Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/6c1c301d1bb0fd968260093a3a30f6/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusionreport.tsv
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/c3/51622c45135197ce557ffa994ab92d/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/0faa8085f85772578f5ea42afefb18/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/0faa8085f85772578f5ea42afefb18/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/51622c45135197ce557ffa994ab92d/.command.run
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/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 = 0.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf > /tmp/nxf.ip1B8zh3GJ/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf > /tmp/nxf.ip1B8zh3GJ/cytoBand.txt
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed
-parsing GTF file: /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.ip1B8zh3GJ/fi_workdir --reads "/tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:53:55 ..... started STAR run
Jun 08 09:53:55 ..... loading genome
Jun 08 09:56:08 ... generating Suffix Array index
Jun 08 09:59:43 ... completed Suffix Array index
Jun 08 09:59:43 ..... processing annotations GTF
Jun 08 09:59:43 ..... inserting junctions into the genome indices
Jun 08 10:01:00 ..... started mapping
Jun 08 11:15:14 ..... finished mapping
Jun 08 11:15:17 ..... started sorting BAM
Jun 08 11:15:19 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
Execution Time = 81.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.ip1B8zh3GJ/fi_workdir --reads "/tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:15:46 : INFO : Done.
Execution Time = 0.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[3590000] -done parsing /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 7010,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 80,
'seq-similar region overlap' => 1540,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 525,
'low complexity anchor region' => 5,
'num genes matched < 2' => 291,
'excessive soft clipping' => 28003,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 99,
'exons hit < 2' => 8,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 64,
'per_id < 96' => 13895,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 55,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 81,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15,
'small anchor length' => 88,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 130
};
-writing fusion junction support info.
Execution Time = 2.44 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[145000] -fusion SPANNING read extraction for scaff: CD2AP--AL451166.1
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[34000] -fusion SPANNING read extraction for scaff: CHIC2--HDAC9
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[25000] -fusion SPANNING read extraction for scaff: COL9A3--TRHDE
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[79000] -fusion SPANNING read extraction for scaff: ELOVL5--CLIC5
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[34000] -fusion SPANNING read extraction for scaff: GNE--MROH2B
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[11000] -fusion SPANNING read extraction for scaff: GPR149--ARHGEF26-AS1
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[166000] -fusion SPANNING read extraction for scaff: GRK2--SSH3
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[106000] -fusion SPANNING read extraction for scaff: HELZ--CCR10
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[146000] -fusion SPANNING read extraction for scaff: IQGAP1--BLM
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[57000] -fusion SPANNING read extraction for scaff: KDM4C--RCL1
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[244000] -fusion SPANNING read extraction for scaff: KIAA1549--ZC3HAV1
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[11000] -fusion SPANNING read extraction for scaff: LCORL--LINC02438
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[83000] -fusion SPANNING read extraction for scaff: LRRC1--HCRTR2
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[28000] -fusion SPANNING read extraction for scaff: MED20--AL031767.2
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[28000] -fusion SPANNING read extraction for scaff: MED20--LINC00581
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[9000] -fusion SPANNING read extraction for scaff: N6AMT1--HUNK
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[26000] -fusion SPANNING read extraction for scaff: NDFIP1--SPRY4-AS1
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[29000] -fusion SPANNING read extraction for scaff: NOCT--NAA15
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[23000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHA13
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[23000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC1
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[18000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC2
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[27000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[32000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[32000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[23000] -fusion SPANNING read extraction for scaff: PICK1--HORMAD2-AS1
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[33000] -fusion SPANNING read extraction for scaff: PIP5K1A--AL031599.1
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[34000] -fusion SPANNING read extraction for scaff: PIP5K1A--GOT2P2
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[24000] -fusion SPANNING read extraction for scaff: PMS2P7--CCDC146
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[87000] -fusion SPANNING read extraction for scaff: SBNO1--AC117503.5
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[50000] -fusion SPANNING read extraction for scaff: SFI1--BPIFC
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[19000] -fusion SPANNING read extraction for scaff: SH2D4A--AC087269.1
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[260000] -fusion SPANNING read extraction for scaff: SKAP2--HNRNPA2B1
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[43000] -fusion SPANNING read extraction for scaff: SNHG14--HTR4
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[84000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[44000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[69000] -fusion SPANNING read extraction for scaff: TMEM165--TBL1X
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[84000] -fusion SPANNING read extraction for scaff: TSEN2--PPARG
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[31000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[113000] -fusion SPANNING read extraction for scaff: UBAP1--PTPRD
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[110000] -fusion SPANNING read extraction for scaff: URB1--N6AMT1
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[21000] -fusion SPANNING read extraction for scaff: ZCCHC7--AL354977.2
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[21000] -fusion SPANNING read extraction for scaff: ZCCHC7--RFX3-AS1
[1000]
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[4000] -fusion SPANNING read extraction for scaff: ZNF257--AC074135.1
[1000]
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[37000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610
[1000]
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[53000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 99021,
'lacks exon overlap' => 76178
};
Execution Time = 6.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -12025.002784
EM: Round [1] log likelihood: -12021.409928
EM: Round [2] log likelihood: -12021.267832
EM: Round [3] log likelihood: -12021.262865
EM: Round [4] log likelihood: -12021.262698
EM: Round [5] log likelihood: -12021.262693
EM: Stopping iterations at round 5 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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa > /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir
-done, see /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -9923.169679
EM: Round [1] log likelihood: -9923.048128
EM: Round [2] log likelihood: -9923.048065
EM: Stopping iterations at round 2 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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296790345
Execution Time = 6.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf > /tmp/nxf.ip1B8zh3GJ/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf > /tmp/nxf.ip1B8zh3GJ/fi_workdir/microH.dat
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.ip1B8zh3GJ/fi_workdir/microH.dat /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/fi_workdir/microH.dat /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.ip1B8zh3GJ --json_outfile /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-fa55c3-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.ip1B8zh3GJ --json_outfile /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-fa55c3-R1_A23YTGFLT4_1
Running: touch /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-fa55c3-R1_A23YTGFLT4_1 --html_output /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.03 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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-fa55c3-R1_A23YTGFLT4_1 --html_output /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000229018.5]
WARNING, no entry stored in dbm for [ENSG00000229018.5]
WARNING, no entry stored in dbm for [ENSG00000229018.5]
WARNING, no entry stored in dbm for [ENSG00000229018.5]
WARNING, no entry stored in dbm for [ENSG00000286092.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
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 [ENSG00000231185.7]
WARNING, no entry stored in dbm for [ENSG00000231185.7]
WARNING, no entry stored in dbm for [ENSG00000279973.2]
WARNING, no entry stored in dbm for [ENSG00000279973.2]
WARNING, no entry stored in dbm for [ENSG00000279973.2]
WARNING, no entry stored in dbm for [ENSG00000254367.5]
WARNING, no entry stored in dbm for [ENSG00000254367.5]
WARNING, no entry stored in dbm for [ENSG00000248238.2]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000267886.1]
WARNING, no entry stored in dbm for [ENSG00000267886.1]
WARNING, no entry stored in dbm for [ENSG00000267886.1]
WARNING, no entry stored in dbm for [ENSG00000267886.1]
WARNING, no entry stored in dbm for [ENSG00000267886.1]
WARNING, no entry stored in dbm for [ENSG00000248103.1]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000243069.8]
WARNING, no entry stored in dbm for [ENSG00000243069.8]
WARNING, no entry stored in dbm for [ENSG00000243069.8]
WARNING, no entry stored in dbm for [ENSG00000243069.8]
WARNING, no entry stored in dbm for [ENSG00000237359.2]
WARNING, no entry stored in dbm for [ENSG00000232104.3]
WARNING, no entry stored in dbm for [ENSG00000232104.3]
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.ip1B8zh3GJ/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory