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/e7/939073e94389f625b1fd62467f5353/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/7ce28938a0d11a6c29a7dda4d89229/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/7ce28938a0d11a6c29a7dda4d89229/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/7d6e3eef06bd4a9ae7ddf3fea87e21/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/7d6e3eef06bd4a9ae7ddf3fea87e21/aih-tih-sc-96d0f6-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-96d0f6-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf > /tmp/nxf.nPMYJDuozx/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf > /tmp/nxf.nPMYJDuozx/cytoBand.txt Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.nPMYJDuozx/fi_workdir --reads "/tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 03 21:39:30 ..... started STAR run Jun 03 21:39:30 ..... loading genome Jun 03 21:41:09 ... generating Suffix Array index Jun 03 21:45:05 ... completed Suffix Array index Jun 03 21:45:06 ..... processing annotations GTF Jun 03 21:45:06 ..... inserting junctions into the genome indices Jun 03 21:46:06 ..... started mapping Jun 03 22:38:52 ..... finished mapping Jun 03 22:38:54 ..... started sorting BAM Jun 03 22:38:54 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 59.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.nPMYJDuozx/fi_workdir --reads "/tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 22:38:55 : INFO : Done. Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] -done parsing /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'excessive soft clipping' => 733, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 10, 'seq-similar region overlap' => 19, ' ** passed ** ' => 671, 'per_id < 96' => 347, 'num genes matched < 2' => 2, 'exons hit < 2' => 2 }; -writing fusion junction support info. Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 691, 'seq similar region alignment' => 3815 }; Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -701.559623 EM: Round [1] log likelihood: -701.489914 EM: Round [2] log likelihood: -701.471009 EM: Round [3] log likelihood: -701.453260 EM: Round [4] log likelihood: -701.436573 EM: Round [5] log likelihood: -701.420867 EM: Round [6] log likelihood: -701.406072 EM: Round [7] log likelihood: -701.392122 EM: Round [8] log likelihood: -701.378958 EM: Round [9] log likelihood: -701.366527 EM: Round [10] log likelihood: -701.354779 EM: Round [11] log likelihood: -701.343669 EM: Round [12] log likelihood: -701.333157 EM: Round [13] log likelihood: -701.323204 EM: Round [14] log likelihood: -701.313776 EM: Round [15] log likelihood: -701.304840 EM: Round [16] log likelihood: -701.296367 EM: Round [17] log likelihood: -701.288328 EM: Round [18] log likelihood: -701.280699 EM: Round [19] log likelihood: -701.273456 EM: Round [20] log likelihood: -701.266577 EM: Round [21] log likelihood: -701.260041 EM: Round [22] log likelihood: -701.253828 EM: Round [23] log likelihood: -701.247922 EM: Round [24] log likelihood: -701.242305 EM: Round [25] log likelihood: -701.236961 EM: Round [26] log likelihood: -701.231877 EM: Round [27] log likelihood: -701.227037 EM: Round [28] log likelihood: -701.222430 EM: Round [29] log likelihood: -701.218043 EM: Round [30] log likelihood: -701.213864 EM: Round [31] log likelihood: -701.209884 EM: Round [32] log likelihood: -701.206091 EM: Round [33] log likelihood: -701.202476 EM: Round [34] log likelihood: -701.199031 EM: Round [35] log likelihood: -701.195747 EM: Round [36] log likelihood: -701.192616 EM: Round [37] log likelihood: -701.189630 EM: Round [38] log likelihood: -701.186782 EM: Round [39] log likelihood: -701.184065 EM: Round [40] log likelihood: -701.181474 EM: Round [41] log likelihood: -701.179001 EM: Round [42] log likelihood: -701.176642 EM: Round [43] log likelihood: -701.174390 EM: Round [44] log likelihood: -701.172241 EM: Round [45] log likelihood: -701.170190 EM: Round [46] log likelihood: -701.168232 EM: Round [47] log likelihood: -701.166362 EM: Round [48] log likelihood: -701.164577 EM: Round [49] log likelihood: -701.162873 EM: Round [50] log likelihood: -701.161246 EM: Round [51] log likelihood: -701.159692 EM: Round [52] log likelihood: -701.158207 EM: Round [53] log likelihood: -701.156789 EM: Round [54] log likelihood: -701.155435 EM: Round [55] log likelihood: -701.154141 EM: Round [56] log likelihood: -701.152905 EM: Round [57] log likelihood: -701.151725 EM: Round [58] log likelihood: -701.150597 EM: Round [59] log likelihood: -701.149519 EM: Round [60] log likelihood: -701.148489 EM: Round [61] log likelihood: -701.147505 EM: Round [62] log likelihood: -701.146564 EM: Round [63] log likelihood: -701.145666 EM: Round [64] log likelihood: -701.144807 EM: Round [65] log likelihood: -701.143986 EM: Round [66] log likelihood: -701.143201 EM: Round [67] log likelihood: -701.142452 EM: Round [68] log likelihood: -701.141735 EM: Round [69] log likelihood: -701.141050 EM: Round [70] log likelihood: -701.140395 EM: Round [71] log likelihood: -701.139769 EM: Round [72] log likelihood: -701.139171 EM: Round [73] log likelihood: -701.138599 EM: Round [74] log likelihood: -701.138052 EM: Round [75] log likelihood: -701.137529 EM: Round [76] log likelihood: -701.137029 EM: Round [77] log likelihood: -701.136551 EM: Round [78] log likelihood: -701.136094 EM: Round [79] log likelihood: -701.135657 EM: Round [80] log likelihood: -701.135240 EM: Round [81] log likelihood: -701.134841 EM: Round [82] log likelihood: -701.134459 EM: Round [83] log likelihood: -701.134094 EM: Round [84] log likelihood: -701.133745 EM: Round [85] log likelihood: -701.133411 EM: Round [86] log likelihood: -701.133092 EM: Round [87] log likelihood: -701.132786 EM: Round [88] log likelihood: -701.132495 EM: Round [89] log likelihood: -701.132216 EM: Round [90] log likelihood: -701.131949 EM: Round [91] log likelihood: -701.131693 EM: Round [92] log likelihood: -701.131449 EM: Round [93] log likelihood: -701.131216 EM: Round [94] log likelihood: -701.130993 EM: Round [95] log likelihood: -701.130779 EM: Round [96] log likelihood: -701.130575 EM: Round [97] log likelihood: -701.130380 EM: Round [98] log likelihood: -701.130194 EM: Round [99] log likelihood: -701.130015 EM: Round [100] log likelihood: -701.129844 EM: Round [101] log likelihood: -701.129681 EM: Round [102] log likelihood: -701.129525 EM: Round [103] log likelihood: -701.129376 EM: Round [104] log likelihood: -701.129233 EM: Round [105] log likelihood: -701.129096 EM: Round [106] log likelihood: -701.128965 EM: Round [107] log likelihood: -701.128841 EM: Round [108] log likelihood: -701.128721 EM: Round [109] log likelihood: -701.128607 EM: Round [110] log likelihood: -701.128497 EM: Round [111] log likelihood: -701.128393 EM: Round [112] log likelihood: -701.128293 EM: Stopping iterations at round 112 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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa > /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir -done, see /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -656.365350 EM: Round [1] log likelihood: -656.315789 EM: Round [2] log likelihood: -656.315782 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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296375716 Execution Time = 5.51 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf > /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf > /tmp/nxf.nPMYJDuozx/fi_workdir/microH.dat Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.nPMYJDuozx/fi_workdir/microH.dat /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/microH.dat /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.nPMYJDuozx --json_outfile /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-96d0f6-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.nPMYJDuozx --json_outfile /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-96d0f6-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-96d0f6-R1_A23YTGFLT4_1 --html_output /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-96d0f6-R1_A23YTGFLT4_1 --html_output /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 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 [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000280136.2] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.nPMYJDuozx/ctat_genome_lib_build_dir > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.nPMYJDuozx/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory