Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/d65f6edc84f26d0e0ddbb0e76aafa4/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/225cc6211d6bc826792e2c954efa94/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/d65f6edc84f26d0e0ddbb0e76aafa4/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/225cc6211d6bc826792e2c954efa94/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/3ee5f49de940e0284dc7476408cb61/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf > /tmp/nxf.MytSv7bv3H/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf > /tmp/nxf.MytSv7bv3H/cytoBand.txt
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed
-parsing GTF file: /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.MytSv7bv3H/fi_workdir --reads "/tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:27:30 ..... started STAR run
Jun 08 10:27:30 ..... loading genome
Jun 08 10:29:13 ... generating Suffix Array index
Jun 08 10:33:03 ... completed Suffix Array index
Jun 08 10:33:03 ..... processing annotations GTF
Jun 08 10:33:03 ..... inserting junctions into the genome indices
Jun 08 10:34:04 ..... started mapping
Jun 08 11:58:59 ..... finished mapping
Jun 08 11:59:00 ..... started sorting BAM
Jun 08 11:59:01 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
Execution Time = 91.53 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.MytSv7bv3H/fi_workdir --reads "/tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:59:05 : INFO : Done.
Execution Time = 0.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[720000] -done parsing /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 110,
'low complexity anchor region' => 10,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 21,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
' ** passed ** ' => 8866,
'per_id < 96' => 2418,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
'small anchor length' => 46,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2,
'excessive soft clipping' => 3593,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 36,
'num genes matched < 2' => 15,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 8
};
-writing fusion junction support info.
Execution Time = 0.36 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[27000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 2703,
'seq similar region alignment' => 33639
};
Execution Time = 0.83 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -3749.389101
EM: Round [1] log likelihood: -3748.252192
EM: Round [2] log likelihood: -3747.477766
EM: Round [3] log likelihood: -3746.809832
EM: Round [4] log likelihood: -3746.227212
EM: Round [5] log likelihood: -3745.713703
EM: Round [6] log likelihood: -3745.256683
EM: Round [7] log likelihood: -3744.846208
EM: Round [8] log likelihood: -3744.474372
EM: Round [9] log likelihood: -3744.134843
EM: Round [10] log likelihood: -3743.822519
EM: Round [11] log likelihood: -3743.533264
EM: Round [12] log likelihood: -3743.263715
EM: Round [13] log likelihood: -3743.011123
EM: Round [14] log likelihood: -3742.773236
EM: Round [15] log likelihood: -3742.548201
EM: Round [16] log likelihood: -3742.334490
EM: Round [17] log likelihood: -3742.130838
EM: Round [18] log likelihood: -3741.936197
EM: Round [19] log likelihood: -3741.749691
EM: Round [20] log likelihood: -3741.570590
EM: Round [21] log likelihood: -3741.398281
EM: Round [22] log likelihood: -3741.232247
EM: Round [23] log likelihood: -3741.072051
EM: Round [24] log likelihood: -3740.917319
EM: Round [25] log likelihood: -3740.767731
EM: Round [26] log likelihood: -3740.623011
EM: Round [27] log likelihood: -3740.482919
EM: Round [28] log likelihood: -3740.347243
EM: Round [29] log likelihood: -3740.215797
EM: Round [30] log likelihood: -3740.088414
EM: Round [31] log likelihood: -3739.964942
EM: Round [32] log likelihood: -3739.845245
EM: Round [33] log likelihood: -3739.729197
EM: Round [34] log likelihood: -3739.616679
EM: Round [35] log likelihood: -3739.507584
EM: Round [36] log likelihood: -3739.401807
EM: Round [37] log likelihood: -3739.299252
EM: Round [38] log likelihood: -3739.199824
EM: Round [39] log likelihood: -3739.103434
EM: Round [40] log likelihood: -3739.009996
EM: Round [41] log likelihood: -3738.919426
EM: Round [42] log likelihood: -3738.831644
EM: Round [43] log likelihood: -3738.746571
EM: Round [44] log likelihood: -3738.664131
EM: Round [45] log likelihood: -3738.584248
EM: Round [46] log likelihood: -3738.506851
EM: Round [47] log likelihood: -3738.431866
EM: Round [48] log likelihood: -3738.359226
EM: Round [49] log likelihood: -3738.288862
EM: Round [50] log likelihood: -3738.220706
EM: Round [51] log likelihood: -3738.154695
EM: Round [52] log likelihood: -3738.090764
EM: Round [53] log likelihood: -3738.028851
EM: Round [54] log likelihood: -3737.968895
EM: Round [55] log likelihood: -3737.910837
EM: Round [56] log likelihood: -3737.854618
EM: Round [57] log likelihood: -3737.800182
EM: Round [58] log likelihood: -3737.747474
EM: Round [59] log likelihood: -3737.696440
EM: Round [60] log likelihood: -3737.647026
EM: Round [61] log likelihood: -3737.599183
EM: Round [62] log likelihood: -3737.552860
EM: Round [63] log likelihood: -3737.508008
EM: Round [64] log likelihood: -3737.464581
EM: Round [65] log likelihood: -3737.422532
EM: Round [66] log likelihood: -3737.381817
EM: Round [67] log likelihood: -3737.342393
EM: Round [68] log likelihood: -3737.304216
EM: Round [69] log likelihood: -3737.267247
EM: Round [70] log likelihood: -3737.231446
EM: Round [71] log likelihood: -3737.196774
EM: Round [72] log likelihood: -3737.163194
EM: Round [73] log likelihood: -3737.130670
EM: Round [74] log likelihood: -3737.099166
EM: Round [75] log likelihood: -3737.068648
EM: Round [76] log likelihood: -3737.039084
EM: Round [77] log likelihood: -3737.010442
EM: Round [78] log likelihood: -3736.982690
EM: Round [79] log likelihood: -3736.955799
EM: Round [80] log likelihood: -3736.929740
EM: Round [81] log likelihood: -3736.904484
EM: Round [82] log likelihood: -3736.880005
EM: Round [83] log likelihood: -3736.856277
EM: Round [84] log likelihood: -3736.833274
EM: Round [85] log likelihood: -3736.810971
EM: Round [86] log likelihood: -3736.789345
EM: Round [87] log likelihood: -3736.768373
EM: Round [88] log likelihood: -3736.748033
EM: Round [89] log likelihood: -3736.728303
EM: Round [90] log likelihood: -3736.709163
EM: Round [91] log likelihood: -3736.690593
EM: Round [92] log likelihood: -3736.672574
EM: Round [93] log likelihood: -3736.655086
EM: Round [94] log likelihood: -3736.638112
EM: Round [95] log likelihood: -3736.621635
EM: Round [96] log likelihood: -3736.605637
EM: Round [97] log likelihood: -3736.590103
EM: Round [98] log likelihood: -3736.575017
EM: Round [99] log likelihood: -3736.560364
EM: Round [100] log likelihood: -3736.546129
EM: Round [101] log likelihood: -3736.532299
EM: Round [102] log likelihood: -3736.518859
EM: Round [103] log likelihood: -3736.505796
EM: Round [104] log likelihood: -3736.493099
EM: Round [105] log likelihood: -3736.480754
EM: Round [106] log likelihood: -3736.468750
EM: Round [107] log likelihood: -3736.457076
EM: Round [108] log likelihood: -3736.445720
EM: Round [109] log likelihood: -3736.434673
EM: Round [110] log likelihood: -3736.423923
EM: Round [111] log likelihood: -3736.413462
EM: Round [112] log likelihood: -3736.403279
EM: Round [113] log likelihood: -3736.393365
EM: Round [114] log likelihood: -3736.383712
EM: Round [115] log likelihood: -3736.374311
EM: Round [116] log likelihood: -3736.365154
EM: Round [117] log likelihood: -3736.356232
EM: Round [118] log likelihood: -3736.347539
EM: Round [119] log likelihood: -3736.339066
EM: Round [120] log likelihood: -3736.330808
EM: Round [121] log likelihood: -3736.322755
EM: Round [122] log likelihood: -3736.314904
EM: Round [123] log likelihood: -3736.307245
EM: Round [124] log likelihood: -3736.299775
EM: Round [125] log likelihood: -3736.292486
EM: Round [126] log likelihood: -3736.285372
EM: Round [127] log likelihood: -3736.278429
EM: Round [128] log likelihood: -3736.271651
EM: Round [129] log likelihood: -3736.265033
EM: Round [130] log likelihood: -3736.258570
EM: Round [131] log likelihood: -3736.252256
EM: Round [132] log likelihood: -3736.246088
EM: Round [133] log likelihood: -3736.240060
EM: Round [134] log likelihood: -3736.234169
EM: Round [135] log likelihood: -3736.228410
EM: Round [136] log likelihood: -3736.222780
EM: Round [137] log likelihood: -3736.217274
EM: Round [138] log likelihood: -3736.211888
EM: Round [139] log likelihood: -3736.206620
EM: Round [140] log likelihood: -3736.201465
EM: Round [141] log likelihood: -3736.196420
EM: Round [142] log likelihood: -3736.191481
EM: Round [143] log likelihood: -3736.186647
EM: Round [144] log likelihood: -3736.181913
EM: Round [145] log likelihood: -3736.177277
EM: Round [146] log likelihood: -3736.172735
EM: Round [147] log likelihood: -3736.168286
EM: Round [148] log likelihood: -3736.163926
EM: Round [149] log likelihood: -3736.159653
EM: Round [150] log likelihood: -3736.155464
EM: Round [151] log likelihood: -3736.151357
EM: Round [152] log likelihood: -3736.147330
EM: Round [153] log likelihood: -3736.143380
EM: Round [154] log likelihood: -3736.139506
EM: Round [155] log likelihood: -3736.135705
EM: Round [156] log likelihood: -3736.131975
EM: Round [157] log likelihood: -3736.128314
EM: Round [158] log likelihood: -3736.124721
EM: Round [159] log likelihood: -3736.121193
EM: Round [160] log likelihood: -3736.117729
EM: Round [161] log likelihood: -3736.114326
EM: Round [162] log likelihood: -3736.110985
EM: Round [163] log likelihood: -3736.107702
EM: Round [164] log likelihood: -3736.104476
EM: Round [165] log likelihood: -3736.101306
EM: Round [166] log likelihood: -3736.098191
EM: Round [167] log likelihood: -3736.095128
EM: Round [168] log likelihood: -3736.092117
EM: Round [169] log likelihood: -3736.089156
EM: Round [170] log likelihood: -3736.086244
EM: Round [171] log likelihood: -3736.083380
EM: Round [172] log likelihood: -3736.080563
EM: Round [173] log likelihood: -3736.077791
EM: Round [174] log likelihood: -3736.075063
EM: Round [175] log likelihood: -3736.072379
EM: Round [176] log likelihood: -3736.069736
EM: Round [177] log likelihood: -3736.067135
EM: Round [178] log likelihood: -3736.064575
EM: Round [179] log likelihood: -3736.062053
EM: Round [180] log likelihood: -3736.059570
EM: Round [181] log likelihood: -3736.057124
EM: Round [182] log likelihood: -3736.054715
EM: Round [183] log likelihood: -3736.052342
EM: Round [184] log likelihood: -3736.050003
EM: Round [185] log likelihood: -3736.047699
EM: Round [186] log likelihood: -3736.045428
EM: Round [187] log likelihood: -3736.043190
EM: Round [188] log likelihood: -3736.040984
EM: Round [189] log likelihood: -3736.038809
EM: Round [190] log likelihood: -3736.036665
EM: Round [191] log likelihood: -3736.034550
EM: Round [192] log likelihood: -3736.032465
EM: Round [193] log likelihood: -3736.030408
EM: Round [194] log likelihood: -3736.028380
EM: Round [195] log likelihood: -3736.026379
EM: Round [196] log likelihood: -3736.024404
EM: Round [197] log likelihood: -3736.022457
EM: Round [198] log likelihood: -3736.020535
EM: Round [199] log likelihood: -3736.018638
EM: Round [200] log likelihood: -3736.016766
EM: Round [201] log likelihood: -3736.014919
EM: Round [202] log likelihood: -3736.013095
EM: Round [203] log likelihood: -3736.011294
EM: Round [204] log likelihood: -3736.009517
EM: Round [205] log likelihood: -3736.007762
EM: Round [206] log likelihood: -3736.006029
EM: Round [207] log likelihood: -3736.004318
EM: Round [208] log likelihood: -3736.002628
EM: Round [209] log likelihood: -3736.000959
EM: Round [210] log likelihood: -3735.999310
EM: Round [211] log likelihood: -3735.997681
EM: Round [212] log likelihood: -3735.996072
EM: Round [213] log likelihood: -3735.994483
EM: Round [214] log likelihood: -3735.992912
EM: Round [215] log likelihood: -3735.991361
EM: Round [216] log likelihood: -3735.989827
EM: Round [217] log likelihood: -3735.988312
EM: Round [218] log likelihood: -3735.986814
EM: Round [219] log likelihood: -3735.985334
EM: Round [220] log likelihood: -3735.983871
EM: Round [221] log likelihood: -3735.982425
EM: Round [222] log likelihood: -3735.980995
EM: Round [223] log likelihood: -3735.979582
EM: Round [224] log likelihood: -3735.978185
EM: Round [225] log likelihood: -3735.976804
EM: Round [226] log likelihood: -3735.975438
EM: Round [227] log likelihood: -3735.974087
EM: Round [228] log likelihood: -3735.972752
EM: Round [229] log likelihood: -3735.971431
EM: Round [230] log likelihood: -3735.970125
EM: Round [231] log likelihood: -3735.968833
EM: Round [232] log likelihood: -3735.967555
EM: Round [233] log likelihood: -3735.966291
EM: Round [234] log likelihood: -3735.965041
EM: Round [235] log likelihood: -3735.963805
EM: Round [236] log likelihood: -3735.962582
EM: Round [237] log likelihood: -3735.961372
EM: Round [238] log likelihood: -3735.960174
EM: Round [239] log likelihood: -3735.958990
EM: Round [240] log likelihood: -3735.957818
EM: Round [241] log likelihood: -3735.956658
EM: Round [242] log likelihood: -3735.955511
EM: Round [243] log likelihood: -3735.954376
EM: Round [244] log likelihood: -3735.953252
EM: Round [245] log likelihood: -3735.952140
EM: Round [246] log likelihood: -3735.951040
EM: Round [247] log likelihood: -3735.949951
EM: Round [248] log likelihood: -3735.948873
EM: Round [249] log likelihood: -3735.947807
EM: Round [250] log likelihood: -3735.946751
EM: Round [251] log likelihood: -3735.945706
EM: Round [252] log likelihood: -3735.944672
EM: Round [253] log likelihood: -3735.943648
EM: Round [254] log likelihood: -3735.942634
EM: Round [255] log likelihood: -3735.941631
EM: Round [256] log likelihood: -3735.940638
EM: Round [257] log likelihood: -3735.939654
EM: Round [258] log likelihood: -3735.938681
EM: Round [259] log likelihood: -3735.937717
EM: Round [260] log likelihood: -3735.936763
EM: Round [261] log likelihood: -3735.935818
EM: Round [262] log likelihood: -3735.934883
EM: Round [263] log likelihood: -3735.933956
EM: Round [264] log likelihood: -3735.933039
EM: Round [265] log likelihood: -3735.932131
EM: Round [266] log likelihood: -3735.931232
EM: Round [267] log likelihood: -3735.930341
EM: Round [268] log likelihood: -3735.929460
EM: Round [269] log likelihood: -3735.928586
EM: Round [270] log likelihood: -3735.927722
EM: Round [271] log likelihood: -3735.926865
EM: Round [272] log likelihood: -3735.926017
EM: Round [273] log likelihood: -3735.925177
EM: Round [274] log likelihood: -3735.924345
EM: Round [275] log likelihood: -3735.923522
EM: Round [276] log likelihood: -3735.922706
EM: Round [277] log likelihood: -3735.921897
EM: Round [278] log likelihood: -3735.921097
EM: Round [279] log likelihood: -3735.920304
EM: Round [280] log likelihood: -3735.919519
EM: Round [281] log likelihood: -3735.918741
EM: Round [282] log likelihood: -3735.917970
EM: Round [283] log likelihood: -3735.917207
EM: Round [284] log likelihood: -3735.916451
EM: Round [285] log likelihood: -3735.915702
EM: Round [286] log likelihood: -3735.914960
EM: Round [287] log likelihood: -3735.914225
EM: Round [288] log likelihood: -3735.913497
EM: Round [289] log likelihood: -3735.912776
EM: Round [290] log likelihood: -3735.912061
EM: Round [291] log likelihood: -3735.911353
EM: Round [292] log likelihood: -3735.910652
EM: Round [293] log likelihood: -3735.909957
EM: Round [294] log likelihood: -3735.909269
EM: Round [295] log likelihood: -3735.908587
EM: Round [296] log likelihood: -3735.907912
EM: Round [297] log likelihood: -3735.907242
EM: Round [298] log likelihood: -3735.906579
EM: Round [299] log likelihood: -3735.905922
EM: Round [300] log likelihood: -3735.905271
EM: Round [301] log likelihood: -3735.904626
EM: Round [302] log likelihood: -3735.903987
EM: Round [303] log likelihood: -3735.903354
EM: Round [304] log likelihood: -3735.902726
EM: Round [305] log likelihood: -3735.902104
EM: Round [306] log likelihood: -3735.901488
EM: Round [307] log likelihood: -3735.900878
EM: Round [308] log likelihood: -3735.900273
EM: Round [309] log likelihood: -3735.899674
EM: Round [310] log likelihood: -3735.899080
EM: Round [311] log likelihood: -3735.898491
EM: Round [312] log likelihood: -3735.897908
EM: Round [313] log likelihood: -3735.897330
EM: Round [314] log likelihood: -3735.896758
EM: Round [315] log likelihood: -3735.896190
EM: Round [316] log likelihood: -3735.895628
EM: Round [317] log likelihood: -3735.895071
EM: Round [318] log likelihood: -3735.894519
EM: Round [319] log likelihood: -3735.893971
EM: Round [320] log likelihood: -3735.893429
EM: Round [321] log likelihood: -3735.892892
EM: Round [322] log likelihood: -3735.892359
EM: Round [323] log likelihood: -3735.891831
EM: Round [324] log likelihood: -3735.891308
EM: Round [325] log likelihood: -3735.890790
EM: Round [326] log likelihood: -3735.890276
EM: Round [327] log likelihood: -3735.889767
EM: Round [328] log likelihood: -3735.889262
EM: Round [329] log likelihood: -3735.888762
EM: Round [330] log likelihood: -3735.888267
EM: Round [331] log likelihood: -3735.887775
EM: Round [332] log likelihood: -3735.887289
EM: Round [333] log likelihood: -3735.886806
EM: Round [334] log likelihood: -3735.886328
EM: Round [335] log likelihood: -3735.885854
EM: Round [336] log likelihood: -3735.885384
EM: Round [337] log likelihood: -3735.884919
EM: Round [338] log likelihood: -3735.884457
EM: Round [339] log likelihood: -3735.884000
EM: Round [340] log likelihood: -3735.883547
EM: Round [341] log likelihood: -3735.883097
EM: Round [342] log likelihood: -3735.882652
EM: Round [343] log likelihood: -3735.882211
EM: Round [344] log likelihood: -3735.881773
EM: Round [345] log likelihood: -3735.881340
EM: Round [346] log likelihood: -3735.880910
EM: Round [347] log likelihood: -3735.880484
EM: Round [348] log likelihood: -3735.880062
EM: Round [349] log likelihood: -3735.879643
EM: Round [350] log likelihood: -3735.879228
EM: Round [351] log likelihood: -3735.878817
EM: Round [352] log likelihood: -3735.878410
EM: Round [353] log likelihood: -3735.878006
EM: Round [354] log likelihood: -3735.877605
EM: Round [355] log likelihood: -3735.877208
EM: Round [356] log likelihood: -3735.876815
EM: Round [357] log likelihood: -3735.876425
EM: Round [358] log likelihood: -3735.876038
EM: Round [359] log likelihood: -3735.875655
EM: Round [360] log likelihood: -3735.875275
EM: Round [361] log likelihood: -3735.874899
EM: Round [362] log likelihood: -3735.874526
EM: Round [363] log likelihood: -3735.874156
EM: Round [364] log likelihood: -3735.873789
EM: Round [365] log likelihood: -3735.873426
EM: Round [366] log likelihood: -3735.873065
EM: Round [367] log likelihood: -3735.872708
EM: Round [368] log likelihood: -3735.872354
EM: Round [369] log likelihood: -3735.872003
EM: Round [370] log likelihood: -3735.871655
EM: Round [371] log likelihood: -3735.871310
EM: Round [372] log likelihood: -3735.870968
EM: Round [373] log likelihood: -3735.870629
EM: Round [374] log likelihood: -3735.870293
EM: Round [375] log likelihood: -3735.869960
EM: Round [376] log likelihood: -3735.869630
EM: Round [377] log likelihood: -3735.869303
EM: Round [378] log likelihood: -3735.868978
EM: Round [379] log likelihood: -3735.868657
EM: Round [380] log likelihood: -3735.868338
EM: Round [381] log likelihood: -3735.868022
EM: Round [382] log likelihood: -3735.867709
EM: Round [383] log likelihood: -3735.867398
EM: Round [384] log likelihood: -3735.867090
EM: Round [385] log likelihood: -3735.866785
EM: Round [386] log likelihood: -3735.866482
EM: Round [387] log likelihood: -3735.866182
EM: Round [388] log likelihood: -3735.865885
EM: Round [389] log likelihood: -3735.865590
EM: Round [390] log likelihood: -3735.865298
EM: Round [391] log likelihood: -3735.865008
EM: Round [392] log likelihood: -3735.864721
EM: Round [393] log likelihood: -3735.864436
EM: Round [394] log likelihood: -3735.864154
EM: Round [395] log likelihood: -3735.863874
EM: Round [396] log likelihood: -3735.863596
EM: Round [397] log likelihood: -3735.863321
EM: Round [398] log likelihood: -3735.863048
EM: Round [399] log likelihood: -3735.862778
EM: Round [400] log likelihood: -3735.862510
EM: Round [401] log likelihood: -3735.862244
EM: Round [402] log likelihood: -3735.861981
EM: Round [403] log likelihood: -3735.861720
EM: Round [404] log likelihood: -3735.861461
EM: Round [405] log likelihood: -3735.861204
EM: Round [406] log likelihood: -3735.860950
EM: Round [407] log likelihood: -3735.860697
EM: Round [408] log likelihood: -3735.860447
EM: Round [409] log likelihood: -3735.860199
EM: Round [410] log likelihood: -3735.859954
EM: Round [411] log likelihood: -3735.859710
EM: Round [412] log likelihood: -3735.859468
EM: Round [413] log likelihood: -3735.859229
EM: Round [414] log likelihood: -3735.858991
EM: Round [415] log likelihood: -3735.858756
EM: Round [416] log likelihood: -3735.858522
EM: Round [417] log likelihood: -3735.858291
EM: Round [418] log likelihood: -3735.858061
EM: Round [419] log likelihood: -3735.857834
EM: Round [420] log likelihood: -3735.857608
EM: Round [421] log likelihood: -3735.857385
EM: Round [422] log likelihood: -3735.857163
EM: Round [423] log likelihood: -3735.856943
EM: Round [424] log likelihood: -3735.856725
EM: Round [425] log likelihood: -3735.856509
EM: Round [426] log likelihood: -3735.856295
EM: Round [427] log likelihood: -3735.856082
EM: Round [428] log likelihood: -3735.855872
EM: Round [429] log likelihood: -3735.855663
EM: Round [430] log likelihood: -3735.855456
EM: Round [431] log likelihood: -3735.855251
EM: Round [432] log likelihood: -3735.855047
EM: Round [433] log likelihood: -3735.854846
EM: Round [434] log likelihood: -3735.854646
EM: Round [435] log likelihood: -3735.854447
EM: Round [436] log likelihood: -3735.854251
EM: Round [437] log likelihood: -3735.854056
EM: Round [438] log likelihood: -3735.853863
EM: Round [439] log likelihood: -3735.853671
EM: Round [440] log likelihood: -3735.853481
EM: Round [441] log likelihood: -3735.853293
EM: Round [442] log likelihood: -3735.853106
EM: Round [443] log likelihood: -3735.852921
EM: Round [444] log likelihood: -3735.852737
EM: Round [445] log likelihood: -3735.852555
EM: Round [446] log likelihood: -3735.852375
EM: Round [447] log likelihood: -3735.852196
EM: Round [448] log likelihood: -3735.852018
EM: Round [449] log likelihood: -3735.851842
EM: Round [450] log likelihood: -3735.851668
EM: Round [451] log likelihood: -3735.851495
EM: Round [452] log likelihood: -3735.851324
EM: Round [453] log likelihood: -3735.851154
EM: Round [454] log likelihood: -3735.850985
EM: Round [455] log likelihood: -3735.850818
EM: Round [456] log likelihood: -3735.850652
EM: Round [457] log likelihood: -3735.850488
EM: Round [458] log likelihood: -3735.850325
EM: Round [459] log likelihood: -3735.850164
EM: Round [460] log likelihood: -3735.850004
EM: Round [461] log likelihood: -3735.849845
EM: Round [462] log likelihood: -3735.849687
EM: Round [463] log likelihood: -3735.849531
EM: Round [464] log likelihood: -3735.849377
EM: Round [465] log likelihood: -3735.849223
EM: Round [466] log likelihood: -3735.849071
EM: Round [467] log likelihood: -3735.848920
EM: Round [468] log likelihood: -3735.848771
EM: Round [469] log likelihood: -3735.848622
EM: Round [470] log likelihood: -3735.848475
EM: Round [471] log likelihood: -3735.848329
EM: Round [472] log likelihood: -3735.848185
EM: Round [473] log likelihood: -3735.848042
EM: Round [474] log likelihood: -3735.847899
EM: Round [475] log likelihood: -3735.847758
EM: Round [476] log likelihood: -3735.847619
EM: Round [477] log likelihood: -3735.847480
EM: Round [478] log likelihood: -3735.847343
EM: Round [479] log likelihood: -3735.847207
EM: Round [480] log likelihood: -3735.847072
EM: Round [481] log likelihood: -3735.846938
EM: Round [482] log likelihood: -3735.846805
EM: Round [483] log likelihood: -3735.846673
EM: Round [484] log likelihood: -3735.846543
EM: Round [485] log likelihood: -3735.846413
EM: Round [486] log likelihood: -3735.846285
EM: Round [487] log likelihood: -3735.846158
EM: Round [488] log likelihood: -3735.846032
EM: Round [489] log likelihood: -3735.845907
EM: Round [490] log likelihood: -3735.845782
EM: Round [491] log likelihood: -3735.845659
EM: Round [492] log likelihood: -3735.845538
EM: Round [493] log likelihood: -3735.845417
EM: Round [494] log likelihood: -3735.845297
EM: Round [495] log likelihood: -3735.845178
EM: Round [496] log likelihood: -3735.845060
EM: Round [497] log likelihood: -3735.844943
EM: Round [498] log likelihood: -3735.844827
EM: Round [499] log likelihood: -3735.844712
EM: Round [500] log likelihood: -3735.844598
EM: Round [501] log likelihood: -3735.844485
EM: Round [502] log likelihood: -3735.844373
EM: Round [503] log likelihood: -3735.844262
EM: Round [504] log likelihood: -3735.844152
EM: Round [505] log likelihood: -3735.844043
EM: Round [506] log likelihood: -3735.843935
EM: Round [507] log likelihood: -3735.843827
EM: Round [508] log likelihood: -3735.843721
EM: Round [509] log likelihood: -3735.843615
EM: Round [510] log likelihood: -3735.843510
EM: Round [511] log likelihood: -3735.843407
EM: Round [512] log likelihood: -3735.843304
EM: Round [513] log likelihood: -3735.843202
EM: Round [514] log likelihood: -3735.843100
EM: Round [515] log likelihood: -3735.843000
EM: Round [516] log likelihood: -3735.842901
EM: Stopping iterations at round 516 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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa > /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir
-done, see /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2520.458624
EM: Round [1] log likelihood: -2520.234213
EM: Round [2] log likelihood: -2520.234136
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.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296655419
Execution Time = 5.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf > /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf > /tmp/nxf.MytSv7bv3H/fi_workdir/microH.dat
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.MytSv7bv3H/fi_workdir/microH.dat /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.MytSv7bv3H/fi_workdir/microH.dat /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.MytSv7bv3H --json_outfile /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-fe8311-R1_A23YTGFLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.MytSv7bv3H --json_outfile /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-fe8311-R1_A23YTGFLT4_1
Running: touch /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-fe8311-R1_A23YTGFLT4_1 --html_output /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_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.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-fe8311-R1_A23YTGFLT4_1 --html_output /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
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]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [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]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.MytSv7bv3H/ctat_genome_lib_build_dir > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.MytSv7bv3H/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory