Getting "Segmentation fault (core dumped)" when running against some bam files.

[MurphyDavid]

Hi
Running the scramle docker, it seems to randomly fail for some bam files with a seg fault.
This doesn't seem to be for all bam files but I can't identify any common aspect of the ones for which it does fail vs succeed.

I don't see any core dump file to include (where would these save to?)

Docker command used:

docker run -v /mnt/qsg-results-3/:/LIfolder -it --rm scramble:latest bash

Command used:

root@2704cc4af852:/# /app/cluster_identifier/src/build/cluster_identifier /LIfolder/LI6073/Sorted_LI6073.bam

output:

chr1:189991284 right 6 cctgccacaaccactccccagtgcctttaagagtttctacacctgcatccagatgtttaaatacaggaaactgctgt ttttc 
chr1:200911586 right 6 cctgccactcctgctcagaagacagtggctctgacgtctccagcatctcccaccccacttcgccgggcagcagcagccccgacatctcctttctgca ccc
chr1:201048681 right 10 ccagccgctgtacagggagacgcagtggcctgccgctgagctgggaccaggccaagcttggcaagtcatcctcacccggtctgtggaccgggagg cccc
chr1:201066388 right 9 ccagccatatcctgccctccacaccagctgcctttctgcctgaaaacactcccaccttccccttccctttcctccagccgtgagagtgtgccc ccc
chr1:201782348 right 12 cctgccacaggcacagccactgtcatgcaaactggtggttcagccactctcagcaagatccagaagtcctcaggcatccctgtca ccc
chr1:203498891 right 10 ccctgccactaggacagtcaccaacactgtgttagtgccccccgtgttagctctttcctgttggctctcagtccctccagctgtcaaaggga ccc
chr1:204249208 right 6 ccagccggtcctgctccctcaccaccttgttctgctcacacaattttcccagcagcttctagggacccagagagtggagaaggagagggagaaa cc
chr1:204460083 right 7 tgaaggagggagagtcttt gccctgggaaacccattttctccctccctctcctcagctcacactctgatttaaaggagttcccactctttctatatgtcctgtgaagac
chr1:205065724 left 15 tcatgtctcatggcctgctgcactggtcagggccggtggtc tggcctgctgcactggtcagggccggtggtctgacctgctgcccctaactgtccccgtgtgcagaaggagaccattggggatctgacca
chr1:205065766 right 11 actggtcagggccggtggtctgacc ccatggatgtcatggagtaggggactcccaagcgctgcctcatgtctcatggcctgctgcactggtcagggccggtggtctggcctgctgc
chr1:205069461 right 7 aagccatatcggtgtcccttggcccttgacagccccctcggtggcaccctcaggactcagcggaggaggtggagcccccggagagct aaa
chr1:205339789 right 8 cctgccgcatatactcggtaatctaagaagaaaggccatacatgcccctggcttagctca ccc
chr1:205339790 right 9 cctgccgcatatactcggtaatctaagaagaaaggccatacatgcccctggcttagctcacaggtacagcaagacaggcccaccagtatctattg cccc
chr1:205662050 right 7 ccagccggtccatgaccagagagaagaccagggagatggcgcactgcaggaacagccccaggctgcccatccgaacgcctgcagagggagaggggcc cc
chr1:206730053 right 5 ccagccacaactctttgaccactccttgttatacaccgtactatgtgggtaagtccacagggggcccagggacctaggcttttcccagaactttt ccc
chr1:208103054 left 8 aggacaattcctct ctctctctgcaaagtactgtcatatcccatcattcccggaaagccccggtcttctgcatgccaaacccttttccagtataccccaaactta
chr1:208267465 left 10 tcataagattactttccagcagcagcagcagcagcagcagcagcagcagcagcag cagcagcagcagcagcagcagcagcagcgatgtaattgacccccatttacagatgatgcagctttaaggcagagaattccatggctg
chr1:209432319 right 6 agagtaactctg catggagctgacaaccatgaggcctcggcagccaccgccaccaccgccgccgccaccaccgtagcagcagcagcagcagcagcagcagca
chr1:209788627 right 5 gagccactactggaatgacctgttcaggacacagaacacaggtgtatcctctgaggaaaaggtatttttaaatagcacaatggacccaagatt cg
chr1:214464832 right 13 gcctatcctggcgcacacgcccctgagatggccttagcagtttcgtgactggaaaattacactatcacctgtgctcctccaggcaggga cct
chr1:214464835 right 8 gcctatcctggcgcacacgcccctgagatggccttagcagtttcgtgactggaaaattacactatcacctgtgctcctccaggcagggaaaagg ccgcct
chr1:215786813 right 12 cctgccacaatgttctgtggcttccatagatgctgggcagaggatcctgcactctttggtttcctgagtcaagtggcag cc
chr1:224114452 right 5 gaggagaaggga ttatgtcctacgacgaaattagccagctccgcctggtgaggcccccgcagaactcctgcctccctctccccccggccgaggtctgggagat
chr1:224330143 right 6 caagccacagctcggaccgccagctcctagtcaaccgggggcctcgtaggggttgcccgccgcgttcgccgggccagttgcacctgaaa ttt
chr1:227925467 right 14 gccgcctctggctccagggtcagcgggaggatggtcaggggctcgctgcccgtcagcctgggcacagagaggccagcatgagcccggcccc gggcg
chr1:229647493 left 5 ttttcctctatc ttattttgccctttagctcttaaaccgagaagcttctcaggagcagcctgtgtccctcacagtggtcgggcctgtcttagatgtcctggct
chr1:230710052 right 11 tcagggagcagccagtcttccatcctgtcacagcctgcatgaacctgtcaatcttctcagcagcaacatccagttctgtgaagtccagagagcgt cccg
chr1:232515127 right 5 ttgggcacagctggggtaccattagccggaccaccaccgccagtctcattggaattcgaggcatttaaagaagtagtgggtcccatgttgccat cccatt
chr1:233379357 right 5 gtggggaggccagcagccccccctccctgccactgtcaagtgccctgggcatcctctccacaccttctttctccacaaagtgcctgctgcagatggac g
chr1:233614150 left 10 cggcgttggccttggctttggct ttggcggcggcggtggagaagatgctgcagtccctggccggcagctcgtgcgtgcgcctggtggagcggcaccgctcggcctggtgctt
chr1:236540468 left 6 caagcacacgcacatatacttatgactgcctgtttgtctggggagagacag ggacgcaaggaaacatttaaatttggataataagttaatttattaactgtttttttttggtggcgggggggg
chr1:240207330 right 6 agccacgaacactctgtttcctctgcctttaaaaacagctgtaacatcccatctccaccacctctgccttgcacagag g
chr1:247434047 left 11 gtgttctgaggccttctctattcca gagctctctggtcagatgtgttctgatgctttctgcctctgttcttggcatgaaggttggggcgctgtggcctctcgcatgagtgctgctt
chr1:248858387 right 11 cctgccgttagggcctcagtttcctcatcagtgaactggggcaagactaaactatttcaatagcagtggcaggtgtggagccaaaccccgtcctt ccc
chr2:676478 left 12 cagaactcctgtaa gtgtcactactctctgctggggaccgcagcggcttctccagagccgcgccatgacataaggacacaagcgcatctactcccatcaatgcac
chr2:1638773 left 11 ggaataaaacgttatacg cagaaggttcgggcagggctgtgctgctgtggaatcttggagtggggggacacaggccgccaggcacctcacctgtgttctgaggtctg
chr2:6910472 right 7 acattagtgggtgcagcgcaccagcatggcac gtagaaagagagagagagaggagtttttaagtactgtatgtattttaaggagattgaataatctaaggtgaggagcatttaaaataata
chr2:9843465 right 7 gcttctccagcctttcccggaagctgcgctcgc aaggtttccctgccgcgcaggcgcacggaatcctaggcgcggatctcgcgtttgcggccggaag
chr2:10122796 right 5 ccactatgctctccctccgtgtcccgctcgcgcccatcacggacccgcagcagctgcagctctcgccgctgaaggggctcagcttggtcgacaagg ccg
chr2:15393610 left 6 gtctgagagaaatgaaagcgtatgtctacac aaatgaaagcgtatgtctacacaaacacttgcatatgaaaagtcatagcaactttatttgtaaaagccaaaactcaaaataacccaaat
chr2:15942065 right 6 gagccgatgccgagctgctccacgtccaccatgccgggcatgatctgcaagaacccagacctcgagtttgactcgctacagccctgcttct ggggggg
chr2:16239536 left 7 acaacaagctacaacagcagcagcagcagcag cagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagaatgaaggaatgaatgaatgaatgagcgagtgagtgag
chr2:20102729 left 11 atggggagaaggagaagaagaagaagaagaaga agaagaagaagaagaagaagaagaagaagaagaagacgacgacaacggtggtgagggggatggtaccagtctgaggttcgacaggcagtt
chr2:20618698 left 5 ggggctgggcatcta gttggcaaggcatccccacaccctccctccccttcatgtccacggggaataagacacattgggctctggctcctagggtgagagccgctcc
chr2:20640843 right 6 cctgcctcaccagcctggctgaagcctccaggctgcagaggcagctgtggacatgctcccactggggcacggcagcggggcctagttctgggc ccc
chr2:24054101 right 6 cccagccagtctagtgggaatgataaaggaggcttggaaggccaactctttccctcttctaccagcaagggccatccatggtgccagcttctaggt ccc
chr2:27205506 right 6 ccctgcaaggaaagcacagcaaccctgccacagaggccttctaaacccagcttgtccaacctgccttattttgttgttgc cccc
chr2:27629250 right 13 ggtcttcgaggatttggagggt ttttgtacaggtgacgtacacagcatgggtgtagtaggggagcgcaaaaggttgcctccggcaggcggaaggccaggaagaaagggaggga
chr2:28632222 right 5 tttttttttttttaaccatctctctccaagaggattcctgagggtggctttttccacattacctccttt t
chr2:29144009 right 6 acagacagtatg gatcgtgttgttattgcaggacagaaggtacagtaagtaactgcagtctctgaagccagggttgttatgtccatgacctatgttcaaggac
Segmentation fault (core dumped)

Bam files are built against GRCH38, aligned with novoalign.

[qingyun039]

可能是某一区间的深度太高了，导致cluster_identifier栈内存溢出，这种情况可以用ulimit -s提高栈内存限制来解决