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/38/1062cf9bd01508e001320160fcc078/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/1062cf9bd01508e001320160fcc078/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/de06854f62171807c2e65c46fba1c7/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/4d0cdbb115dc7efebd72bc8f9f68f4/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/de06854f62171807c2e65c46fba1c7/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.5N6GvMo3vq/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/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.5N6GvMo3vq/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5N6GvMo3vq/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5N6GvMo3vq/cytoBand.txt Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir --reads "/tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 03 21:14:29 ..... started STAR run Jun 03 21:14:29 ..... loading genome Jun 03 21:16:14 ... generating Suffix Array index Jun 03 21:20:04 ... completed Suffix Array index Jun 03 21:20:04 ..... processing annotations GTF Jun 03 21:20:05 ..... inserting junctions into the genome indices Jun 03 21:21:06 ..... started mapping Jun 03 22:28:31 ..... finished mapping Jun 03 22:28:32 ..... started sorting BAM Jun 03 22:28:33 ..... 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 = 74.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir --reads "/tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 22:28:44 : INFO : Done. Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.5N6GvMo3vq/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] -done parsing /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 263, 'num genes matched < 2' => 418, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 110, 'excessive soft clipping' => 11431, 'per_id < 96' => 5576, 'small anchor length' => 3, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 174, 'low complexity anchor region' => 2, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 58, ' ** passed ** ' => 5062, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2 }; -writing fusion junction support info. Execution Time = 0.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L [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] -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] [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] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [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] [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] [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' => 23063 }; Execution Time = 2.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -6241.600875 EM: Round [1] log likelihood: -6211.980654 EM: Round [2] log likelihood: -6211.571012 EM: Round [3] log likelihood: -6211.569022 EM: Round [4] log likelihood: -6211.569015 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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.FusionJuncSpan Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa > /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/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.5N6GvMo3vq/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.5N6GvMo3vq/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.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir -done, see /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -6071.361764 EM: Round [1] log likelihood: -6044.208990 EM: Round [2] log likelihood: -6043.725135 EM: Round [3] log likelihood: -6043.722447 EM: Round [4] log likelihood: -6043.722436 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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296664875 Execution Time = 5.99 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5N6GvMo3vq/fi_workdir/microH.dat Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.5N6GvMo3vq/fi_workdir/microH.dat /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/fi_workdir/microH.dat /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.5N6GvMo3vq --json_outfile /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq --json_outfile /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-a8a787-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/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.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/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 [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 [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 [ENSG00000225393.1] WARNING, no entry stored in dbm for [ENSG00000225393.1] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.5N6GvMo3vq/ctat_genome_lib_build_dir > /tmp/nxf.5N6GvMo3vq/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.5N6GvMo3vq/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory