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/11/4e3387652e5ad6250e89b8cd95eb1e/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/fa26a0f7cf084461246a67bf4b77e3/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/ae0ba399bfdd6d3c9bfef7e4042d51/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/fa26a0f7cf084461246a67bf4b77e3/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/4e3387652e5ad6250e89b8cd95eb1e/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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-2d4b78-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf > /tmp/nxf.lk0fC5CYP2/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf > /tmp/nxf.lk0fC5CYP2/cytoBand.txt
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed
-parsing GTF file: /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.lk0fC5CYP2/fi_workdir --reads "/tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:13:05 ..... started STAR run
Jun 08 10:13:05 ..... loading genome
Jun 08 10:14:51 ... generating Suffix Array index
Jun 08 10:18:44 ... completed Suffix Array index
Jun 08 10:18:45 ..... processing annotations GTF
Jun 08 10:18:45 ..... inserting junctions into the genome indices
Jun 08 10:19:46 ..... started mapping
Jun 08 11:41:12 ..... finished mapping
Jun 08 11:41:14 ..... started sorting BAM
Jun 08 11:41:16 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
Execution Time = 88.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.lk0fC5CYP2/fi_workdir --reads "/tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:41:37 : INFO : Done.
Execution Time = 0.29 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[3090000] -done parsing /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 754,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'small anchor length' => 52,
'per_id < 96' => 12863,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20,
'low complexity anchor region' => 10,
'exons hit < 2' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
'excessive soft clipping' => 23284,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2,
'seq-similar region overlap' => 208,
'num genes matched < 2' => 41,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 106,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 46,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 12,
' ** passed ** ' => 6146,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 27
};
-writing fusion junction support info.
Execution Time = 1.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[26000] -fusion SPANNING read extraction for scaff: AGAP12P--FRMPD2
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[10000] -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180
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[25000] -fusion SPANNING read extraction for scaff: AP001347.1--ANKRD20A11P
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[11000] -fusion SPANNING read extraction for scaff: ASTN2--AL138749.1
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[11000] -fusion SPANNING read extraction for scaff: ASTN2--RPS20P25
[1000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
-fusion SPANNING read extraction for scaff: CHRDL2--P4HA3-AS1
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[1510000] -fusion SPANNING read extraction for scaff: COL1A1--SLC45A4
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[12000] -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B
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[52000] -fusion SPANNING read extraction for scaff: FAM168A--ASIC2
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[226000] -fusion SPANNING read extraction for scaff: GUSB--NAIP
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[7000] -fusion SPANNING read extraction for scaff: LRRC55--MS4A4E
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[12000] -fusion SPANNING read extraction for scaff: LRRC55--MS4A4A
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[4000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[3000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
[1000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
[1000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
[1000]
[2000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
[1000]
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[3000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[3000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[3000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[2000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[8000] -fusion SPANNING read extraction for scaff: PGM2L1--MOGAT2
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[14000] -fusion SPANNING read extraction for scaff: PMS2P5--CCDC146
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[58000] -fusion SPANNING read extraction for scaff: RBM4--MS4A6E
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[44000] -fusion SPANNING read extraction for scaff: RNF169--SLCO2B1
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[653000] -fusion SPANNING read extraction for scaff: SHANK2--AP000439.2
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[39000] -fusion SPANNING read extraction for scaff: SLCO2B1--SPCS2
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[43000] -fusion SPANNING read extraction for scaff: SLCO2B1--RNF169
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[128000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[32000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[34000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[19000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[36000] -fusion SPANNING read extraction for scaff: UVRAG--POLD3
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[13000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610
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[15000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 28573,
'seq similar region alignment' => 105065
};
Execution Time = 5.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -6731.513897
EM: Round [1] log likelihood: -6725.448812
EM: Round [2] log likelihood: -6724.458778
EM: Round [3] log likelihood: -6724.243606
EM: Round [4] log likelihood: -6724.191464
EM: Round [5] log likelihood: -6724.174446
EM: Round [6] log likelihood: -6724.165084
EM: Round [7] log likelihood: -6724.157458
EM: Round [8] log likelihood: -6724.150291
EM: Round [9] log likelihood: -6724.143305
EM: Round [10] log likelihood: -6724.136440
EM: Round [11] log likelihood: -6724.129679
EM: Round [12] log likelihood: -6724.123018
EM: Round [13] log likelihood: -6724.116455
EM: Round [14] log likelihood: -6724.109986
EM: Round [15] log likelihood: -6724.103611
EM: Round [16] log likelihood: -6724.097327
EM: Round [17] log likelihood: -6724.091132
EM: Round [18] log likelihood: -6724.085024
EM: Round [19] log likelihood: -6724.079003
EM: Round [20] log likelihood: -6724.073065
EM: Round [21] log likelihood: -6724.067210
EM: Round [22] log likelihood: -6724.061435
EM: Round [23] log likelihood: -6724.055740
EM: Round [24] log likelihood: -6724.050122
EM: Round [25] log likelihood: -6724.044581
EM: Round [26] log likelihood: -6724.039114
EM: Round [27] log likelihood: -6724.033721
EM: Round [28] log likelihood: -6724.028399
EM: Round [29] log likelihood: -6724.023148
EM: Round [30] log likelihood: -6724.017967
EM: Round [31] log likelihood: -6724.012853
EM: Round [32] log likelihood: -6724.007807
EM: Round [33] log likelihood: -6724.002826
EM: Round [34] log likelihood: -6723.997909
EM: Round [35] log likelihood: -6723.993056
EM: Round [36] log likelihood: -6723.988265
EM: Round [37] log likelihood: -6723.983535
EM: Round [38] log likelihood: -6723.978865
EM: Round [39] log likelihood: -6723.974254
EM: Round [40] log likelihood: -6723.969701
EM: Round [41] log likelihood: -6723.965205
EM: Round [42] log likelihood: -6723.960765
EM: Round [43] log likelihood: -6723.956380
EM: Round [44] log likelihood: -6723.952049
EM: Round [45] log likelihood: -6723.947772
EM: Round [46] log likelihood: -6723.943547
EM: Round [47] log likelihood: -6723.939373
EM: Round [48] log likelihood: -6723.935251
