Open info-97 opened 4 years ago
Hello,
As pointed out in previous threads ---- https://github.com/arq5x/lumpy-sv/issues/314 https://github.com/arq5x/lumpy-sv/issues/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!
Hello,
As pointed out in previous threads ---- https://github.com/arq5x/lumpy-sv/issues/314 https://github.com/arq5x/lumpy-sv/issues/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!