Hi @vinjana,

I have generated this example from the public SEQC2 data for Sophia/35 module in the cluster. I have tried to change the chr prefix on the go so that Sophia will recognise the reads. And then the segmentation fault happens.

samtools view -F 0x600 -f 0x001 /omics/odcf/project/public_data/seqc2/sequencing/whole_genome_sequencing/view-by-pid/SEQC2_IL2/tumor0
1/paired/merged-alignment/tumor01_SEQC2_IL2_merged.mdup.bam | \
sed 's/chr//g' | \
sophia --medianisize 395.0 --stdisizepercentage 21.0 --properpairpercentage 92.02 --defaultreadlength 101 --
clipsize 10 --basequality 23 --basequalitylow 12 --lowqualclipsize 5 --isizesigma 5 --bpsupport 3

And here is the error message:

[[clipped]]
1       31788   31789   0,0,0,1,0,0,36,6,5,0,0,0        36,36   .       .       .
1       33528   33529   0,0,1,0,0,0,44,41,3,0,1,0       44,44   .       .       .
1       33546   33547   0,0,2,0,0,0,54,26,2,13,2,0      50,54   .       .       .
1       33547   33548   0,0,4,0,0,0,55,17,1,11,0,0      54,55   |4:25808805_INV(0,1,4?/8)       .       .
1       34045   34046   5,2,17,0,0,0,96,1,0,2,0,0       92,101  1:35362_INV|(4,1,!/0);12:31020091-31020162_INV|(5,1,7?/14);X:68605275-68605276_INV|(0,1,2?/4);9:1862015-1862016_INV|(0,2,4?
/8)     1:205884_INV|(4,0,1?/2);19:75792-75844|(4,0,2?/4);2:113579039-113579040_INV|(4,0,1?/2)  >120_1:GGCCTCAAGCGATCCTCCCACCTTAGCCTCCCAAAGTGTTGGGATTATAGGCATGAGCCACTGCACCTGGCT|(4)
1       35362   35363   3,2,8,0,0,0,83,3,0,1,1,0        84,86   19:75654_INV|(3,1,2?/4);1:34045_INV|(3,2,!/0);2:113579421|(0,2,3?/6)    6:99450064-99450065|(3,0,1?/2);1:205883-205884|(3,0
,1?/2);X:68605275-68605276|(3,0,1?/2)   >124_1:GTGGGCATTTAGTGCTATAAATTTCTCTTTACACACTGCTTTAAATGCGTCCC|(3)
1       39262   39263   0,0,0,1,0,0,187,23,0,0,0,0      187,188 .       .       .
1       50482   50483   0,0,0,2,0,21,48,2,0,2,0,0       44,50   .       .       .
1       50605   50606   0,0,0,0,0,0,80,18,0,41,1,0      79,80   #       #       #
1       51611   51612   0,0,1,0,0,0,14,10,0,1,1,0       14,14   .       .       .
1       54778   54779   0,0,0,0,1,0,5,20,1,0,0,0        7,7     .       .       .
1       61352   61353   0,0,0,0,0,0,0,36,2,0,1,0        0,0     #       #       #
Segmentation fault

I assume the error is because of different columns in the SAM file in this new hg38 alignments compared to the hg19 ones. I am trying to figure this out.

Failure for chromosomes with "chr" prefix #4

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