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/f9/16645d4365c10e4d215adf2b297b3a/tih_rna_sample_00163_B23WHTKLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/a87dfaac344d2855d933580fb03698/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/866e41695733d677115b04e18ce039/tih_rna_sample_00163_B23WHTKLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/a87dfaac344d2855d933580fb03698/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/866e41695733d677115b04e18ce039/tih_rna_sample_00163_B23WHTKLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00163_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00163_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf > /tmp/nxf.Iz2yB19JfN/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf > /tmp/nxf.Iz2yB19JfN/cytoBand.txt
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00163_B23WHTKLT4_1.star --out_dir /tmp/nxf.Iz2yB19JfN/fi_workdir --reads "/tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 08:56:01 ..... started STAR run
Jun 08 08:56:01 ..... loading genome
Jun 08 08:57:39 ... generating Suffix Array index
Jun 08 09:01:18 ... completed Suffix Array index
Jun 08 09:01:19 ..... processing annotations GTF
Jun 08 09:01:19 ..... inserting junctions into the genome indices
Jun 08 09:02:19 ..... started mapping
Jun 08 09:44:41 ..... finished mapping
Jun 08 09:44:42 ..... started sorting BAM
Jun 08 09:44:42 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00163_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00163_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 48.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00163_B23WHTKLT4_1.star --out_dir /tmp/nxf.Iz2yB19JfN/fi_workdir --reads "/tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
09:44:46 : INFO : Done.
Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
[10000]
[20000]
[30000]
[40000]
[50000]
[60000]
[70000]
[80000]
[90000]
[100000]
[110000]
[120000]
[130000]
[140000]
[150000]
[160000]
[170000]
[180000]
[190000]
[200000]
[210000]
[220000]
[230000]
[240000]
[250000]
[260000]
[270000]
[280000]
[290000]
[300000]
[310000]
[320000]
[330000]
[340000]
[350000]
[360000]
[370000]
[380000]
[390000]
[400000]
[410000]
[420000]
[430000]
[440000]
[450000]
[460000]
[470000]
[480000]
[490000]
[500000]
[510000]
[520000]
[530000]
[540000] -done parsing /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 34,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 22,
'num genes matched < 2' => 35,
'seq-similar region overlap' => 99,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 39,
'low complexity anchor region' => 6,
'per_id < 96' => 3683,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 4,
'excessive soft clipping' => 5438,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 56,
' ** passed ** ' => 3103
};
-writing fusion junction support info.
Execution Time = 0.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
[2000]
[3000]
[4000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000] -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000] -fusion SPANNING read extraction for scaff: LINC01674--POTED
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000]
[75000]
[76000]
[77000]
[78000]
[79000]
[80000]
[81000]
[82000]
[83000] -fusion SPANNING read extraction for scaff: RUNX1--LINC01674
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000]
[75000]
[76000]
[77000]
[78000]
[79000]
[80000]
[81000]
[82000]
[83000]
[84000]
[85000]
[86000]
[87000]
[88000]
[89000]
[90000]
[91000]
[92000]
[93000]
[94000]
[95000]
[96000]
[97000]
[98000]
[99000]
[100000]
[101000]
[102000]
[103000] -fusion SPANNING read extraction for scaff: RUNX1--POTED
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000]
[75000]
[76000]
[77000]
[78000]
[79000]
[80000]
[81000]
[82000]
[83000] -fusion SPANNING read extraction for scaff: RUNX1--GTF2IP2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000] -fusion SPANNING read extraction for scaff: SCARF2--EHMT1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
[1000]
[2000]
[3000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000] -fusion SPANNING read extraction for scaff: TPD52L1--HDDC2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000] -fusion SPANNING read extraction for scaff: ZNF44--AC024563.1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 9337,
'lacks exon overlap' => 6171
};
Execution Time = 0.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4649.446790
EM: Round [1] log likelihood: -4647.168424
EM: Round [2] log likelihood: -4647.050761
EM: Round [3] log likelihood: -4646.943859
EM: Round [4] log likelihood: -4646.845782
EM: Round [5] log likelihood: -4646.755660
EM: Round [6] log likelihood: -4646.672728
EM: Round [7] log likelihood: -4646.596314
EM: Round [8] log likelihood: -4646.525824
EM: Round [9] log likelihood: -4646.460729
EM: Round [10] log likelihood: -4646.400558
EM: Round [11] log likelihood: -4646.344890
EM: Round [12] log likelihood: -4646.293346
EM: Round [13] log likelihood: -4646.245586
EM: Round [14] log likelihood: -4646.201302
EM: Round [15] log likelihood: -4646.160216
EM: Round [16] log likelihood: -4646.122074
EM: Round [17] log likelihood: -4646.086647
EM: Round [18] log likelihood: -4646.053727
EM: Round [19] log likelihood: -4646.023122
EM: Round [20] log likelihood: -4645.994657
EM: Round [21] log likelihood: -4645.968173
EM: Round [22] log likelihood: -4645.943523
EM: Round [23] log likelihood: -4645.920573
EM: Round [24] log likelihood: -4645.899199
EM: Round [25] log likelihood: -4645.879287
EM: Round [26] log likelihood: -4645.860733
EM: Round [27] log likelihood: -4645.843439
EM: Round [28] log likelihood: -4645.827317
EM: Round [29] log likelihood: -4645.812284
EM: Round [30] log likelihood: -4645.798263
EM: Round [31] log likelihood: -4645.785185
EM: Round [32] log likelihood: -4645.772983
EM: Round [33] log likelihood: -4645.761597
EM: Round [34] log likelihood: -4645.750972
EM: Round [35] log likelihood: -4645.741054
EM: Round [36] log likelihood: -4645.731797
EM: Round [37] log likelihood: -4645.723154
EM: Round [38] log likelihood: -4645.715084
EM: Round [39] log likelihood: -4645.707548
EM: Round [40] log likelihood: -4645.700510
EM: Round [41] log likelihood: -4645.693938
EM: Round [42] log likelihood: -4645.687799
EM: Round [43] log likelihood: -4645.682064
EM: Round [44] log likelihood: -4645.676707
EM: Round [45] log likelihood: -4645.671702
EM: Round [46] log likelihood: -4645.667026
EM: Round [47] log likelihood: -4645.662657
EM: Round [48] log likelihood: -4645.658574
EM: Round [49] log likelihood: -4645.654759
EM: Round [50] log likelihood: -4645.651194
EM: Round [51] log likelihood: -4645.647863
EM: Round [52] log likelihood: -4645.644749
EM: Round [53] log likelihood: -4645.641839
EM: Round [54] log likelihood: -4645.639119
EM: Round [55] log likelihood: -4645.636577
EM: Round [56] log likelihood: -4645.634201
EM: Round [57] log likelihood: -4645.631979
EM: Round [58] log likelihood: -4645.629903
EM: Round [59] log likelihood: -4645.627962
EM: Round [60] log likelihood: -4645.626148
EM: Round [61] log likelihood: -4645.624452
EM: Round [62] log likelihood: -4645.622866
EM: Round [63] log likelihood: -4645.621384
EM: Round [64] log likelihood: -4645.619998
EM: Round [65] log likelihood: -4645.618703
EM: Round [66] log likelihood: -4645.617491
EM: Round [67] log likelihood: -4645.616359
EM: Round [68] log likelihood: -4645.615300
EM: Round [69] log likelihood: -4645.614310
EM: Round [70] log likelihood: -4645.613385
EM: Round [71] log likelihood: -4645.612520
EM: Round [72] log likelihood: -4645.611710
EM: Round [73] log likelihood: -4645.610954
EM: Round [74] log likelihood: -4645.610247
EM: Round [75] log likelihood: -4645.609585
EM: Round [76] log likelihood: -4645.608967
EM: Round [77] log likelihood: -4645.608389
EM: Round [78] log likelihood: -4645.607848
EM: Round [79] log likelihood: -4645.607343
EM: Round [80] log likelihood: -4645.606870
EM: Round [81] log likelihood: -4645.606428
EM: Round [82] log likelihood: -4645.606015
EM: Round [83] log likelihood: -4645.605628
EM: Round [84] log likelihood: -4645.605267
EM: Round [85] log likelihood: -4645.604929
EM: Round [86] log likelihood: -4645.604613
EM: Round [87] log likelihood: -4645.604318
EM: Round [88] log likelihood: -4645.604042
EM: Round [89] log likelihood: -4645.603783
EM: Round [90] log likelihood: -4645.603542
EM: Round [91] log likelihood: -4645.603316
EM: Round [92] log likelihood: -4645.603105
EM: Round [93] log likelihood: -4645.602907
EM: Round [94] log likelihood: -4645.602723
EM: Round [95] log likelihood: -4645.602550
EM: Round [96] log likelihood: -4645.602388
EM: Round [97] log likelihood: -4645.602237
EM: Round [98] log likelihood: -4645.602096
EM: Round [99] log likelihood: -4645.601964
EM: Round [100] log likelihood: -4645.601841
EM: Round [101] log likelihood: -4645.601725
EM: Round [102] log likelihood: -4645.601617
EM: Round [103] log likelihood: -4645.601516
EM: Round [104] log likelihood: -4645.601422
EM: Stopping iterations at round 104 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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa > /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -4414.825998
EM: Round [1] log likelihood: -4414.547973
EM: Round [2] log likelihood: -4414.547836
EM: Round [3] log likelihood: -4414.547835
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.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_1.fastp.fastq.gz: 186358289
Execution Time = 3.72 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa --gtf /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf > /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fa --gtf /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf > /tmp/nxf.Iz2yB19JfN/fi_workdir/microH.dat
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Iz2yB19JfN/fi_workdir/microH.dat /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Iz2yB19JfN/fi_workdir/microH.dat /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Iz2yB19JfN --json_outfile /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00163_B23WHTKLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Iz2yB19JfN --json_outfile /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00163_B23WHTKLT4_1
Running: touch /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00163_B23WHTKLT4_1 --html_output /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_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.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00163_B23WHTKLT4_1 --html_output /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
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 [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000268981.5]
WARNING, no entry stored in dbm for [ENSG00000268981.5]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Iz2yB19JfN/ctat_genome_lib_build_dir > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.Iz2yB19JfN/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory