Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/835cfc5ca1ba3fde291d7e3c937c91/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/835cfc5ca1ba3fde291d7e3c937c91/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/56b054d50bdfaaf63c5276a1be4864/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/05d1bba6bd2966cdbc714f1b9f725c/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/56b054d50bdfaaf63c5276a1be4864/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Error, strand conflict in gtf info for chr1 ENSEMBL exon 43716467 43716556 . + . gene_id "U6^ENSG00000283414.1"; transcript_id "ENST00000637979.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.104-201"; exon_number 1; exon_id "ENSE00003791911.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283414.1"; orig_coord_info "chr1,43716467,43716556,+"; Error, strand conflict in gtf info for chr1 ENSEMBL exon 180758722 180758817 . + . gene_id "U6^ENSG00000283575.1"; transcript_id "ENST00000636407.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.114-201"; exon_number 1; exon_id "ENSE00003794679.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283575.1"; orig_coord_info "chr1,180758722,180758817,+"; Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 47781379 47781465 . + . gene_id "U6^ENSG00000283502.1"; transcript_id "ENST00000636749.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.109-201"; exon_number 1; exon_id "ENSE00003797274.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283502.1"; orig_coord_info "chr2,47781379,47781465,+"; Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 88367793 88367862 . - . gene_id "U6^ENSG00000283262.1"; transcript_id "ENST00000636931.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.95-201"; exon_number 1; exon_id "ENSE00003794432.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283262.1"; orig_coord_info "chr2,88367793,88367862,-"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 129819777 129819876 . + . gene_id "U6^ENSG00000283509.1"; transcript_id "ENST00000637725.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.110-201"; exon_number 1; exon_id "ENSE00003800884.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283509.1"; orig_coord_info "chr3,129819777,129819876,+"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 139388277 139388364 . + . gene_id "U6^ENSG00000283418.1"; transcript_id "ENST00000637379.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.105-201"; exon_number 1; exon_id "ENSE00003796411.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283418.1"; orig_coord_info "chr3,139388277,139388364,+"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 13051342 13051411 . + . gene_id "U6^ENSG00000283271.1"; transcript_id "ENST00000636425.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.96-201"; exon_number 1; exon_id "ENSE00003794917.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283271.1"; orig_coord_info "chr4,13051342,13051411,+"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 29510635 29510737 . + . gene_id "U6^ENSG00000283666.1"; transcript_id "ENST00000636045.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.115-201"; exon_number 1; exon_id "ENSE00003798657.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283666.1"; orig_coord_info "chr4,29510635,29510737,+"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 48109353 48109410 . - . gene_id "U6^ENSG00000283499.1"; transcript_id "ENST00000637764.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.108-201"; exon_number 1; exon_id "ENSE00003792913.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283499.1"; orig_coord_info "chr4,48109353,48109410,-"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 70848136 70848218 . - . gene_id "U6^ENSG00000283313.1"; transcript_id "ENST00000637524.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.99-201"; exon_number 1; exon_id "ENSE00003794269.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283313.1"; orig_coord_info "chr4,70848136,70848218,-"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 135315418 135315522 . - . gene_id "U6^ENSG00000283432.1"; transcript_id "ENST00000636360.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.106-201"; exon_number 1; exon_id "ENSE00003800825.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283432.1"; orig_coord_info "chr4,135315418,135315522,-"; Error, chr discrepancy in gtf info for chr9 ENSEMBL exon 64082429 64082534 . + . gene_id "U6^ENSG00000275068.1"; transcript_id "ENST00000618523.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.48-201"; exon_number 1; exon_id "ENSE00003712247.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000275068.1"; orig_coord_info "chr9,64082429,64082534,+"; Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 102868421 102868519 . + . gene_id "U6^ENSG00000283337.1"; transcript_id "ENST00000636230.