Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/586932ce49d1279d9feacd56a1b60f/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz 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/9b/99d0b92f6047b9fa925cf00bf907af/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/99d0b92f6047b9fa925cf00bf907af/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/3d1514a7a0c106bfedbae0229e51df/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/586932ce49d1279d9feacd56a1b60f/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_2.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-a97ce1-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 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-a97ce1-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf > /tmp/nxf.dIpS1I9D8d/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf > /tmp/nxf.dIpS1I9D8d/cytoBand.txt Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.dIpS1I9D8d/fi_workdir --reads "/tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 03 20:44:59 ..... started STAR run Jun 03 20:44:59 ..... loading genome Jun 03 20:46:42 ... generating Suffix Array index Jun 03 20:50:37 ... completed Suffix Array index Jun 03 20:50:37 ..... processing annotations GTF Jun 03 20:50:38 ..... inserting junctions into the genome indices Jun 03 20:51:38 ..... started mapping Jun 03 21:37:48 ..... finished mapping Jun 03 21:37:49 ..... started sorting BAM Jun 03 21:37:49 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 52.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.dIpS1I9D8d/fi_workdir --reads "/tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 21:37:50 : INFO : Done. Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] -done parsing /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 11, 'per_id < 96' => 364, ' ** passed ** ' => 1042, 'excessive soft clipping' => 913, 'seq-similar region overlap' => 37, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 30, 'low complexity anchor region' => 1 }; -writing fusion junction support info. Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PRCP--RAB30 [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] -fusion SPANNING read extraction for scaff: TLK2--AL669831.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 10336, 'lacks exon overlap' => 644 }; Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -506.204039 EM: Round [1] log likelihood: -506.188481 EM: Round [2] log likelihood: -506.173288 EM: Round [3] log likelihood: -506.158451 EM: Round [4] log likelihood: -506.143958 EM: Round [5] log likelihood: -506.129798 EM: Round [6] log likelihood: -506.115962 EM: Round [7] log likelihood: -506.102441 EM: Round [8] log likelihood: -506.089224 EM: Round [9] log likelihood: -506.076303 EM: Round [10] log likelihood: -506.063671 EM: Round [11] log likelihood: -506.051317 EM: Round [12] log likelihood: -506.039236 EM: Round [13] log likelihood: -506.027418 EM: Round [14] log likelihood: -506.015858 EM: Round [15] log likelihood: -506.004547 EM: Round [16] log likelihood: -505.993479 EM: Round [17] log likelihood: -505.982648 EM: Round [18] log likelihood: -505.972047 EM: Round [19] log likelihood: -505.961670 EM: Round [20] log likelihood: -505.951512 EM: Round [21] log likelihood: -505.941566 EM: Round [22] log likelihood: -505.931827 EM: Round [23] log likelihood: -505.922290 EM: Round [24] log likelihood: -505.912950 EM: Round [25] log likelihood: -505.903802 EM: Round [26] log likelihood: -505.894841 EM: Round [27] log likelihood: -505.886062 EM: Round [28] log likelihood: -505.877461 EM: Round [29] log likelihood: -505.869034 EM: Round [30] log likelihood: -505.860776 EM: Round [31] log likelihood: -505.852684 EM: Round [32] log likelihood: -505.844752 EM: Round [33] log likelihood: -505.836979 EM: Round [34] log likelihood: -505.829358 EM: Round [35] log likelihood: -505.821889 EM: Round [36] log likelihood: -505.814565 EM: Round [37] log likelihood: -505.807385 EM: Round [38] log likelihood: -505.800345 EM: Round [39] log likelihood: -505.793442 EM: Round [40] log likelihood: -505.786672 EM: Round [41] log likelihood: -505.780033 EM: Round [42] log likelihood: -505.773522 EM: Round [43] log likelihood: -505.767135 EM: Round [44] log likelihood: -505.760871 EM: Round [45] log likelihood: -505.754725 EM: Round [46] log likelihood: -505.748697 EM: Round [47] log likelihood: -505.742782 EM: Round [48] log likelihood: -505.736980 EM: Round [49] log likelihood: -505.731286 EM: Round [50] log likelihood: -505.725699 EM: Round [51] log likelihood: -505.720217 EM: Round [52] log likelihood: -505.714838 EM: Round [53] log likelihood: -505.709558 EM: Round [54] log likelihood: -505.704377 EM: Round [55] log likelihood: -505.699291 EM: Round [56] log likelihood: -505.694300 EM: Round [57] log likelihood: -505.689400 EM: Round [58] log likelihood: -505.684590 EM: Round [59] log likelihood: -505.679869 EM: Round [60] log likelihood: -505.675234 EM: Round [61] log likelihood: -505.670684 EM: Round [62] log likelihood: -505.666217 EM: Round [63] log likelihood: -505.661830 EM: Round [64] log likelihood: -505.657524 EM: Round [65] log likelihood: -505.653295 EM: Round [66] log likelihood: -505.649143 EM: Round [67] log likelihood: -505.645065 EM: Round [68] log likelihood: -505.641061 EM: Round [69] log likelihood: -505.637129 EM: Round [70] log likelihood: -505.633267 EM: Round [71] log likelihood: -505.629474 EM: Round [72] log likelihood: -505.625749 EM: Round [73] log likelihood: -505.622090 EM: Round [74] log likelihood: -505.618497 EM: Round [75] log likelihood: -505.614967 EM: Round [76] log likelihood: -505.611499 EM: Round [77] log likelihood: -505.608093 EM: Round [78] log likelihood: -505.604748 EM: Round [79] log likelihood: -505.601461 EM: Round [80] log likelihood: -505.598232 EM: Round [81] log likelihood: -505.595059 EM: Round [82] log likelihood: -505.591943 EM: Round [83] log likelihood: -505.588881 EM: Round [84] log likelihood: -505.585872 EM: Round [85] log likelihood: -505.582917 EM: Round [86] log likelihood: -505.580012 EM: Round [87] log likelihood: -505.577158 EM: Round [88] log likelihood: -505.574354 EM: Round [89] log likelihood: -505.571599 EM: Round [90] log likelihood: -505.568891 EM: Round [91] log likelihood: -505.566230 EM: Round [92] log likelihood: -505.563616 EM: Round [93] log likelihood: -505.561046 EM: Round [94] log likelihood: -505.558521 EM: Round [95] log likelihood: -505.556039 EM: Round [96] log likelihood: -505.553600 EM: Round [97] log likelihood: -505.551203 EM: Round [98] log likelihood: -505.548847 EM: Round [99] log likelihood: -505.546532 EM: Round [100] log likelihood: -505.544256 EM: Round [101] log likelihood: -505.542019 EM: Round [102] log likelihood: -505.539820 EM: Round [103] log likelihood: -505.537659 EM: Round [104] log likelihood: -505.535535 EM: Round [105] log likelihood: -505.533447 EM: Round [106] log likelihood: -505.531394 EM: Round [107] log likelihood: -505.529376 EM: Round [108] log likelihood: -505.527393 EM: Round [109] log likelihood: -505.525443 EM: Round [110] log likelihood: -505.523526 EM: Round [111] log likelihood: -505.521642 EM: Round [112] log likelihood: -505.519790 EM: Round [113] log likelihood: -505.517969 EM: Round [114] log likelihood: -505.516178 EM: Round [115] log likelihood: -505.514418 EM: Round [116] log likelihood: -505.512688 EM: Round [117] log likelihood: -505.510987 EM: Round [118] log likelihood: -505.509314 EM: Round [119] log likelihood: -505.507670 EM: Round [120] log likelihood: -505.506053 EM: Round [121] log likelihood: -505.504463 EM: Round [122] log likelihood: -505.502900 EM: Round [123] log likelihood: -505.501363 EM: Round [124] log likelihood: -505.499852 EM: Round [125] log likelihood: -505.498366 EM: Round [126] log likelihood: -505.496905 EM: Round [127] log likelihood: -505.495468 EM: Round [128] log likelihood: -505.494056 EM: Round [129] log likelihood: -505.492667 EM: Round [130] log likelihood: -505.491301 EM: Round [131] log likelihood: -505.489958 EM: Round [132] log likelihood: -505.488637 EM: Round [133] log likelihood: -505.487338 EM: Round [134] log likelihood: -505.486061 EM: Round [135] log likelihood: -505.484805 EM: Round [136] log likelihood: -505.483570 EM: Round [137] log likelihood: -505.482356 EM: Round [138] log likelihood: -505.481161 EM: Round [139] log likelihood: -505.479987 EM: Round [140] log likelihood: -505.478832 EM: Round [141] log likelihood: -505.477696 EM: Round [142] log likelihood: -505.476579 EM: Round [143] log likelihood: -505.475480 EM: Round [144] log likelihood: -505.474399 EM: Round [145] log likelihood: -505.473337 EM: Round [146] log likelihood: -505.472292 EM: Round [147] log likelihood: -505.471264 EM: Round [148] log likelihood: -505.470253 EM: Round [149] log likelihood: -505.469259 EM: Round [150] log likelihood: -505.468281 EM: Round [151] log likelihood: -505.467319 EM: Round [152] log likelihood: -505.466373 EM: Round [153] log likelihood: -505.465443 EM: Round [154] log likelihood: -505.464528 EM: Round [155] log likelihood: -505.463628 EM: Round [156] log likelihood: -505.462743 EM: Round [157] log likelihood: -505.461872 EM: Round [158] log likelihood: -505.461016 EM: Round [159] log likelihood: -505.460174 EM: Round [160] log likelihood: -505.459345 EM: Round [161] log likelihood: -505.458530 EM: Round [162] log likelihood: -505.457729 EM: Round [163] log likelihood: -505.456941 EM: Round [164] log likelihood: -505.456165 EM: Round [165] log likelihood: -505.455402 EM: Round [166] log likelihood: -505.454652 EM: Round [167] log likelihood: -505.453914 EM: Round [168] log likelihood: -505.453188 EM: Round [169] log likelihood: -505.452474 EM: Round [170] log likelihood: -505.451772 EM: Round [171] log likelihood: -505.451081 EM: Round [172] log likelihood: -505.450402 EM: Round [173] log likelihood: -505.449733 EM: Round [174] log likelihood: -505.449075 EM: Round [175] log likelihood: -505.448429 EM: Round [176] log likelihood: -505.447792 EM: Round [177] log likelihood: -505.447166 EM: Round [178] log likelihood: -505.446551 EM: Round [179] log likelihood: -505.445945 EM: Round [180] log likelihood: -505.445349 EM: Round [181] log likelihood: -505.444763 EM: Round [182] log likelihood: -505.444187 EM: Round [183] log likelihood: -505.443620 EM: Round [184] log likelihood: -505.443062 EM: Round [185] log likelihood: -505.442513 EM: Round [186] log likelihood: -505.441973 EM: Round [187] log likelihood: -505.441442 EM: Round [188] log likelihood: -505.440919 EM: Round [189] log likelihood: -505.440405 EM: Round [190] log likelihood: -505.439900 EM: Round [191] log likelihood: -505.439402 EM: Round [192] log likelihood: -505.438913 EM: Round [193] log likelihood: -505.438431 EM: Round [194] log likelihood: -505.437958 EM: Round [195] log likelihood: -505.437492 EM: Round [196] log likelihood: -505.437033 EM: Round [197] log likelihood: -505.436583 EM: Round [198] log likelihood: -505.436139 EM: Round [199] log likelihood: -505.435703 EM: Round [200] log likelihood: -505.435273 EM: Round [201] log likelihood: -505.434851 EM: Round [202] log likelihood: -505.434435 EM: Round [203] log likelihood: -505.434027 EM: Round [204] log likelihood: -505.433624 EM: Round [205] log likelihood: -505.433229 EM: Round [206] log likelihood: -505.432839 EM: Round [207] log likelihood: -505.432457 EM: Round [208] log likelihood: -505.432080 EM: Round [209] log likelihood: -505.431709 EM: Round [210] log likelihood: -505.431344 EM: Round [211] log likelihood: -505.430986 EM: Round [212] log likelihood: -505.430633 EM: Round [213] log likelihood: -505.430286 EM: Round [214] log likelihood: -505.429944 EM: Round [215] log likelihood: -505.429608 EM: Round [216] log likelihood: -505.429277 EM: Round [217] log likelihood: -505.428952 EM: Round [218] log likelihood: -505.428632 EM: Round [219] log likelihood: -505.428317 EM: Round [220] log likelihood: -505.428007 EM: Round [221] log likelihood: -505.427702 EM: Round [222] log likelihood: -505.427402 EM: Round [223] log likelihood: -505.427107 EM: Round [224] log likelihood: -505.426817 EM: Round [225] log likelihood: -505.426531 EM: Round [226] log likelihood: -505.426250 EM: Round [227] log likelihood: -505.425974 EM: Round [228] log likelihood: -505.425702 EM: Round [229] log likelihood: -505.425434 EM: Round [230] log likelihood: -505.425171 EM: Round [231] log likelihood: -505.424912 EM: Round [232] log likelihood: -505.424657 EM: Round [233] log likelihood: -505.424406 EM: Round [234] log likelihood: -505.424160 EM: Round [235] log likelihood: -505.423917 EM: Round [236] log likelihood: -505.423678 EM: Round [237] log likelihood: -505.423443 EM: Round [238] log likelihood: -505.423212 EM: Round [239] log likelihood: -505.422984 EM: Round [240] log likelihood: -505.422761 EM: Round [241] log likelihood: -505.422541 EM: Round [242] log likelihood: -505.422324 EM: Round [243] log likelihood: -505.422111 EM: Round [244] log likelihood: -505.421901 EM: Round [245] log likelihood: -505.421695 EM: Round [246] log likelihood: -505.421492 EM: Round [247] log likelihood: -505.421292 EM: Round [248] log likelihood: -505.421095 EM: Round [249] log likelihood: -505.420902 EM: Round [250] log likelihood: -505.420712 EM: Round [251] log likelihood: -505.420524 EM: Round [252] log likelihood: -505.420340 EM: Round [253] log likelihood: -505.420159 EM: Round [254] log likelihood: -505.419981 EM: Round [255] log likelihood: -505.419805 EM: Round [256] log likelihood: -505.419633 EM: Round [257] log likelihood: -505.419463 EM: Round [258] log likelihood: -505.419296 EM: Round [259] log likelihood: -505.419131 EM: Round [260] log likelihood: -505.418970 EM: Round [261] log likelihood: -505.418810 EM: Round [262] log likelihood: -505.418654 EM: Round [263] log likelihood: -505.418500 EM: Round [264] log likelihood: -505.418348 EM: Round [265] log likelihood: -505.418199 EM: Round [266] log likelihood: -505.418052 EM: Round [267] log likelihood: -505.417908 EM: Round [268] log likelihood: -505.417765 EM: Round [269] log likelihood: -505.417626 EM: Round [270] log likelihood: -505.417488 EM: Round [271] log likelihood: -505.417353 EM: Round [272] log likelihood: -505.417220 EM: Round [273] log likelihood: -505.417088 EM: Round [274] log likelihood: -505.416960 EM: Round [275] log likelihood: -505.416833 EM: Round [276] log likelihood: -505.416708 EM: Round [277] log likelihood: -505.416585 EM: Round [278] log likelihood: -505.416464 EM: Round [279] log likelihood: -505.416345 EM: Round [280] log likelihood: -505.416228 EM: Round [281] log likelihood: -505.416113 EM: Round [282] log likelihood: -505.416000 EM: Round [283] log likelihood: -505.415888 EM: Round [284] log likelihood: -505.415779 EM: Round [285] log likelihood: -505.415671 EM: Round [286] log likelihood: -505.415564 EM: Round [287] log likelihood: -505.415460 EM: Round [288] log likelihood: -505.415357 EM: Round [289] log likelihood: -505.415256 EM: Round [290] log likelihood: -505.415157 EM: Stopping iterations at round 290 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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.FusionJuncSpan Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa > /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir -done, see /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -505.409045 EM: Round [1] log likelihood: -505.409045 EM: Stopping iterations at round 1 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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 216439276 Execution Time = 4.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf > /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf > /tmp/nxf.dIpS1I9D8d/fi_workdir/microH.dat Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.dIpS1I9D8d/fi_workdir/microH.dat /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/microH.dat /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.dIpS1I9D8d --json_outfile /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-a97ce1-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.dIpS1I9D8d --json_outfile /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-a97ce1-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-a97ce1-R1_A23YTGFLT4_1 --html_output /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.00 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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-a97ce1-R1_A23YTGFLT4_1 --html_output /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000228327.3] WARNING, no entry stored in dbm for [ENSG00000228327.3] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.dIpS1I9D8d/ctat_genome_lib_build_dir > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.dIpS1I9D8d/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory