LASER Error: signal 6

[Roland Wittler]

The command:

laser -T 4 GRCh38_full_analysis_set_plus_decoy_hla.fa ERR992656_1.fastq.gz ERR992656_2.fastq.gz ERR992656.laser

(Data from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/hgsv_sv_discovery/illumina_wgs.GRCh38.alignment.index and clever-toolkit-v2.1)

aborts with the following error (full log attached):

[...] Reading reference sequence "HLA-DRB115:03:01:01" Reading reference sequence "HLA-DRB115:03:01:02" Reading reference sequence "HLA-DRB1*16:02:01" Read 3366 reference sequences. laser-core: /prj/cancersv/tools/clever-toolkit-v2.1/src/ShortDnaSequence.cpp:103: char ShortDnaSequence::operator const: Assertion `pos < forward->size()' failed. Error: signal 6: /prj/cancersv/tools/clever-toolkit-v2.1/src/laser-core(_Z14signal_handleri+0x18)[0x424fc8] /lib64/libc.so.6(+0x35990)[0x2b4939df3990] /lib64/libc.so.6(gsignal+0x9f)[0x2b4939df391f] /lib64/libc.so.6(abort+0x16a)[0x2b4939df551a] /lib64/libc.so.6(+0x2dda7)[0x2b4939debda7] /lib64/libc.so.6(+0x2de52)[0x2b4939debe52] /prj/cancersv/tools/clever-toolkit-v2.1/src/libclever.so.2.0.0(+0x7c2cd)[0x2b49381bd2cd] /prj/cancersv/tools/clever-toolkit-v2.1/src/laser-core(_ZN10NfaMatcherC1I16ShortDnaSequenceEERKT_mmb+0xb6)[0x454b96] /prj/cancersv/tools/clever-toolkit-v2.1/src/laser-core[0x452b21] /prj/cancersv/tools/clever-toolkit-v2.1/src/laser-core(_ZN4Read14findNewAnchorsERKNS_23anchor_search_regions_tERKSt6vectorIP16NamedDnaSequenceSaIS5_EEii+0x2a)[0x453a9a] /prj/cancersv/tools/clever-toolkit-v2.1/src/laser-core(_Z17process_read_pairR18read_pair_record_tR13read_output_tRK12parameters_t+0x5e5)[0x428135] /prj/cancersv/tools/clever-toolkit-v2.1/src/laser-core(_ZN10ThreadPoolI14work_package_t15output_writer_tE11thread_mainEPv+0x142)[0x43d0c2] /lib64/libpthread.so.0(+0x76ca)[0x2b49384246ca] /lib64/libc.so.6(clone+0x5f)[0x2b4939ec5f7f]