Segmentation fault

[husamia]

I ran three samples simultanously. One of them processed to completion but two failed due to Segmentation fault during the Building graph step

2021-07-27 16:01:08,978 [INFO   ]  [dysgu-run] Version: 1.1.7
2021-07-27 16:01:08,980 [INFO   ]  run -p5 GRCh38_full_analysis_set_plus_decoy_hla.fa X_dysgu X.cram.bam
2021-07-27 16:01:08,980 [INFO   ]  Destination: X_dysgu
2021-07-27 20:52:22,501 [INFO   ]  dysgu fetch X.cram.bam written to X_dysgu/X.cram.dysgu_reads.bam, n=32435857, time=4:51:13 h:m:s
2021-07-27 20:52:22,501 [INFO   ]  Input file is: X_dysgu/X.cram.dysgu_reads.bam
[E::idx_find_and_load] Could not retrieve index file for 'X_dysgu/X.cram.dysgu_reads.bam'
2021-07-27 20:52:22,715 [INFO   ]  Input file has index False
2021-07-27 20:52:23,231 [WARNING]  Warning: more than one @RG, using first sample (SM) for output: X
2021-07-27 20:52:23,231 [INFO   ]  Sample name: X
2021-07-27 20:52:23,231 [INFO   ]  Writing vcf to stdout
2021-07-27 20:52:23,231 [INFO   ]  Running pipeline
2021-07-27 20:52:26,642 [INFO   ]  Removed 55 outliers with insert size >= 1661
2021-07-27 20:52:26,659 [INFO   ]  Inferred read length 151.0, insert median 444, insert stdev 202
2021-07-27 20:52:26,660 [INFO   ]  Max clustering dist 1454
2021-07-27 20:52:26,660 [INFO   ]  Minimum support 3
2021-07-27 20:52:26,660 [INFO   ]  Building graph with clustering distance 1454 bp, scope length 1454 bp
Segmentation fault

[kcleal]

Hi, thanks for reporting this. If possible, would you be able to test some different options to try and help me track down the cause of the bug? Please could you try using -p1, and if the bug persists please try setting --contigs False. Thanks

[husamia]

I was using the wrong reference. I will close this issue. Thank you