EM: Round [49] log likelihood: -6723.931178
EM: Round [50] log likelihood: -6723.927154
EM: Round [51] log likelihood: -6723.923178
EM: Round [52] log likelihood: -6723.919250
EM: Round [53] log likelihood: -6723.915369
EM: Round [54] log likelihood: -6723.911534
EM: Round [55] log likelihood: -6723.907744
EM: Round [56] log likelihood: -6723.903998
EM: Round [57] log likelihood: -6723.900297
EM: Round [58] log likelihood: -6723.896639
EM: Round [59] log likelihood: -6723.893023
EM: Round [60] log likelihood: -6723.889450
EM: Round [61] log likelihood: -6723.885917
EM: Round [62] log likelihood: -6723.882426
EM: Round [63] log likelihood: -6723.878974
EM: Round [64] log likelihood: -6723.875562
EM: Round [65] log likelihood: -6723.872189
EM: Round [66] log likelihood: -6723.868854
EM: Round [67] log likelihood: -6723.865557
EM: Round [68] log likelihood: -6723.862297
EM: Round [69] log likelihood: -6723.859074
EM: Round [70] log likelihood: -6723.855887
EM: Round [71] log likelihood: -6723.852736
EM: Round [72] log likelihood: -6723.849619
EM: Round [73] log likelihood: -6723.846538
EM: Round [74] log likelihood: -6723.843490
EM: Round [75] log likelihood: -6723.840476
EM: Round [76] log likelihood: -6723.837496
EM: Round [77] log likelihood: -6723.834548
EM: Round [78] log likelihood: -6723.831632
EM: Round [79] log likelihood: -6723.828748
EM: Round [80] log likelihood: -6723.825895
EM: Round [81] log likelihood: -6723.823074
EM: Round [82] log likelihood: -6723.820283
EM: Round [83] log likelihood: -6723.817522
EM: Round [84] log likelihood: -6723.814791
EM: Round [85] log likelihood: -6723.812089
EM: Round [86] log likelihood: -6723.809416
EM: Round [87] log likelihood: -6723.806772
EM: Round [88] log likelihood: -6723.804155
EM: Round [89] log likelihood: -6723.801567
EM: Round [90] log likelihood: -6723.799006
EM: Round [91] log likelihood: -6723.796472
EM: Round [92] log likelihood: -6723.793964
EM: Round [93] log likelihood: -6723.791483
EM: Round [94] log likelihood: -6723.789028
EM: Round [95] log likelihood: -6723.786599
EM: Round [96] log likelihood: -6723.784195
EM: Round [97] log likelihood: -6723.781816
EM: Round [98] log likelihood: -6723.779462
EM: Round [99] log likelihood: -6723.777132
EM: Round [100] log likelihood: -6723.774827
EM: Round [101] log likelihood: -6723.772545
EM: Round [102] log likelihood: -6723.770286
EM: Round [103] log likelihood: -6723.768051
EM: Round [104] log likelihood: -6723.765839
EM: Round [105] log likelihood: -6723.763649
EM: Round [106] log likelihood: -6723.761482
EM: Round [107] log likelihood: -6723.759336
EM: Round [108] log likelihood: -6723.757213
EM: Round [109] log likelihood: -6723.755111
EM: Round [110] log likelihood: -6723.753030
EM: Round [111] log likelihood: -6723.750970
EM: Round [112] log likelihood: -6723.748931
EM: Round [113] log likelihood: -6723.746912
EM: Round [114] log likelihood: -6723.744914
EM: Round [115] log likelihood: -6723.742936
EM: Round [116] log likelihood: -6723.740977
EM: Round [117] log likelihood: -6723.739038
EM: Round [118] log likelihood: -6723.737119
EM: Round [119] log likelihood: -6723.735218
EM: Round [120] log likelihood: -6723.733336
EM: Round [121] log likelihood: -6723.731473
EM: Round [122] log likelihood: -6723.729628
EM: Round [123] log likelihood: -6723.727802
EM: Round [124] log likelihood: -6723.725993
EM: Round [125] log likelihood: -6723.724202
EM: Round [126] log likelihood: -6723.722429
EM: Round [127] log likelihood: -6723.720673
EM: Round [128] log likelihood: -6723.718934
EM: Round [129] log likelihood: -6723.717213
EM: Round [130] log likelihood: -6723.715508
EM: Round [131] log likelihood: -6723.713819
EM: Round [132] log likelihood: -6723.712147
EM: Round [133] log likelihood: -6723.710491
EM: Round [134] log likelihood: -6723.708851
EM: Round [135] log likelihood: -6723.707227
EM: Round [136] log likelihood: -6723.705619
EM: Round [137] log likelihood: -6723.704026
EM: Round [138] log likelihood: -6723.702449
EM: Round [139] log likelihood: -6723.700886
EM: Round [140] log likelihood: -6723.699339
EM: Round [141] log likelihood: -6723.697806
EM: Round [142] log likelihood: -6723.696288
EM: Round [143] log likelihood: -6723.694785
EM: Round [144] log likelihood: -6723.693296
EM: Round [145] log likelihood: -6723.691821
EM: Round [146] log likelihood: -6723.690360
EM: Round [147] log likelihood: -6723.688913
EM: Round [148] log likelihood: -6723.687479
EM: Round [149] log likelihood: -6723.686059
EM: Round [150] log likelihood: -6723.684653
EM: Round [151] log likelihood: -6723.683259
EM: Round [152] log likelihood: -6723.681879
EM: Round [153] log likelihood: -6723.680512
EM: Round [154] log likelihood: -6723.679158
EM: Round [155] log likelihood: -6723.677816
EM: Round [156] log likelihood: -6723.676487
EM: Round [157] log likelihood: -6723.675171
EM: Round [158] log likelihood: -6723.673866
EM: Round [159] log likelihood: -6723.672574
EM: Round [160] log likelihood: -6723.671294
EM: Round [161] log likelihood: -6723.670026
EM: Round [162] log likelihood: -6723.668769
EM: Round [163] log likelihood: -6723.667525
EM: Round [164] log likelihood: -6723.666292
EM: Round [165] log likelihood: -6723.665070
EM: Round [166] log likelihood: -6723.663859
EM: Round [167] log likelihood: -6723.662660
EM: Round [168] log likelihood: -6723.661472
EM: Round [169] log likelihood: -6723.660294
EM: Round [170] log likelihood: -6723.659128
EM: Round [171] log likelihood: -6723.657972
EM: Round [172] log likelihood: -6723.656827
EM: Round [173] log likelihood: -6723.655692
EM: Round [174] log likelihood: -6723.654568
EM: Round [175] log likelihood: -6723.653454
EM: Round [176] log likelihood: -6723.652350
EM: Round [177] log likelihood: -6723.651257
EM: Round [178] log likelihood: -6723.650173
EM: Round [179] log likelihood: -6723.649099
EM: Round [180] log likelihood: -6723.648035
EM: Round [181] log likelihood: -6723.646981
EM: Round [182] log likelihood: -6723.645936
EM: Round [183] log likelihood: -6723.644900
EM: Round [184] log likelihood: -6723.643874
EM: Round [185] log likelihood: -6723.642858
EM: Round [186] log likelihood: -6723.641850
EM: Round [187] log likelihood: -6723.640852
EM: Round [188] log likelihood: -6723.639862
EM: Round [189] log likelihood: -6723.638882
EM: Round [190] log likelihood: -6723.637910
EM: Round [191] log likelihood: -6723.636948
EM: Round [192] log likelihood: -6723.635993
EM: Round [193] log likelihood: -6723.635048
EM: Round [194] log likelihood: -6723.634111
EM: Round [195] log likelihood: -6723.633182
EM: Round [196] log likelihood: -6723.632261
EM: Round [197] log likelihood: -6723.631349
EM: Round [198] log likelihood: -6723.630445
EM: Round [199] log likelihood: -6723.629549
EM: Round [200] log likelihood: -6723.628661
EM: Round [201] log likelihood: -6723.627781
EM: Round [202] log likelihood: -6723.626909
EM: Round [203] log likelihood: -6723.626044
EM: Round [204] log likelihood: -6723.625188
EM: Round [205] log likelihood: -6723.624339
EM: Round [206] log likelihood: -6723.623497
EM: Round [207] log likelihood: -6723.622663
EM: Round [208] log likelihood: -6723.621836
EM: Round [209] log likelihood: -6723.621017
EM: Round [210] log likelihood: -6723.620204
EM: Round [211] log likelihood: -6723.619400
EM: Round [212] log likelihood: -6723.618602
EM: Round [213] log likelihood: -6723.617811
EM: Round [214] log likelihood: -6723.617027
EM: Round [215] log likelihood: -6723.616250
EM: Round [216] log likelihood: -6723.615480
EM: Round [217] log likelihood: -6723.614717
EM: Round [218] log likelihood: -6723.613960
EM: Round [219] log likelihood: -6723.613210
EM: Round [220] log likelihood: -6723.612467
EM: Round [221] log likelihood: -6723.611730
EM: Round [222] log likelihood: -6723.610999
EM: Round [223] log likelihood: -6723.610275
EM: Round [224] log likelihood: -6723.609558
EM: Round [225] log likelihood: -6723.608846
EM: Round [226] log likelihood: -6723.608141
EM: Round [227] log likelihood: -6723.607442
EM: Round [228] log likelihood: -6723.606749
EM: Round [229] log likelihood: -6723.606062
EM: Round [230] log likelihood: -6723.605382
EM: Round [231] log likelihood: -6723.604707
EM: Round [232] log likelihood: -6723.604038
EM: Round [233] log likelihood: -6723.603374
EM: Round [234] log likelihood: -6723.602717
EM: Round [235] log likelihood: -6723.602065
EM: Round [236] log likelihood: -6723.601419
EM: Round [237] log likelihood: -6723.600779
EM: Round [238] log likelihood: -6723.600144
EM: Round [239] log likelihood: -6723.599514
EM: Round [240] log likelihood: -6723.598890
EM: Round [241] log likelihood: -6723.598272
EM: Round [242] log likelihood: -6723.597659
EM: Round [243] log likelihood: -6723.597051
EM: Round [244] log likelihood: -6723.596448
EM: Round [245] log likelihood: -6723.595850
EM: Round [246] log likelihood: -6723.595258
EM: Round [247] log likelihood: -6723.594671
EM: Round [248] log likelihood: -6723.594089
EM: Round [249] log likelihood: -6723.593512
EM: Round [250] log likelihood: -6723.592940
EM: Round [251] log likelihood: -6723.592372
EM: Round [252] log likelihood: -6723.591810
EM: Round [253] log likelihood: -6723.591253
EM: Round [254] log likelihood: -6723.590700
EM: Round [255] log likelihood: -6723.590152
EM: Round [256] log likelihood: -6723.589609
EM: Round [257] log likelihood: -6723.589070
EM: Round [258] log likelihood: -6723.588536
EM: Round [259] log likelihood: -6723.588007
EM: Round [260] log likelihood: -6723.587482
EM: Round [261] log likelihood: -6723.586961
EM: Round [262] log likelihood: -6723.586445
EM: Round [263] log likelihood: -6723.585934
EM: Round [264] log likelihood: -6723.585427
EM: Round [265] log likelihood: -6723.584924
EM: Round [266] log likelihood: -6723.584425
EM: Round [267] log likelihood: -6723.583931
EM: Round [268] log likelihood: -6723.583441
EM: Round [269] log likelihood: -6723.582955
EM: Round [270] log likelihood: -6723.582473
EM: Round [271] log likelihood: -6723.581996
EM: Round [272] log likelihood: -6723.581522
EM: Round [273] log likelihood: -6723.581053
EM: Round [274] log likelihood: -6723.580587
EM: Round [275] log likelihood: -6723.580125
EM: Round [276] log likelihood: -6723.579668
EM: Round [277] log likelihood: -6723.579214
EM: Round [278] log likelihood: -6723.578764
EM: Round [279] log likelihood: -6723.578318
EM: Round [280] log likelihood: -6723.577876
EM: Round [281] log likelihood: -6723.577437
EM: Round [282] log likelihood: -6723.577002
EM: Round [283] log likelihood: -6723.576571
EM: Round [284] log likelihood: -6723.576143
EM: Round [285] log likelihood: -6723.575719
EM: Round [286] log likelihood: -6723.575299
EM: Round [287] log likelihood: -6723.574882
EM: Round [288] log likelihood: -6723.574469
EM: Round [289] log likelihood: -6723.574059
EM: Round [290] log likelihood: -6723.573653
EM: Round [291] log likelihood: -6723.573250
EM: Round [292] log likelihood: -6723.572851
EM: Round [293] log likelihood: -6723.572455
EM: Round [294] log likelihood: -6723.572062
EM: Round [295] log likelihood: -6723.571672
EM: Round [296] log likelihood: -6723.571286
EM: Round [297] log likelihood: -6723.570903
EM: Round [298] log likelihood: -6723.570524
EM: Round [299] log likelihood: -6723.570147
EM: Round [300] log likelihood: -6723.569774
EM: Round [301] log likelihood: -6723.569404
EM: Round [302] log likelihood: -6723.569037
EM: Round [303] log likelihood: -6723.568673
EM: Round [304] log likelihood: -6723.568312
EM: Round [305] log likelihood: -6723.567954
EM: Round [306] log likelihood: -6723.567599
EM: Round [307] log likelihood: -6723.567247
EM: Round [308] log likelihood: -6723.566898
EM: Round [309] log likelihood: -6723.566552
EM: Round [310] log likelihood: -6723.566209
EM: Round [311] log likelihood: -6723.565868
EM: Round [312] log likelihood: -6723.565531
EM: Round [313] log likelihood: -6723.565196
EM: Round [314] log likelihood: -6723.564865
EM: Round [315] log likelihood: -6723.564536
EM: Round [316] log likelihood: -6723.564209
EM: Round [317] log likelihood: -6723.563886
EM: Round [318] log likelihood: -6723.563565
EM: Round [319] log likelihood: -6723.563247
EM: Round [320] log likelihood: -6723.562931
EM: Round [321] log likelihood: -6723.562619
EM: Round [322] log likelihood: -6723.562308
EM: Round [323] log likelihood: -6723.562001
EM: Round [324] log likelihood: -6723.561696
EM: Round [325] log likelihood: -6723.561393
EM: Round [326] log likelihood: -6723.561093
EM: Round [327] log likelihood: -6723.560796
EM: Round [328] log likelihood: -6723.560500
EM: Round [329] log likelihood: -6723.560208
EM: Round [330] log likelihood: -6723.559918
EM: Round [331] log likelihood: -6723.559630
EM: Round [332] log likelihood: -6723.559345
EM: Round [333] log likelihood: -6723.559062
EM: Round [334] log likelihood: -6723.558781
EM: Round [335] log likelihood: -6723.558503
EM: Round [336] log likelihood: -6723.558227
EM: Round [337] log likelihood: -6723.557953
EM: Round [338] log likelihood: -6723.557682
EM: Round [339] log likelihood: -6723.557413
EM: Round [340] log likelihood: -6723.557146
EM: Round [341] log likelihood: -6723.556881
EM: Round [342] log likelihood: -6723.556619
EM: Round [343] log likelihood: -6723.556358
EM: Round [344] log likelihood: -6723.556100
EM: Round [345] log likelihood: -6723.555844
EM: Round [346] log likelihood: -6723.555590
EM: Round [347] log likelihood: -6723.555339
EM: Round [348] log likelihood: -6723.555089
EM: Round [349] log likelihood: -6723.554841
EM: Round [350] log likelihood: -6723.554596
EM: Round [351] log likelihood: -6723.554352
EM: Round [352] log likelihood: -6723.554111
EM: Round [353] log likelihood: -6723.553871
EM: Round [354] log likelihood: -6723.553634
EM: Round [355] log likelihood: -6723.553398
EM: Round [356] log likelihood: -6723.553165
EM: Round [357] log likelihood: -6723.552933
EM: Round [358] log likelihood: -6723.552703
EM: Round [359] log likelihood: -6723.552475
EM: Round [360] log likelihood: -6723.552249
EM: Round [361] log likelihood: -6723.552025
EM: Round [362] log likelihood: -6723.551803
EM: Round [363] log likelihood: -6723.551582
EM: Round [364] log likelihood: -6723.551364
EM: Round [365] log likelihood: -6723.551147
EM: Round [366] log likelihood: -6723.550932
EM: Round [367] log likelihood: -6723.550719
EM: Round [368] log likelihood: -6723.550507
EM: Round [369] log likelihood: -6723.550298
EM: Round [370] log likelihood: -6723.550090
EM: Round [371] log likelihood: -6723.549883
EM: Round [372] log likelihood: -6723.549679
EM: Round [373] log likelihood: -6723.549476
EM: Round [374] log likelihood: -6723.549275
EM: Round [375] log likelihood: -6723.549075
EM: Round [376] log likelihood: -6723.548877
EM: Round [377] log likelihood: -6723.548681
EM: Round [378] log likelihood: -6723.548486
EM: Round [379] log likelihood: -6723.548293
EM: Round [380] log likelihood: -6723.548101
EM: Round [381] log likelihood: -6723.547912
EM: Round [382] log likelihood: -6723.547723
EM: Round [383] log likelihood: -6723.547536
EM: Round [384] log likelihood: -6723.547351
EM: Round [385] log likelihood: -6723.547167
EM: Round [386] log likelihood: -6723.546985
EM: Round [387] log likelihood: -6723.546804
EM: Round [388] log likelihood: -6723.546625
EM: Round [389] log likelihood: -6723.546447
EM: Round [390] log likelihood: -6723.546271
EM: Round [391] log likelihood: -6723.546096
EM: Round [392] log likelihood: -6723.545923
EM: Round [393] log likelihood: -6723.545751
EM: Round [394] log likelihood: -6723.545580
EM: Round [395] log likelihood: -6723.545411
EM: Round [396] log likelihood: -6723.545243
EM: Round [397] log likelihood: -6723.545077
EM: Round [398] log likelihood: -6723.544912
EM: Round [399] log likelihood: -6723.544748
EM: Round [400] log likelihood: -6723.544586
EM: Round [401] log likelihood: -6723.544425
EM: Round [402] log likelihood: -6723.544265
EM: Round [403] log likelihood: -6723.544107
EM: Round [404] log likelihood: -6723.543949
EM: Round [405] log likelihood: -6723.543794
EM: Round [406] log likelihood: -6723.543639
EM: Round [407] log likelihood: -6723.543486
EM: Round [408] log likelihood: -6723.543334
EM: Round [409] log likelihood: -6723.543183
EM: Round [410] log likelihood: -6723.543033
EM: Round [411] log likelihood: -6723.542885
EM: Round [412] log likelihood: -6723.542738
EM: Round [413] log likelihood: -6723.542592
EM: Round [414] log likelihood: -6723.542447
EM: Round [415] log likelihood: -6723.542304
EM: Round [416] log likelihood: -6723.542162
EM: Round [417] log likelihood: -6723.542020
EM: Round [418] log likelihood: -6723.541880
EM: Round [419] log likelihood: -6723.541742
EM: Round [420] log likelihood: -6723.541604
EM: Round [421] log likelihood: -6723.541467
EM: Round [422] log likelihood: -6723.541332
EM: Round [423] log likelihood: -6723.541197
EM: Round [424] log likelihood: -6723.541064
EM: Round [425] log likelihood: -6723.540932
EM: Round [426] log likelihood: -6723.540801
EM: Round [427] log likelihood: -6723.540671
EM: Round [428] log likelihood: -6723.540542
EM: Round [429] log likelihood: -6723.540414
EM: Round [430] log likelihood: -6723.540287
EM: Round [431] log likelihood: -6723.540161
EM: Round [432] log likelihood: -6723.540036
EM: Round [433] log likelihood: -6723.539912
EM: Round [434] log likelihood: -6723.539790
EM: Round [435] log likelihood: -6723.539668
EM: Round [436] log likelihood: -6723.539547
EM: Round [437] log likelihood: -6723.539427
EM: Round [438] log likelihood: -6723.539308
EM: Round [439] log likelihood: -6723.539190
EM: Round [440] log likelihood: -6723.539074
EM: Round [441] log likelihood: -6723.538958
EM: Round [442] log likelihood: -6723.538843
EM: Round [443] log likelihood: -6723.538728
EM: Round [444] log likelihood: -6723.538615
EM: Round [445] log likelihood: -6723.538503
EM: Round [446] log likelihood: -6723.538392
EM: Round [447] log likelihood: -6723.538281
EM: Round [448] log likelihood: -6723.538172
EM: Round [449] log likelihood: -6723.538063
EM: Round [450] log likelihood: -6723.537956
EM: Round [451] log likelihood: -6723.537849
EM: Round [452] log likelihood: -6723.537743
EM: Round [453] log likelihood: -6723.537638
EM: Round [454] log likelihood: -6723.537533
EM: Round [455] log likelihood: -6723.537430
EM: Round [456] log likelihood: -6723.537327
EM: Round [457] log likelihood: -6723.537226
EM: Round [458] log likelihood: -6723.537125
EM: Round [459] log likelihood: -6723.537025
EM: Round [460] log likelihood: -6723.536926
EM: Stopping iterations at round 460 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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa > /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir
-done, see /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -6110.177372
EM: Round [1] log likelihood: -6109.998040
EM: Round [2] log likelihood: -6109.996901
EM: Round [3] log likelihood: -6109.996887
EM: Stopping iterations at round 3 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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 296632708
Execution Time = 5.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf > /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gtf > /tmp/nxf.lk0fC5CYP2/fi_workdir/microH.dat
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.lk0fC5CYP2/fi_workdir/microH.dat /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_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.lk0fC5CYP2/fi_workdir/microH.dat /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.lk0fC5CYP2 --json_outfile /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-2d4b78-R1_A23WJ53LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.lk0fC5CYP2 --json_outfile /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-2d4b78-R1_A23WJ53LT4_1
Running: touch /tmp/nxf.lk0fC5CYP2/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.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-2d4b78-R1_A23WJ53LT4_1 --html_output /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-2d4b78-R1_A23WJ53LT4_1 --html_output /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000123965.13]
WARNING, no entry stored in dbm for [ENSG00000123965.13]
WARNING, no entry stored in dbm for [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000255980.1]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.lk0fC5CYP2/ctat_genome_lib_build_dir > /tmp/nxf.lk0fC5CYP2/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.lk0fC5CYP2/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory