Error while using v1.0.15 on GSNAP aligned bam files

[napr]

I am using strelka v1.0.15 on GSNAP aligned RNA-Seq data and i'm getting this error

ERROR: Failed system call: '/data2/bsi/staff_analysis/m081429/Somatic_workflow_paper/install_tools1/STRELKA/strelka_workflow-1.0.15/libexec/strelka2 -clobber -filter-unanchored -min-paired-align-score 20 -min-single-align-score 10 -min-qscore 0 -report-range-begin 25000001 -report-range-end 50000000 -samtools-reference '/data2/bsi/staff_analysis/m081429/Somatic_workflow_paper/ref_files/GRCh37_gencode_v19_CTAT_lib_July272016/ref_genome.fa' -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name 'chr6' -genome-size 2861343699 -max-indel-size 50 -indel-nonsite-match-prob 0.5 --min-contig-open-end-support 35 --somatic-snv-rate 0.000001 --shared-site-error-rate 0.0000005 --shared-site-error-strand-bias-fraction 0.5 --somatic-indel-rate 0.000001 --shared-indel-error-rate 0.000001 --tier2-min-single-align-score 5 --tier2-min-paired-align-score 5 --tier2-single-align-score-rescue-mode --tier2-mismatch-density-filter-count 10 --tier2-no-filter-unanchored --tier2-indel-nonsite-match-prob 0.25 --tier2-include-singleton --tier2-include-anomalous -bam-file /data2/external_data/Sun_Zhifu_zxs01/GSE40419/ERP001058_analysis_run_tum_pair_with_gsnap/ALIGNMENT/GSNAP/ERR164479_1.GSNAP.gatkin.splitNC.realign.recaliber.bam --tumor-bam-file /data2/external_data/Sun_Zhifu_zxs01/GSE40419/ERP001058_analysis_run_tum_pair_with_gsnap/ALIGNMENT/GSNAP/ERR164559_1.tumor.GSNAP.gatkin.splitNC.realign.recaliber.bam --somatic-snv-file /data2/external_data/Sun_Zhifu_zxs01/GSE40419/ERP001058_analysis_run_tum_pair_with_gsnap/SOMATIC_SNVINDEL/GSNAP/ERR164559_1.tumor.GSNAP.gatkin.splitNC.realign.recaliber.strelka/chromosomes/chr6/bins/0001/somatic.snvs.unfiltered.vcf --somatic-indel-file /data2/external_data/Sun_Zhifu_zxs01/GSE40419/ERP001058_analysis_run_tum_pair_with_gsnap/SOMATIC_SNVINDEL/GSNAP/ERR164559_1.tumor.GSNAP.gatkin.splitNC.realign.recaliber.strelka/chromosomes/chr6/bins/0001/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 /data2/external_data/Sun_Zhifu_zxs01/GSE40419/ERP001058_analysis_run_tum_pair_with_gsnap/SOMATIC_SNVINDEL/GSNAP/ERR164559_1.tumor.GSNAP.gatkin.splitNC.realign.recaliber.strelka/chromosomes/chr6/bins/0001/somatic.indels.unfiltered.vcf.window --max-input-depth 10000 --ignore-conflicting-read-names --report-file /data2/external_data/Sun_Zhifu_zxs01/GSE40419/ERP001058_analysis_run_tum_pair_with_gsnap/SOMATIC_SNVINDEL/GSNAP/ERR164559_1.tumor.GSNAP.gatkin.splitNC.realign.recaliber.strelka/chromosomes/chr6/bins/0001/strelka.stats >| /data2/external_data/Sun_Zhifu_zxs01/GSE40419/ERP001058_analysis_run_tum_pair_with_gsnap/SOMATIC_SNVINDEL/GSNAP/ERR164559_1.tumor.GSNAP.gatkin.splitNC.realign.recaliber.strelka/chromosomes/chr6/bins/0001/strelka.stdout 2>| /data2/external_data/Sun_Zhifu_zxs01/GSE40419/ERP001058_analysis_run_tum_pair_with_gsnap/SOMATIC_SNVINDEL/GSNAP/ERR164559_1.tumor.GSNAP.gatkin.splitNC.realign.recaliber.strelka/chromosomes/chr6/bins/0001/strelka.stderr'

 at /data2/bsi/staff_analysis/m081429/Somatic_workflow_paper/install_tools1/STRELKA/strelka_workflow-1.0.15/libexec/../lib/Utils.pm line 44

        Utils::errorX('Failed system call: \'/data2/bsi/staff_analysis/m081429/Somat...') called at /data2/bsi/staff_analysis/m081429/Somatic_workflow_paper/install_tools1/STRELKA/strelka_workflow-1.0.15/libexec/../lib/Utils.pm line 57

        Utils::executeCmd('/data2/bsi/staff_analysis/m081429/Somatic_workflow_paper/inst...', 0) called at /data2/bsi/staff_analysis/m081429/Somatic_workflow_paper/install_tools1/STRELKA/strelka_workflow-1.0.15/libexec/callSomaticVariants.pl line 225

make: *** [/data2/external_data/Sun_Zhifu_zxs01/GSE40419/ERP001058_analysis_run_tum_pair_with_gsnap/SOMATIC_SNVINDEL/GSNAP/ERR164559_1.tumor.GSNAP.gatkin.splitNC.realign.recaliber.strelka/chromosomes/chr6/bins/0001/task.complete] Error 1

ERROR: Exception caught in align_pos() while realigning segment: 2 of read: STARLING_READ id: 718369 genomic_mapping?: tier1-mapped

full_segment_info:

key: ERR164479.10781396/1

id: 718369

seq:  GGGCTGTCTCTCCACCTCCTCACATTATGCTAACAGGAACGCAGACAGGCGTGACAGGAAAGATGATCGGGGAGGGAACACAGGTCAGTGTGGGGACAGGG

qual: CCCFFFFFGHHHHJJIIIHIIIJIIJGJJJJIJJJJJGIHGIGIGJJGEGG';FHGEGHFFEEDBECDBA>@BDD<B??????8@>ACCCCC@>@?BB?@B

GENOME ALIGNMENT pos: 31236721 strand: F path: 15S3M6N35I48M

is_realigned? 0

buffer_pos: 0

partial_segment 1 :

GENOME ALIGNMENT pos: 31236721 strand: F path: 15S3M

is_realigned? 0

buffer_pos: 31236706

partial_segment 2 :

GENOME ALIGNMENT pos: 31236730 strand: F path: 35I48M

is_realigned? 0

buffer_pos: 31236695

FATAL_ERROR: strelka EXCEPTION: ERROR: Exemplar alignment contains indel not found in the overlap indel set

        Indel: INDEL pos: 31236730 type: INSERT len: 35 swap_dlen: 0