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/b7/0df0944f66ea8532fa257b3236219b/tih_rna_sample_00150_B23WHTKLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/ae1b14f182e865592385f2ba3070df/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/4ab818477ae782480e1a646963ad0a/tih_rna_sample_00150_B23WHTKLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/ae1b14f182e865592385f2ba3070df/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/0df0944f66ea8532fa257b3236219b/tih_rna_sample_00150_B23WHTKLT4_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 tih_rna_sample_00150_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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 tih_rna_sample_00150_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fa Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf > /tmp/nxf.8Y0BsPg7Kt/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf > /tmp/nxf.8Y0BsPg7Kt/cytoBand.txt Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed -parsing GTF file: /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed.sorted.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed.sorted.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00150_B23WHTKLT4_1.star --out_dir /tmp/nxf.8Y0BsPg7Kt/fi_workdir --reads "/tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 09:57:31 ..... started STAR run Jun 08 09:57:31 ..... loading genome Jun 08 09:59:15 ... generating Suffix Array index Jun 08 10:03:06 ... completed Suffix Array index Jun 08 10:03:06 ..... processing annotations GTF Jun 08 10:03:07 ..... inserting junctions into the genome indices Jun 08 10:04:07 ..... started mapping Jun 08 10:58:34 ..... finished mapping Jun 08 10:58:36 ..... started sorting BAM Jun 08 10:58:36 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00150_B23WHTKLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index tih_rna_sample_00150_B23WHTKLT4_1.star.sortedByCoord.out.bam Execution Time = 61.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00150_B23WHTKLT4_1.star --out_dir /tmp/nxf.8Y0BsPg7Kt/fi_workdir --reads "/tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups 10:58:37 : INFO : Done. Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf -parsing /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] -done parsing /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num genes matched < 2' => 6, 'per_id < 96' => 550, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4, 'excessive soft clipping' => 1539, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 440, 'seq-similar region overlap' => 190, ' ** passed ** ' => 1614, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 14 }; -writing fusion junction support info. Execution Time = 0.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_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] -fusion SPANNING read extraction for scaff: AP000347.1--IGLL1 [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] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 372, 'seq similar region alignment' => 10164 }; Execution Time = 0.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -967.193665 EM: Round [1] log likelihood: -966.888224 EM: Round [2] log likelihood: -966.818459 EM: Round [3] log likelihood: -966.754080 EM: Round [4] log likelihood: -966.694521 EM: Round [5] log likelihood: -966.639336 EM: Round [6] log likelihood: -966.588133 EM: Round [7] log likelihood: -966.540563 EM: Round [8] log likelihood: -966.496319 EM: Round [9] log likelihood: -966.455124 EM: Round [10] log likelihood: -966.416729 EM: Round [11] log likelihood: -966.380914 EM: Round [12] log likelihood: -966.347476 EM: Round [13] log likelihood: -966.316235 EM: Round [14] log likelihood: -966.287025 EM: Round [15] log likelihood: -966.259696 EM: Round [16] log likelihood: -966.234113 EM: Round [17] log likelihood: -966.210149 EM: Round [18] log likelihood: -966.187691 EM: Round [19] log likelihood: -966.166634 EM: Round [20] log likelihood: -966.146882 EM: Round [21] log likelihood: -966.128346 EM: Round [22] log likelihood: -966.110944 EM: Round [23] log likelihood: -966.094601 EM: Round [24] log likelihood: -966.079247 EM: Round [25] log likelihood: -966.064818 EM: Round [26] log likelihood: -966.051254 EM: Round [27] log likelihood: -966.038500 EM: Round [28] log likelihood: -966.026503 EM: Round [29] log likelihood: -966.015218 EM: Round [30] log likelihood: -966.004598 EM: Round [31] log likelihood: -965.994602 EM: Round [32] log likelihood: -965.985192 EM: Round [33] log likelihood: -965.976332 EM: Round [34] log likelihood: -965.967988 EM: Round [35] log likelihood: -965.960129 EM: Round [36] log likelihood: -965.952726 EM: Round [37] log likelihood: -965.945750 EM: Round [38] log likelihood: -965.939177 EM: Round [39] log likelihood: -965.932982 EM: Round [40] log likelihood: -965.927143 EM: Round [41] log likelihood: -965.921639 EM: Round [42] log likelihood: -965.916450 EM: Round [43] log likelihood: -965.911558 EM: Round [44] log likelihood: -965.906944 EM: Round [45] log likelihood: -965.902594 EM: Round [46] log likelihood: -965.898491 EM: Round [47] log likelihood: -965.894621 EM: Round [48] log likelihood: -965.890970 EM: Round [49] log likelihood: -965.887527 EM: Round [50] log likelihood: -965.884278 EM: Round [51] log likelihood: -965.881213 EM: Round [52] log likelihood: -965.878321 EM: Round [53] log likelihood: -965.875593 EM: Round [54] log likelihood: -965.873018 EM: Round [55] log likelihood: -965.870588 EM: Round [56] log likelihood: -965.868295 EM: Round [57] log likelihood: -965.866131 EM: Round [58] log likelihood: -965.864089 EM: Round [59] log likelihood: -965.862162 EM: Round [60] log likelihood: -965.860343 EM: Round [61] log likelihood: -965.858625 EM: Round [62] log likelihood: -965.857004 EM: Round [63] log likelihood: -965.855474 EM: Round [64] log likelihood: -965.854030 EM: Round [65] log likelihood: -965.852667 EM: Round [66] log likelihood: -965.851380 EM: Round [67] log likelihood: -965.850164 EM: Round [68] log likelihood: -965.849017 EM: Round [69] log likelihood: -965.847934 EM: Round [70] log likelihood: -965.846912 EM: Round [71] log likelihood: -965.845946 EM: Round [72] log likelihood: -965.845035 EM: Round [73] log likelihood: -965.844174 EM: Round [74] log likelihood: -965.843362 EM: Round [75] log likelihood: -965.842595 EM: Round [76] log likelihood: -965.841870 EM: Round [77] log likelihood: -965.841186 EM: Round [78] log likelihood: -965.840541 EM: Round [79] log likelihood: -965.839931 EM: Round [80] log likelihood: -965.839355 EM: Round [81] log likelihood: -965.838811 EM: Round [82] log likelihood: -965.838298 EM: Round [83] log likelihood: -965.837813 EM: Round [84] log likelihood: -965.837355 EM: Round [85] log likelihood: -965.836923 EM: Round [86] log likelihood: -965.836514 EM: Round [87] log likelihood: -965.836129 EM: Round [88] log likelihood: -965.835765 EM: Round [89] log likelihood: -965.835421 EM: Round [90] log likelihood: -965.835096 EM: Round [91] log likelihood: -965.834790 EM: Round [92] log likelihood: -965.834500 EM: Round [93] log likelihood: -965.834227 EM: Round [94] log likelihood: -965.833969 EM: Round [95] log likelihood: -965.833725 EM: Round [96] log likelihood: -965.833495 EM: Round [97] log likelihood: -965.833277 EM: Round [98] log likelihood: -965.833072 EM: Round [99] log likelihood: -965.832878 EM: Round [100] log likelihood: -965.832695 EM: Round [101] log likelihood: -965.832522 EM: Round [102] log likelihood: -965.832358 EM: Round [103] log likelihood: -965.832204 EM: Round [104] log likelihood: -965.832058 EM: Round [105] log likelihood: -965.831921 EM: Round [106] log likelihood: -965.831791 EM: Round [107] log likelihood: -965.831668 EM: Round [108] log likelihood: -965.831552 EM: Round [109] log likelihood: -965.831443 EM: Round [110] log likelihood: -965.831339 EM: Round [111] log likelihood: -965.831242 EM: Stopping iterations at round 111 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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam" Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/tih_rna_sample_00150_B23WHTKLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir -done, see /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -681.783093 EM: Round [1] log likelihood: -681.782283 EM: Round [2] log likelihood: -681.782282 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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_1.fastp.fastq.gz: 247680642 Execution Time = 5.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa --gtf /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf > /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fa --gtf /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf > /tmp/nxf.8Y0BsPg7Kt/fi_workdir/microH.dat Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.8Y0BsPg7Kt/fi_workdir/microH.dat /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/fi_workdir/microH.dat /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.8Y0BsPg7Kt --json_outfile /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00150_B23WHTKLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.8Y0BsPg7Kt --json_outfile /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00150_B23WHTKLT4_1 Running: touch /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00150_B23WHTKLT4_1 --html_output /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00150_B23WHTKLT4_1 --html_output /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000272578.5] WARNING, no entry stored in dbm for [ENSG00000272578.5] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.8Y0BsPg7Kt/ctat_genome_lib_build_dir > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.8Y0BsPg7Kt/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory