.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00766_B23MVV7LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/180e5d94607dd74b3fc64de0f2538a/.command.log
Size: 61.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00766_B23MVV7LT4_1)
Attempt
Content

  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/56/4d5cd7c99b970a9a3ad5168704774d/tih_rna_sample_00766_B23MVV7LT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/180e5d94607dd74b3fc64de0f2538a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/180e5d94607dd74b3fc64de0f2538a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/df7312405d0fde5a2fecf816f75c5b/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/df7312405d0fde5a2fecf816f75c5b/tih_rna_sample_00766_B23MVV7LT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00766_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00766_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/cytoBand.txt
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00766_B23MVV7LT4_1.star --out_dir /tmp/nxf.k6iMamKp4Y/fi_workdir --reads "/tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:21:32 ..... started STAR run
Jun 08 09:21:32 ..... loading genome
Jun 08 09:23:10 ... generating Suffix Array index
Jun 08 09:27:04 ... completed Suffix Array index
Jun 08 09:27:04 ..... processing annotations GTF
Jun 08 09:27:04 ..... inserting junctions into the genome indices
Jun 08 09:28:05 ..... started mapping
Jun 08 10:05:00 ..... finished mapping
Jun 08 10:05:02 ..... started sorting BAM
Jun 08 10:05:02 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 43.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00766_B23MVV7LT4_1.star --out_dir /tmp/nxf.k6iMamKp4Y/fi_workdir --reads "/tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
10:05:08 : INFO : Done.
Execution Time = 0.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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]   
[550000]   
[560000]   
[570000]   
[580000]   
[590000]   
[600000]   
[610000]   
[620000]   
[630000]   
[640000]   
[650000]   
[660000]   
[670000]   
[680000]   
[690000]   
[700000]   
[710000]   
[720000]   
[730000]   
[740000]   
[750000]   
[760000]   
[770000]   
[780000]   
[790000]   
[800000]   
[810000]   
[820000]   
[830000]   
[840000]   
[850000]   
[860000]   
[870000]   
[880000]   
[890000]   
[900000]   
[910000]   
[920000]   
[930000]   
[940000]   
[950000]   
[960000]   
[970000]   
[980000]   
[990000]   
[1000000]   
[1010000]   
[1020000]   
[1030000]   
[1040000]   -done parsing /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'seq-similar region overlap' => 547,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 56,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
          ' ** passed ** ' => 1147,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 81,
          'per_id < 96' => 5998,
          'small anchor length' => 2,
          'low complexity anchor region' => 3,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 7,
          'num genes matched < 2' => 30,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 18,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
          'excessive soft clipping' => 10146,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 16
        };
-writing fusion junction support info.
Execution Time = 0.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[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]   -fusion SPANNING read extraction for scaff: AC211476.4--CLIP2

[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]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   
[120000]   
[121000]   
[122000]   
[123000]   
[124000]   
[125000]   
[126000]   
[127000]   
[128000]   
[129000]   
[130000]   
[131000]   
[132000]   
[133000]   -fusion SPANNING read extraction for scaff: CDKAL1--E2F3

[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]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   
[120000]   
[121000]   
[122000]   
[123000]   
[124000]   
[125000]   
[126000]   
[127000]   
[128000]   
[129000]   
[130000]   
[131000]   
[132000]   
[133000]   
[134000]   
[135000]   
[136000]   
[137000]   
[138000]   
[139000]   
[140000]   
[141000]   
[142000]   
[143000]   
[144000]   
[145000]   
[146000]   
[147000]   
[148000]   
[149000]   
[150000]   
[151000]   
[152000]   
[153000]   
[154000]   
[155000]   
[156000]   
[157000]   
[158000]   
[159000]   
[160000]   
[161000]   
[162000]   
[163000]   -fusion SPANNING read extraction for scaff: FBRS--ITGAL

[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]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   
[120000]   -fusion SPANNING read extraction for scaff: FBRS--SEPHS2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[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]   -fusion SPANNING read extraction for scaff: LARS1--AC011396.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[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]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   
[120000]   
[121000]   
[122000]   
[123000]   
[124000]   
[125000]   
[126000]   
[127000]   
[128000]   
[129000]   
[130000]   
[131000]   
[132000]   
[133000]   
[134000]   
[135000]   
[136000]   
[137000]   
[138000]   
[139000]   
[140000]   
[141000]   
[142000]   
[143000]   
[144000]   
[145000]   
[146000]   
[147000]   
[148000]   
[149000]   
[150000]   
[151000]   
[152000]   
[153000]   
[154000]   
[155000]   
[156000]   
[157000]   
[158000]   
[159000]   
[160000]   
[161000]   
[162000]   
[163000]   
[164000]   
[165000]   
[166000]   
[167000]   
[168000]   
[169000]   
[170000]   
[171000]   
[172000]   
[173000]   
[174000]   
[175000]   
[176000]   
[177000]   
[178000]   
[179000]   
[180000]   
[181000]   
[182000]   
[183000]   
[184000]   
[185000]   
[186000]   
[187000]   
[188000]   
[189000]   
[190000]   
[191000]   
[192000]   
[193000]   
[194000]   
[195000]   
[196000]   
[197000]   
[198000]   
[199000]   
[200000]   
[201000]   
[202000]   
[203000]   
[204000]   
[205000]   
[206000]   
[207000]   
[208000]   
[209000]   
[210000]   
[211000]   
[212000]   
[213000]   
[214000]   
[215000]   
[216000]   
[217000]   
[218000]   -fusion SPANNING read extraction for scaff: LARS1--TCERG1

[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]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[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]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   -fusion SPANNING read extraction for scaff: PCDHA11--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]   -fusion SPANNING read extraction for scaff: RRP36--PEX6

[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]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 39001,
          'lacks exon overlap' => 11793
        };
Execution Time = 1.38 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -1192.060136
EM: Round [1] log likelihood: -1192.049448
EM: Round [2] log likelihood: -1192.039108
EM: Round [3] log likelihood: -1192.029099
EM: Round [4] log likelihood: -1192.019409
EM: Round [5] log likelihood: -1192.010024
EM: Round [6] log likelihood: -1192.000932
EM: Round [7] log likelihood: -1191.992121
EM: Round [8] log likelihood: -1191.983581
EM: Round [9] log likelihood: -1191.975300
EM: Round [10] log likelihood: -1191.967269
EM: Round [11] log likelihood: -1191.959478
EM: Round [12] log likelihood: -1191.951919
EM: Round [13] log likelihood: -1191.944582
EM: Round [14] log likelihood: -1191.937460
EM: Round [15] log likelihood: -1191.930546
EM: Round [16] log likelihood: -1191.923830
EM: Round [17] log likelihood: -1191.917308
EM: Round [18] log likelihood: -1191.910971
EM: Round [19] log likelihood: -1191.904813
EM: Round [20] log likelihood: -1191.898829
EM: Round [21] log likelihood: -1191.893012
EM: Round [22] log likelihood: -1191.887357
EM: Round [23] log likelihood: -1191.881859
EM: Round [24] log likelihood: -1191.876511
EM: Round [25] log likelihood: -1191.871310
EM: Round [26] log likelihood: -1191.866251
EM: Round [27] log likelihood: -1191.861329
EM: Round [28] log likelihood: -1191.856539
EM: Round [29] log likelihood: -1191.851878
EM: Round [30] log likelihood: -1191.847341
EM: Round [31] log likelihood: -1191.842925
EM: Round [32] log likelihood: -1191.838626
EM: Round [33] log likelihood: -1191.834441
EM: Round [34] log likelihood: -1191.830365
EM: Round [35] log likelihood: -1191.826395
EM: Round [36] log likelihood: -1191.822529
EM: Round [37] log likelihood: -1191.818764
EM: Round [38] log likelihood: -1191.815096
EM: Round [39] log likelihood: -1191.811522
EM: Round [40] log likelihood: -1191.808040
EM: Round [41] log likelihood: -1191.804647
EM: Round [42] log likelihood: -1191.801340
EM: Round [43] log likelihood: -1191.798118
EM: Round [44] log likelihood: -1191.794977
EM: Round [45] log likelihood: -1191.791915
EM: Round [46] log likelihood: -1191.788931
EM: Round [47] log likelihood: -1191.786021
EM: Round [48] log likelihood: -1191.783184
EM: Round [49] log likelihood: -1191.780418
EM: Round [50] log likelihood: -1191.777721
EM: Round [51] log likelihood: -1191.775091
EM: Round [52] log likelihood: -1191.772526
EM: Round [53] log likelihood: -1191.770024
EM: Round [54] log likelihood: -1191.767584
EM: Round [55] log likelihood: -1191.765204
EM: Round [56] log likelihood: -1191.762882
EM: Round [57] log likelihood: -1191.760617
EM: Round [58] log likelihood: -1191.758408
EM: Round [59] log likelihood: -1191.756252
EM: Round [60] log likelihood: -1191.754148
EM: Round [61] log likelihood: -1191.752096
EM: Round [62] log likelihood: -1191.750093
EM: Round [63] log likelihood: -1191.748139
EM: Round [64] log likelihood: -1191.746232
EM: Round [65] log likelihood: -1191.744370
EM: Round [66] log likelihood: -1191.742553
EM: Round [67] log likelihood: -1191.740780
EM: Round [68] log likelihood: -1191.739050
EM: Round [69] log likelihood: -1191.737360
EM: Round [70] log likelihood: -1191.735711
EM: Round [71] log likelihood: -1191.734101
EM: Round [72] log likelihood: -1191.732530
EM: Round [73] log likelihood: -1191.730996
EM: Round [74] log likelihood: -1191.729498
EM: Round [75] log likelihood: -1191.728036
EM: Round [76] log likelihood: -1191.726608
EM: Round [77] log likelihood: -1191.725214
EM: Round [78] log likelihood: -1191.723852
EM: Round [79] log likelihood: -1191.722523
EM: Round [80] log likelihood: -1191.721225
EM: Round [81] log likelihood: -1191.719958
EM: Round [82] log likelihood: -1191.718720
EM: Round [83] log likelihood: -1191.717511
EM: Round [84] log likelihood: -1191.716331
EM: Round [85] log likelihood: -1191.715178
EM: Round [86] log likelihood: -1191.714052
EM: Round [87] log likelihood: -1191.712952
EM: Round [88] log likelihood: -1191.711878
EM: Round [89] log likelihood: -1191.710828
EM: Round [90] log likelihood: -1191.709804
EM: Round [91] log likelihood: -1191.708803
EM: Round [92] log likelihood: -1191.707825
EM: Round [93] log likelihood: -1191.706870
EM: Round [94] log likelihood: -1191.705936
EM: Round [95] log likelihood: -1191.705025
EM: Round [96] log likelihood: -1191.704135
EM: Round [97] log likelihood: -1191.703265
EM: Round [98] log likelihood: -1191.702415
EM: Round [99] log likelihood: -1191.701585
EM: Round [100] log likelihood: -1191.700774
EM: Round [101] log likelihood: -1191.699981
EM: Round [102] log likelihood: -1191.699207
EM: Round [103] log likelihood: -1191.698450
EM: Round [104] log likelihood: -1191.697711
EM: Round [105] log likelihood: -1191.696989
EM: Round [106] log likelihood: -1191.696284
EM: Round [107] log likelihood: -1191.695594
EM: Round [108] log likelihood: -1191.694921
EM: Round [109] log likelihood: -1191.694262
EM: Round [110] log likelihood: -1191.693619
EM: Round [111] log likelihood: -1191.692991
EM: Round [112] log likelihood: -1191.692376
EM: Round [113] log likelihood: -1191.691776
EM: Round [114] log likelihood: -1191.691190
EM: Round [115] log likelihood: -1191.690617
EM: Round [116] log likelihood: -1191.690057
EM: Round [117] log likelihood: -1191.689509
EM: Round [118] log likelihood: -1191.688975
EM: Round [119] log likelihood: -1191.688452
EM: Round [120] log likelihood: -1191.687941
EM: Round [121] log likelihood: -1191.687442
EM: Round [122] log likelihood: -1191.686954
EM: Round [123] log likelihood: -1191.686477
EM: Round [124] log likelihood: -1191.686011
EM: Round [125] log likelihood: -1191.685556
EM: Round [126] log likelihood: -1191.685111
EM: Round [127] log likelihood: -1191.684676
EM: Round [128] log likelihood: -1191.684251
EM: Round [129] log likelihood: -1191.683835
EM: Round [130] log likelihood: -1191.683429
EM: Round [131] log likelihood: -1191.683032
EM: Round [132] log likelihood: -1191.682644
EM: Round [133] log likelihood: -1191.682265
EM: Round [134] log likelihood: -1191.681894
EM: Round [135] log likelihood: -1191.681532
EM: Round [136] log likelihood: -1191.681178
EM: Round [137] log likelihood: -1191.680832
EM: Round [138] log likelihood: -1191.680493
EM: Round [139] log likelihood: -1191.680163
EM: Round [140] log likelihood: -1191.679840
EM: Round [141] log likelihood: -1191.679524
EM: Round [142] log likelihood: -1191.679215
EM: Round [143] log likelihood: -1191.678913
EM: Round [144] log likelihood: -1191.678618
EM: Round [145] log likelihood: -1191.678330
EM: Round [146] log likelihood: -1191.678048
EM: Round [147] log likelihood: -1191.677772
EM: Round [148] log likelihood: -1191.677503
EM: Round [149] log likelihood: -1191.677239
EM: Round [150] log likelihood: -1191.676982
EM: Round [151] log likelihood: -1191.676730
EM: Round [152] log likelihood: -1191.676484
EM: Round [153] log likelihood: -1191.676244
EM: Round [154] log likelihood: -1191.676009
EM: Round [155] log likelihood: -1191.675779
EM: Round [156] log likelihood: -1191.675554
EM: Round [157] log likelihood: -1191.675335
EM: Round [158] log likelihood: -1191.675120
EM: Round [159] log likelihood: -1191.674910
EM: Round [160] log likelihood: -1191.674705
EM: Round [161] log likelihood: -1191.674505
EM: Round [162] log likelihood: -1191.674309
EM: Round [163] log likelihood: -1191.674117
EM: Round [164] log likelihood: -1191.673930
EM: Round [165] log likelihood: -1191.673746
EM: Round [166] log likelihood: -1191.673567
EM: Round [167] log likelihood: -1191.673392
EM: Round [168] log likelihood: -1191.673221
EM: Round [169] log likelihood: -1191.673054
EM: Round [170] log likelihood: -1191.672890
EM: Round [171] log likelihood: -1191.672730
EM: Round [172] log likelihood: -1191.672574
EM: Round [173] log likelihood: -1191.672421
EM: Round [174] log likelihood: -1191.672272
EM: Round [175] log likelihood: -1191.672126
EM: Round [176] log likelihood: -1191.671983
EM: Round [177] log likelihood: -1191.671843
EM: Round [178] log likelihood: -1191.671707
EM: Round [179] log likelihood: -1191.671574
EM: Round [180] log likelihood: -1191.671443
EM: Round [181] log likelihood: -1191.671316
EM: Round [182] log likelihood: -1191.671191
EM: Round [183] log likelihood: -1191.671069
EM: Round [184] log likelihood: -1191.670950
EM: Round [185] log likelihood: -1191.670833
EM: Round [186] log likelihood: -1191.670719
EM: Round [187] log likelihood: -1191.670608
EM: Round [188] log likelihood: -1191.670499
EM: Round [189] log likelihood: -1191.670393
EM: Round [190] log likelihood: -1191.670289
EM: Round [191] log likelihood: -1191.670187
EM: Round [192] log likelihood: -1191.670088
EM: Stopping iterations at round 192 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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir
-done, see /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1131.300251
EM: Round [1] log likelihood: -1131.300251
EM: Stopping iterations at round 1 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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz: 202924806
Execution Time = 3.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa --gtf /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf  > /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa --gtf /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf  > /tmp/nxf.k6iMamKp4Y/fi_workdir/microH.dat
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.k6iMamKp4Y/fi_workdir/microH.dat /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/microH.dat /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.k6iMamKp4Y --json_outfile /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00766_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.k6iMamKp4Y --json_outfile /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00766_B23MVV7LT4_1
Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00766_B23MVV7LT4_1 --html_output /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00766_B23MVV7LT4_1 --html_output /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
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 [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory