumpyExpress run.

Thanks for help!