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.100-201"; exon_number 1; exon_id "ENSE00003800313.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283337.1"; orig_coord_info "chr10,102868421,102868519,+"; Error, chr discrepancy in gtf info for chr11 ENSEMBL exon 87648489 87648549 . - . gene_id "U6^ENSG00000283412.1"; transcript_id "ENST00000637085.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.103-201"; exon_number 1; exon_id "ENSE00003793834.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283412.1"; orig_coord_info "chr11,87648489,87648549,-"; Error, chr discrepancy in gtf info for chr11 ENSEMBL exon 132525809 132525887 . + . gene_id "U6^ENSG00000283489.1"; transcript_id "ENST00000637108.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.107-201"; exon_number 1; exon_id "ENSE00003795495.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283489.1"; orig_coord_info "chr11,132525809,132525887,+"; Error, chr discrepancy in gtf info for chr12 ENSEMBL exon 31366288 31366366 . + . gene_id "U6^ENSG00000283256.1"; transcript_id "ENST00000635778.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.94-201"; exon_number 1; exon_id "ENSE00003799600.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283256.1"; orig_coord_info "chr12,31366288,31366366,+"; Error, chr discrepancy in gtf info for chr12 ENSEMBL exon 45554590 45554659 . - . gene_id "U6^ENSG00000283545.1"; transcript_id "ENST00000384129.2"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.112-201"; exon_number 1; exon_id "ENSE00001808939.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283545.1"; orig_coord_info "chr12,45554590,45554659,-"; Error, chr discrepancy in gtf info for chr13 ENSEMBL exon 18418526 18418632 . + . gene_id "U6^ENSG00000276183.1"; transcript_id "ENST00000615686.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.59-201"; exon_number 1; exon_id "ENSE00003719890.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000276183.1"; orig_coord_info "chr13,18418526,18418632,+"; Error, chr discrepancy in gtf info for chr14 ENSEMBL exon 24352057 24352157 . - . gene_id "U6^ENSG00000283290.1"; transcript_id "ENST00000636904.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.97-201"; exon_number 1; exon_id "ENSE00003800280.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283290.1"; orig_coord_info "chr14,24352057,24352157,-"; Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 21428879 21428985 . - . gene_id "U6^ENSG00000275174.1"; transcript_id "ENST00000612037.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.50-201"; exon_number 1; exon_id "ENSE00003750231.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000275174.1"; orig_coord_info "chr15,21428879,21428985,-"; Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 65843484 65843558 . + . gene_id "U6^ENSG00000283249.1"; transcript_id "ENST00000636829.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.93-201"; exon_number 1; exon_id "ENSE00003798324.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283249.1"; orig_coord_info "chr15,65843484,65843558,+"; Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 98026042 98026139 . + . gene_id "U6^ENSG00000283372.1"; transcript_id "ENST00000637737.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.102-201"; exon_number 1; exon_id "ENSE00003800921.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283372.1"; orig_coord_info "chr15,98026042,98026139,+"; Error, chr discrepancy in gtf info for chr16 ENSEMBL exon 72376704 72376760 . + . gene_id "U6^ENSG00000283564.1"; transcript_id "ENST00000637761.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.113-201"; exon_number 1; exon_id "ENSE00003793842.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283564.1"; orig_coord_info "chr16,72376704,72376760,+"; Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 90796 90899 . - . gene_id "U6^ENSG00000277613.1"; transcript_id "ENST00000620287.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.70-201"; exon_number 1; exon_id "ENSE00003744841.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000277613.1"; orig_coord_info "chr17,90796,90899,-"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 30713240 30713346 . - . gene_id "U6^ENSG00000274385.1"; transcript_id "ENST00000618440.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.42-201"; exon_number 1; exon_id "ENSE00003712066.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000274385.1"; orig_coord_info "chr20,30713240,30713346,-"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 35769785 35769867 . - . gene_id "U6^ENSG00000283527.1"; transcript_id "ENST00000636093.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.111-201"; exon_number 1; exon_id "ENSE00003795784.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283527.1"; orig_coord_info "chr20,35769785,35769867,-"; Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 28743208 28743291 . + . gene_id "U6^ENSG00000283300.1"; transcript_id "ENST00000637157.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.98-201"; exon_number 1; exon_id "ENSE00003800948.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283300.1"; orig_coord_info "chr21,28743208,28743291,+"; Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 15273855 15273961 . + . gene_id "U6^ENSG00000276138.1"; transcript_id "ENST00000613107.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.58-201"; exon_number 1; exon_id "ENSE00003736970.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000276138.1"; orig_coord_info "chr22,15273855,15273961,+"; Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 16141767 16141872 . + . gene_id "U6^ENSG00000278188.1"; transcript_id "ENST00000612550.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.81-201"; exon_number 1; exon_id "ENSE00003714392.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000278188.1"; orig_coord_info "chr22,16141767,16141872,+"; Error, chr discrepancy in gtf info for chrX ENSEMBL exon 86481028 86481130 . + . gene_id "U6^ENSG00000277717.1"; transcript_id "ENST00000619194.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.73-201"; exon_number 1; exon_id "ENSE00003738865.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000277717.1"; orig_coord_info "chrX,86481028,86481130,+"; Error - no gene spans 100M bases in length.... likely problem at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 589. main::get_gene_span_info("chr1\x{9}ENSEMBL\x{9}exon\x{9}516376\x{9}516479\x{9}.\x{9}-\x{9}.\x{9}gene_id \"U6^ENSG0000027"...) called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 417 main::get_gene_contig_gtf("chr1\x{9}ENSEMBL\x{9}exon\x{9}516376\x{9}516479\x{9}.\x{9}-\x{9}.\x{9}gene_id \"U6^ENSG0000027"..., "/tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir/ref_genome.fa") called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 214 eval {...} called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 210 Done. Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.hpsEvEZN4q/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.hpsEvEZN4q/cytoBand.txt Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.hpsEvEZN4q/fi_workdir --reads "/tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:17:46 ..... started STAR run Jun 08 10:17:46 ..... loading genome Jun 08 10:19:34 ... generating Suffix Array index Jun 08 10:23:39 ... completed Suffix Array index Jun 08 10:23:39 ..... processing annotations GTF Jun 08 10:23:40 ..... inserting junctions into the genome indices Jun 08 10:24:49 ..... started mapping Jun 08 11:41:59 ..... finished mapping Jun 08 11:42:02 ..... started sorting BAM Jun 08 11:42:04 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 84.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.hpsEvEZN4q/fi_workdir --reads "/tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:42:35 : INFO : Done. Execution Time = 0.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/mark_dups_reads.index.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] [940000] [950000] [960000] [970000] [980000] [990000] [1000000] [1010000] [1020000] [1030000] [1040000] [1050000] [1060000] [1070000] [1080000] [1090000] [1100000] [1110000] [1120000] [1130000] [1140000] [1150000] [1160000] [1170000] [1180000] [1190000] [1200000] [1210000] [1220000] [1230000] [1240000] [1250000] [1260000] [1270000] [1280000] [1290000] [1300000] [1310000] [1320000] [1330000] [1340000] [1350000] [1360000] [1370000] [1380000] [1390000] [1400000] [1410000] [1420000] [1430000] [1440000] [1450000] [1460000] [1470000] [1480000] [1490000] [1500000] [1510000] [1520000] [1530000] [1540000] [1550000] [1560000] [1570000] [1580000] [1590000] [1600000] [1610000] [1620000] [1630000] [1640000] [1650000] [1660000] [1670000] [1680000] [1690000] [1700000] [1710000] [1720000] [1730000] [1740000] [1750000] [1760000] [1770000] [1780000] [1790000] [1800000] [1810000] [1820000] [1830000] [1840000] [1850000] [1860000] [1870000] [1880000] [1890000] [1900000] [1910000] [1920000] [1930000] [1940000] [1950000] [1960000] [1970000] [1980000] [1990000] [2000000] [2010000] [2020000] [2030000] [2040000] [2050000] [2060000] [2070000] [2080000] [2090000] [2100000] [2110000] [2120000] [2130000] [2140000] [2150000] [2160000] [2170000] [2180000] [2190000] [2200000] [2210000] [2220000] [2230000] [2240000] [2250000] [2260000] [2270000] [2280000] [2290000] [2300000] [2310000] [2320000] [2330000] [2340000] [2350000] [2360000] [2370000] [2380000] [2390000] [2400000] [2410000] [2420000] [2430000] [2440000] [2450000] [2460000] [2470000] [2480000] [2490000] [2500000] [2510000] [2520000] [2530000] [2540000] [2550000] [2560000] [2570000] [2580000] [2590000] [2600000] [2610000] [2620000] [2630000] [2640000] [2650000] [2660000] [2670000] [2680000] [2690000] [2700000] [2710000] [2720000] [2730000] [2740000] [2750000] [2760000] [2770000] [2780000] [2790000] [2800000] [2810000] [2820000] [2830000] [2840000] [2850000] [2860000] [2870000] [2880000] [2890000] [2900000] [2910000] [2920000] [2930000] [2940000] [2950000] [2960000] [2970000] [2980000] [2990000] [3000000] [3010000] [3020000] [3030000] [3040000] [3050000] [3060000] [3070000] [3080000] [3090000] [3100000] [3110000] [3120000] [3130000] [3140000] [3150000] [3160000] [3170000] [3180000] [3190000] [3200000] [3210000] [3220000] [3230000] [3240000] [3250000] [3260000] [3270000] [3280000] [3290000] [3300000] [3310000] [3320000] [3330000] [3340000] [3350000] [3360000] [3370000] [3380000] [3390000] [3400000] [3410000] [3420000] [3430000] [3440000] [3450000] [3460000] [3470000] [3480000] [3490000] [3500000] [3510000] [3520000] [3530000] [3540000] [3550000] [3560000] [3570000] [3580000] [3590000] [3600000] [3610000] [3620000] [3630000] [3640000] [3650000] [3660000] [3670000] [3680000] [3690000] [3700000] [3710000] [3720000] [3730000] [3740000] [3750000] [3760000] [3770000] [3780000] [3790000] [3800000] [3810000] [3820000] [3830000] -done parsing /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'excessive soft clipping' => 23319, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2, 'small anchor length' => 4, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9, 'num genes matched < 2' => 418, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 114, ' ** passed ** ' => 5305, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 58, 'low complexity anchor region' => 3, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 174, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 474, 'per_id < 96' => 12612 }; -writing fusion junction support info. Execution Time = 2.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. 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[557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] [573000] [574000] [575000] [576000] [577000] [578000] [579000] [580000] [581000] [582000] [583000] [584000] [585000] [586000] [587000] [588000] [589000] [590000] [591000] [592000] [593000] [594000] [595000] [596000] [597000] [598000] [599000] [600000] [601000] [602000] [603000] [604000] [605000] [606000] [607000] [608000] [609000] [610000] [611000] [612000] [613000] [614000] [615000] [616000] [617000] [618000] [619000] [620000] [621000] [622000] [623000] [624000] [625000] [626000] [627000] [628000] [629000] [630000] [631000] [632000] [633000] [634000] [635000] [636000] [637000] [638000] [639000] [640000] [641000] [642000] [643000] [644000] [645000] [646000] [647000] [648000] [649000] [650000] [651000] [652000] [653000] [654000] [655000] [656000] [657000] [658000] [659000] [660000] [661000] [662000] [663000] [664000] [665000] [666000] [667000] [668000] [669000] [670000] [671000] [672000] [673000] [674000] [675000] [676000] [677000] [678000] [679000] [680000] [681000] [682000] [683000] [684000] [685000] [686000] [687000] [688000] [689000] [690000] [691000] [692000] [693000] [694000] [695000] [696000] [697000] [698000] [699000] [700000] [701000] [702000] [703000] [704000] [705000] [706000] [707000] [708000] [709000] [710000] [711000] [712000] [713000] [714000] [715000] [716000] [717000] [718000] [719000] [720000] [721000] [722000] [723000] [724000] [725000] [726000] [727000] [728000] [729000] [730000] [731000] [732000] [733000] [734000] [735000] [736000] [737000] [738000] [739000] [740000] [741000] [742000] [743000] [744000] [745000] [746000] [747000] [748000] [749000] [750000] [751000] [752000] [753000] [754000] [755000] [756000] [757000] [758000] [759000] [760000] [761000] [762000] [763000] [764000] [765000] [766000] [767000] [768000] [769000] [770000] [771000] [772000] [773000] [774000] [775000] [776000] [777000] [778000] [779000] [780000] [781000] [782000] [783000] [784000] [785000] [786000] [787000] [788000] [789000] [790000] [791000] [792000] [793000] [794000] [795000] [796000] [797000] [798000] [799000] [800000] [801000] [802000] [803000] [804000] [805000] [806000] [807000] [808000] [809000] [810000] [811000] [812000] [813000] [814000] [815000] [816000] [817000] [818000] [819000] [820000] [821000] [822000] [823000] [824000] [825000] [826000] [827000] [828000] [829000] [830000] [831000] [832000] [833000] [834000] [835000] [836000] [837000] [838000] [839000] [840000] [841000] [842000] [843000] [844000] [845000] [846000] [847000] [848000] [849000] [850000] [851000] [852000] [853000] [854000] [855000] [856000] [857000] [858000] [859000] [860000] [861000] [862000] [863000] [864000] [865000] [866000] [867000] [868000] [869000] [870000] [871000] [872000] [873000] [874000] [875000] [876000] [877000] [878000] [879000] [880000] [881000] [882000] [883000] [884000] [885000] [886000] [887000] [888000] [889000] [890000] [891000] [892000] [893000] [894000] [895000] [896000] [897000] [898000] [899000] [900000] [901000] [902000] [903000] [904000] [905000] [906000] [907000] [908000] [909000] [910000] [911000] [912000] [913000] [914000] [915000] [916000] [917000] [918000] [919000] [920000] [921000] [922000] [923000] [924000] [925000] [926000] [927000] [928000] [929000] [930000] [931000] [932000] [933000] [934000] [935000] [936000] [937000] [938000] [939000] [940000] [941000] [942000] [943000] [944000] [945000] [946000] [947000] [948000] [949000] [950000] [951000] [952000] [953000] [954000] [955000] [956000] [957000] [958000] [959000] [960000] [961000] [962000] [963000] [964000] [965000] [966000] [967000] [968000] [969000] [970000] [971000] [972000] [973000] [974000] [975000] [976000] [977000] [978000] [979000] [980000] [981000] [982000] [983000] [984000] [985000] [986000] [987000] [988000] [989000] [990000] [991000] [992000] [993000] [994000] [995000] [996000] [997000] [998000] [999000] [1000000] [1001000] [1002000] [1003000] [1004000] [1005000] [1006000] [1007000] [1008000] [1009000] [1010000] [1011000] [1012000] [1013000] [1014000] [1015000] [1016000] [1017000] [1018000] [1019000] [1020000] [1021000] [1022000] [1023000] [1024000] [1025000] [1026000] [1027000] [1028000] [1029000] [1030000] [1031000] [1032000] [1033000] [1034000] [1035000] [1036000] [1037000] [1038000] [1039000] [1040000] [1041000] [1042000] [1043000] [1044000] [1045000] [1046000] [1047000] [1048000] [1049000] [1050000] [1051000] [1052000] [1053000] [1054000] [1055000] [1056000] [1057000] [1058000] [1059000] [1060000] [1061000] [1062000] [1063000] [1064000] [1065000] [1066000] [1067000] [1068000] [1069000] [1070000] [1071000] [1072000] [1073000] -fusion SPANNING read extraction for scaff: ACTBP6--ACTB [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] -fusion SPANNING read extraction for scaff: ATAD2--AL365295.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] -fusion SPANNING read extraction for scaff: ATAD2--AL138479.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] -fusion SPANNING read extraction for scaff: ATAD2--MIR5580 [1000] [2000] -fusion SPANNING read extraction for scaff: CLIC2--BX571846.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] -fusion SPANNING read extraction for scaff: CNST--SMYD3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] -fusion SPANNING read extraction for scaff: DNM2--ADGRE4P [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] -fusion SPANNING read extraction for scaff: FRMD6--ABHD12B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] -fusion SPANNING read extraction for scaff: FRMD6--LINC00964 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] -fusion SPANNING read extraction for scaff: FTO--FRG1GP [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: FTO--MIR663AHG [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: FTO--FRG1CP [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] -fusion SPANNING read extraction for scaff: HSD17B4--MT-RNR2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] -fusion SPANNING read extraction for scaff: IGF1R--FAM169B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] -fusion SPANNING read extraction for scaff: IGF1R--IRAIN [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: KLF15--AC063919.1 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] -fusion SPANNING read extraction for scaff: MAP4K5--NSMCE2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: NDUFA9--AC092745.5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: NDUFA9--AC024255.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: NDUFA9--AC012150.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] 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[181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] -fusion SPANNING read extraction for scaff: PYGL--FRMD6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] 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[712000] [713000] [714000] [715000] [716000] [717000] [718000] [719000] [720000] [721000] [722000] [723000] [724000] [725000] [726000] [727000] [728000] [729000] [730000] [731000] [732000] [733000] [734000] [735000] [736000] [737000] [738000] [739000] [740000] [741000] [742000] [743000] [744000] [745000] [746000] [747000] [748000] [749000] [750000] [751000] [752000] [753000] [754000] [755000] [756000] [757000] [758000] [759000] [760000] [761000] [762000] [763000] [764000] [765000] [766000] [767000] [768000] [769000] [770000] [771000] [772000] [773000] [774000] [775000] [776000] [777000] [778000] [779000] [780000] [781000] [782000] [783000] [784000] [785000] [786000] [787000] [788000] [789000] [790000] [791000] [792000] [793000] [794000] [795000] [796000] [797000] [798000] [799000] [800000] [801000] [802000] [803000] [804000] [805000] [806000] [807000] [808000] [809000] [810000] [811000] [812000] [813000] [814000] [815000] [816000] [817000] [818000] [819000] [820000] [821000] [822000] [823000] [824000] [825000] [826000] [827000] [828000] [829000] [830000] [831000] [832000] [833000] [834000] [835000] [836000] [837000] [838000] [839000] [840000] [841000] [842000] [843000] [844000] [845000] [846000] [847000] [848000] [849000] [850000] [851000] [852000] [853000] [854000] [855000] [856000] [857000] [858000] [859000] [860000] [861000] [862000] [863000] [864000] [865000] [866000] [867000] [868000] [869000] [870000] [871000] [872000] [873000] [874000] [875000] [876000] [877000] [878000] [879000] [880000] [881000] [882000] [883000] [884000] [885000] [886000] [887000] [888000] [889000] [890000] [891000] [892000] [893000] [894000] [895000] [896000] [897000] [898000] [899000] [900000] [901000] [902000] [903000] [904000] [905000] [906000] [907000] [908000] [909000] [910000] [911000] [912000] [913000] [914000] [915000] [916000] [917000] [918000] [919000] [920000] [921000] [922000] [923000] [924000] [925000] [926000] [927000] [928000] [929000] [930000] [931000] [932000] [933000] -fusion SPANNING read extraction for scaff: SAA2--MT-RNR2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] -fusion SPANNING read extraction for scaff: TATDN1--NSMCE2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 42105 }; Execution Time = 5.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -7193.100127 EM: Round [1] log likelihood: -7163.479190 EM: Round [2] log likelihood: -7163.069547 EM: Round [3] log likelihood: -7163.067557 EM: Round [4] log likelihood: -7163.067550 EM: Stopping iterations at round 4 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/init_EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/prep_igv_extract_junc_reads.ok Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam || : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.98 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/prep_igv_sam_frag_coordss.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.FusionJuncSpan Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/prep_igv_pfam_bed.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/prep_igv_seqsim_bed.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa > /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir -done, see /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -6568.069392 EM: Round [1] log likelihood: -6540.915901 EM: Round [2] log likelihood: -6540.432046 EM: Round [3] log likelihood: -6540.429357 EM: Round [4] log likelihood: -6540.429347 EM: Stopping iterations at round 4 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296664875 Execution Time = 5.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.hpsEvEZN4q/fi_workdir/microH.dat Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.hpsEvEZN4q/fi_workdir/microH.dat Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.hpsEvEZN4q/fi_workdir/microH.dat /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.hpsEvEZN4q/fi_workdir/microH.dat /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.hpsEvEZN4q --json_outfile /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-a8a787-R1_A23YTGFLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.hpsEvEZN4q --json_outfile /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-a8a787-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/create_fi_igvjs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-a8a787-R1_A23YTGFLT4_1 --html_output /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-a8a787-R1_A23YTGFLT4_1 --html_output /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000251448.2] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000210082.2] WARNING, no entry stored in dbm for [ENSG00000210082.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286065.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000286895.1] WARNING, no entry stored in dbm for [ENSG00000286895.1] WARNING, no entry stored in dbm for [ENSG00000286895.1] WARNING, no entry stored in dbm for [ENSG00000249816.7] WARNING, no entry stored in dbm for [ENSG00000210082.2] WARNING, no entry stored in dbm for [ENSG00000225393.1] WARNING, no entry stored in dbm for [ENSG00000225393.1] WARNING, no entry stored in dbm for [ENSG00000203413.3] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.hpsEvEZN4q/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory