Fred-07

[2020-03-04T16:18:07.428228Z] [cpt01.cluster.uni.ch] [34169_1] [TaskManager] Launching command task: 'generateCandidateSV_0000' from master workflow [2020-03-04T16:18:07.449977Z] [cpt01.cluster.uni.ch] [34169_1] [TaskRunner:generateCandidateSV_0000] Task initiated on local node [2020-03-04T16:31:44.504454Z] [cpt01.cluster.uni.ch] [34169_1] [TaskManager] [ERROR] Failed to complete command task:...

The content of the 'result' directory where an anomalous file is created : RunDir_1KG_HG_002/: total 1120142 -rw------- 1 user diag-dpt 1261289472 Mar 4 17:31 **core.51471** -rw-rw-r-- 1 user diag-dpt 220531...

Other option is to convert number to string by interpolation and use "eq" LINE 2107: if ("$chrSample" eq "$chrControl" ......

Thank you for these explanations. Please find below the link for the reference genome (hg19, slightly modified) https://www.dropbox.com/scl/fi/e9imci4i4rkv5vcpgujus/genome_PAR_masked.fasta.gz?rlkey=5fxpz3fbzy70glish6xwhckc9&dl=0