Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/b1eab359874c53aa906b74940e8519/659_Lx-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/b1eab359874c53aa906b74940e8519/659_Lx-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/fdd088f9271ec2a52e77ee2570d9d2/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/fdd088f9271ec2a52e77ee2570d9d2/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/33dad9c664087db246ede3a6f45973/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.U5nUa6x7eF/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.U5nUa6x7eF/cytoBand.txt
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_Lx-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.U5nUa6x7eF/fi_workdir --reads "/tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:40:54 ..... started STAR run
Jun 08 09:40:54 ..... loading genome
Jun 08 09:42:39 ... generating Suffix Array index
Jun 08 09:47:15 ... completed Suffix Array index
Jun 08 09:47:15 ..... processing annotations GTF
Jun 08 09:47:15 ..... inserting junctions into the genome indices
Jun 08 09:48:16 ..... started mapping
Jun 08 10:37:43 ..... finished mapping
Jun 08 10:37:46 ..... started sorting BAM
Jun 08 10:37:47 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 56.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_Lx-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.U5nUa6x7eF/fi_workdir --reads "/tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
10:37:52 : INFO : Done.
Execution Time = 0.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_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]
[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] -done parsing /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 3486,
'small anchor length' => 40,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 41,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 24,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 160,
'seq-similar region overlap' => 167,
'per_id < 96' => 5195,
'low complexity anchor region' => 27,
'excessive soft clipping' => 5997
};
-writing fusion junction support info.
Execution Time = 0.48 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[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]
[219000]
[220000]
[221000]
[222000]
[223000]
[224000]
[225000]
[226000]
[227000]
[228000]
[229000]
[230000]
[231000]
[232000]
[233000]
[234000]
[235000]
[236000]
[237000]
[238000]
[239000]
[240000]
[241000]
[242000]
[243000]
[244000]
[245000]
[246000]
[247000]
[248000]
[249000]
[250000]
[251000]
[252000]
[253000]
[254000]
[255000]
[256000]
[257000]
[258000]
[259000]
[260000]
[261000]
[262000]
[263000]
[264000]
[265000]
[266000]
[267000]
[268000]
[269000]
[270000]
[271000]
[272000]
[273000]
[274000]
[275000]
[276000]
[277000]
[278000]
[279000]
[280000]
[281000]
[282000]
[283000]
[284000]
[285000]
[286000]
[287000]
[288000]
[289000]
[290000]
[291000]
[292000]
[293000]
[294000]
[295000]
[296000]
[297000]
[298000]
[299000]
[300000]
[301000]
[302000]
[303000]
[304000]
[305000]
[306000]
[307000]
[308000]
[309000]
[310000]
[311000]
[312000]
[313000]
[314000]
[315000]
[316000]
[317000]
[318000]
[319000]
[320000]
[321000]
[322000]
[323000]
[324000]
[325000]
[326000]
[327000]
[328000]
[329000]
[330000]
[331000]
[332000]
[333000]
[334000]
[335000]
[336000]
[337000]
[338000]
[339000]
[340000]
[341000]
[342000]
[343000]
[344000]
[345000]
[346000]
[347000]
[348000]
[349000]
[350000]
[351000]
[352000]
[353000]
[354000]
[355000]
[356000]
[357000]
[358000]
[359000]
[360000]
[361000]
[362000]
[363000]
[364000]
[365000]
[366000]
[367000]
[368000]
[369000]
[370000]
[371000]
[372000]
[373000]
[374000]
[375000]
[376000]
[377000]
[378000]
[379000]
[380000]
[381000]
[382000]
[383000]
[384000]
[385000]
[386000]
[387000]
[388000]
[389000]
[390000]
[391000]
[392000]
[393000]
[394000]
[395000]
[396000]
[397000]
[398000]
[399000]
[400000]
[401000]
[402000]
[403000]
[404000]
[405000]
[406000]
[407000]
[408000]
[409000]
[410000]
[411000]
[412000]
[413000]
[414000]
[415000]
[416000]
[417000]
[418000]
[419000]
[420000]
[421000]
[422000]
[423000]
[424000]
[425000]
[426000]
[427000]
[428000]
[429000]
[430000]
[431000]
[432000]
[433000]
[434000]
[435000]
[436000]
[437000]
[438000]
[439000]
[440000]
[441000]
[442000]
[443000]
[444000]
[445000]
[446000]
[447000]
[448000]
[449000]
[450000]
[451000]
[452000]
[453000]
[454000]
[455000]
[456000]
[457000]
[458000]
[459000]
[460000]
[461000]
[462000]
[463000]
[464000]
[465000]
[466000]
[467000]
[468000]
[469000]
[470000]
[471000]
[472000]
[473000]
[474000]
[475000]
[476000]
[477000]
[478000]
[479000]
[480000]
[481000]
[482000]
[483000]
[484000]
[485000]
[486000]
[487000]
[488000]
[489000]
[490000]
[491000]
[492000]
[493000]
[494000]
[495000]
[496000]
[497000]
[498000]
[499000]
[500000]
[501000]
[502000]
[503000]
[504000]
[505000]
[506000]
[507000]
[508000]
[509000]
[510000]
[511000]
[512000]
[513000]
[514000]
[515000]
[516000]
[517000]
[518000]
[519000]
[520000]
[521000]
[522000]
[523000]
[524000]
[525000]
[526000]
[527000]
[528000]
[529000]
[530000]
[531000]
[532000]
[533000]
[534000]
[535000]
[536000]
[537000]
[538000]
[539000]
[540000]
[541000]
[542000]
[543000]
[544000]
[545000]
[546000]
[547000]
[548000]
[549000]
[550000]
[551000]
[552000]
[553000]
[554000]
[555000]
[556000]
[557000]
[558000]
[559000]
[560000]
[561000]
[562000]
[563000]
[564000]
[565000]
[566000]
[567000]
[568000]
[569000]
[570000]
[571000]
[572000]
[573000]
[574000]
[575000]
[576000]
[577000]
[578000]
[579000]
[580000]
[581000]
[582000]
[583000]
[584000]
[585000]
[586000] -fusion SPANNING read extraction for scaff: ACTBP6--ACTB
[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: CCDC6--RET
[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] -fusion SPANNING read extraction for scaff: MTA1--PACS2
[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] -fusion SPANNING read extraction for scaff: PCDHA10--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] -fusion SPANNING read extraction for scaff: PCDHA10--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] -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] -fusion SPANNING read extraction for scaff: TFB2M--CNST
[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: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 580,
'seq similar region alignment' => 19605
};
Execution Time = 1.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2305.900463
EM: Round [1] log likelihood: -2305.890338
EM: Round [2] log likelihood: -2305.880368
EM: Round [3] log likelihood: -2305.870549
EM: Round [4] log likelihood: -2305.860878
EM: Round [5] log likelihood: -2305.851353
EM: Round [6] log likelihood: -2305.841971
EM: Round [7] log likelihood: -2305.832729
EM: Round [8] log likelihood: -2305.823623
EM: Round [9] log likelihood: -2305.814653
EM: Round [10] log likelihood: -2305.805814
EM: Round [11] log likelihood: -2305.797104
EM: Round [12] log likelihood: -2305.788522
EM: Round [13] log likelihood: -2305.780064
EM: Round [14] log likelihood: -2305.771728
EM: Round [15] log likelihood: -2305.763513
EM: Round [16] log likelihood: -2305.755415
EM: Round [17] log likelihood: -2305.747432
EM: Round [18] log likelihood: -2305.739564
EM: Round [19] log likelihood: -2305.731807
EM: Round [20] log likelihood: -2305.724159
EM: Round [21] log likelihood: -2305.716619
EM: Round [22] log likelihood: -2305.709184
EM: Round [23] log likelihood: -2305.701853
EM: Round [24] log likelihood: -2305.694624
EM: Round [25] log likelihood: -2305.687496
EM: Round [26] log likelihood: -2305.680465
EM: Round [27] log likelihood: -2305.673532
EM: Round [28] log likelihood: -2305.666693
EM: Round [29] log likelihood: -2305.659948
EM: Round [30] log likelihood: -2305.653295
EM: Round [31] log likelihood: -2305.646732
EM: Round [32] log likelihood: -2305.640258
EM: Round [33] log likelihood: -2305.633871
EM: Round [34] log likelihood: -2305.627570
EM: Round [35] log likelihood: -2305.621354
EM: Round [36] log likelihood: -2305.615220
EM: Round [37] log likelihood: -2305.609169
EM: Round [38] log likelihood: -2305.603197
EM: Round [39] log likelihood: -2305.597305
EM: Round [40] log likelihood: -2305.591491
EM: Round [41] log likelihood: -2305.585753
EM: Round [42] log likelihood: -2305.580090
EM: Round [43] log likelihood: -2305.574501
EM: Round [44] log likelihood: -2305.568986
EM: Round [45] log likelihood: -2305.563542
EM: Round [46] log likelihood: -2305.558169
EM: Round [47] log likelihood: -2305.552865
EM: Round [48] log likelihood: -2305.547630
EM: Round [49] log likelihood: -2305.542463
EM: Round [50] log likelihood: -2305.537361
EM: Round [51] log likelihood: -2305.532325
EM: Round [52] log likelihood: -2305.527354
EM: Round [53] log likelihood: -2305.522446
EM: Round [54] log likelihood: -2305.517600
EM: Round [55] log likelihood: -2305.512816
EM: Round [56] log likelihood: -2305.508092
EM: Round [57] log likelihood: -2305.503428
EM: Round [58] log likelihood: -2305.498823
EM: Round [59] log likelihood: -2305.494276
EM: Round [60] log likelihood: -2305.489785
EM: Round [61] log likelihood: -2305.485351
EM: Round [62] log likelihood: -2305.480972
EM: Round [63] log likelihood: -2305.476648
EM: Round [64] log likelihood: -2305.472378
EM: Round [65] log likelihood: -2305.468160
EM: Round [66] log likelihood: -2305.463995
EM: Round [67] log likelihood: -2305.459882
EM: Round [68] log likelihood: -2305.455819
EM: Round [69] log likelihood: -2305.451805
EM: Round [70] log likelihood: -2305.447842
EM: Round [71] log likelihood: -2305.443927
EM: Round [72] log likelihood: -2305.440059
EM: Round [73] log likelihood: -2305.436239
EM: Round [74] log likelihood: -2305.432466
EM: Round [75] log likelihood: -2305.428738
EM: Round [76] log likelihood: -2305.425056
EM: Round [77] log likelihood: -2305.421418
EM: Round [78] log likelihood: -2305.417824
EM: Round [79] log likelihood: -2305.414274
EM: Round [80] log likelihood: -2305.410767
EM: Round [81] log likelihood: -2305.407301
EM: Round [82] log likelihood: -2305.403878
EM: Round [83] log likelihood: -2305.400495
EM: Round [84] log likelihood: -2305.397153
EM: Round [85] log likelihood: -2305.393851
EM: Round [86] log likelihood: -2305.390588
EM: Round [87] log likelihood: -2305.387364
EM: Round [88] log likelihood: -2305.384178
EM: Round [89] log likelihood: -2305.381031
EM: Round [90] log likelihood: -2305.377920
EM: Round [91] log likelihood: -2305.374847
EM: Round [92] log likelihood: -2305.371809
EM: Round [93] log likelihood: -2305.368808
EM: Round [94] log likelihood: -2305.365842
EM: Round [95] log likelihood: -2305.362911
EM: Round [96] log likelihood: -2305.360014
EM: Round [97] log likelihood: -2305.357151
EM: Round [98] log likelihood: -2305.354322
EM: Round [99] log likelihood: -2305.351526
EM: Round [100] log likelihood: -2305.348763
EM: Round [101] log likelihood: -2305.346031
EM: Round [102] log likelihood: -2305.343332
EM: Round [103] log likelihood: -2305.340664
EM: Round [104] log likelihood: -2305.338027
EM: Round [105] log likelihood: -2305.335421
EM: Round [106] log likelihood: -2305.332845
EM: Round [107] log likelihood: -2305.330299
EM: Round [108] log likelihood: -2305.327782
EM: Round [109] log likelihood: -2305.325294
EM: Round [110] log likelihood: -2305.322835
EM: Round [111] log likelihood: -2305.320404
EM: Round [112] log likelihood: -2305.318001
EM: Round [113] log likelihood: -2305.315626
EM: Round [114] log likelihood: -2305.313278
EM: Round [115] log likelihood: -2305.310957
EM: Round [116] log likelihood: -2305.308663
EM: Round [117] log likelihood: -2305.306394
EM: Round [118] log likelihood: -2305.304152
EM: Round [119] log likelihood: -2305.301935
EM: Round [120] log likelihood: -2305.299744
EM: Round [121] log likelihood: -2305.297577
EM: Round [122] log likelihood: -2305.295436
EM: Round [123] log likelihood: -2305.293318
EM: Round [124] log likelihood: -2305.291225
EM: Round [125] log likelihood: -2305.289155
EM: Round [126] log likelihood: -2305.287109
EM: Round [127] log likelihood: -2305.285086
EM: Round [128] log likelihood: -2305.283085
EM: Round [129] log likelihood: -2305.281108
EM: Round [130] log likelihood: -2305.279152
EM: Round [131] log likelihood: -2305.277219
EM: Round [132] log likelihood: -2305.275307
EM: Round [133] log likelihood: -2305.273417
EM: Round [134] log likelihood: -2305.271548
EM: Round [135] log likelihood: -2305.269701
EM: Round [136] log likelihood: -2305.267874
EM: Round [137] log likelihood: -2305.266067
EM: Round [138] log likelihood: -2305.264281
EM: Round [139] log likelihood: -2305.262514
EM: Round [140] log likelihood: -2305.260768
EM: Round [141] log likelihood: -2305.259040
EM: Round [142] log likelihood: -2305.257333
EM: Round [143] log likelihood: -2305.255644
EM: Round [144] log likelihood: -2305.253974
EM: Round [145] log likelihood: -2305.252322
EM: Round [146] log likelihood: -2305.250689
EM: Round [147] log likelihood: -2305.249074
EM: Round [148] log likelihood: -2305.247477
EM: Round [149] log likelihood: -2305.245898
EM: Round [150] log likelihood: -2305.244336
EM: Round [151] log likelihood: -2305.242792
EM: Round [152] log likelihood: -2305.241264
EM: Round [153] log likelihood: -2305.239754
EM: Round [154] log likelihood: -2305.238260
EM: Round [155] log likelihood: -2305.236783
EM: Round [156] log likelihood: -2305.235322
EM: Round [157] log likelihood: -2305.233877
EM: Round [158] log likelihood: -2305.232448
EM: Round [159] log likelihood: -2305.231035
EM: Round [160] log likelihood: -2305.229637
EM: Round [161] log likelihood: -2305.228255
EM: Round [162] log likelihood: -2305.226888
EM: Round [163] log likelihood: -2305.225536
EM: Round [164] log likelihood: -2305.224199
EM: Round [165] log likelihood: -2305.222876
EM: Round [166] log likelihood: -2305.221568
EM: Round [167] log likelihood: -2305.220274
EM: Round [168] log likelihood: -2305.218995
EM: Round [169] log likelihood: -2305.217729
EM: Round [170] log likelihood: -2305.216477
EM: Round [171] log likelihood: -2305.215239
EM: Round [172] log likelihood: -2305.214015
EM: Round [173] log likelihood: -2305.212803
EM: Round [174] log likelihood: -2305.211605
EM: Round [175] log likelihood: -2305.210420
EM: Round [176] log likelihood: -2305.209248
EM: Round [177] log likelihood: -2305.208089
EM: Round [178] log likelihood: -2305.206942
EM: Round [179] log likelihood: -2305.205808
EM: Round [180] log likelihood: -2305.204686
EM: Round [181] log likelihood: -2305.203577
EM: Round [182] log likelihood: -2305.202479
EM: Round [183] log likelihood: -2305.201393
EM: Round [184] log likelihood: -2305.200319
EM: Round [185] log likelihood: -2305.199257
EM: Round [186] log likelihood: -2305.198206
EM: Round [187] log likelihood: -2305.197167
EM: Round [188] log likelihood: -2305.196139
EM: Round [189] log likelihood: -2305.195122
EM: Round [190] log likelihood: -2305.194116
EM: Round [191] log likelihood: -2305.193120
EM: Round [192] log likelihood: -2305.192136
EM: Round [193] log likelihood: -2305.191162
EM: Round [194] log likelihood: -2305.190199
EM: Round [195] log likelihood: -2305.189246
EM: Round [196] log likelihood: -2305.188303
EM: Round [197] log likelihood: -2305.187371
EM: Round [198] log likelihood: -2305.186448
EM: Round [199] log likelihood: -2305.185536
EM: Round [200] log likelihood: -2305.184633
EM: Round [201] log likelihood: -2305.183740
EM: Round [202] log likelihood: -2305.182857
EM: Round [203] log likelihood: -2305.181983
EM: Round [204] log likelihood: -2305.181118
EM: Round [205] log likelihood: -2305.180263
EM: Round [206] log likelihood: -2305.179417
EM: Round [207] log likelihood: -2305.178580
EM: Round [208] log likelihood: -2305.177752
EM: Round [209] log likelihood: -2305.176933
EM: Round [210] log likelihood: -2305.176122
EM: Round [211] log likelihood: -2305.175320
EM: Round [212] log likelihood: -2305.174527
EM: Round [213] log likelihood: -2305.173743
EM: Round [214] log likelihood: -2305.172966
EM: Round [215] log likelihood: -2305.172199
EM: Round [216] log likelihood: -2305.171439
EM: Round [217] log likelihood: -2305.170687
EM: Round [218] log likelihood: -2305.169944
EM: Round [219] log likelihood: -2305.169208
EM: Round [220] log likelihood: -2305.168480
EM: Round [221] log likelihood: -2305.167760
EM: Round [222] log likelihood: -2305.167048
EM: Round [223] log likelihood: -2305.166343
EM: Round [224] log likelihood: -2305.165646
EM: Round [225] log likelihood: -2305.164956
EM: Round [226] log likelihood: -2305.164273
EM: Round [227] log likelihood: -2305.163598
EM: Round [228] log likelihood: -2305.162930
EM: Round [229] log likelihood: -2305.162269
EM: Round [230] log likelihood: -2305.161615
EM: Round [231] log likelihood: -2305.160968
EM: Round [232] log likelihood: -2305.160328
EM: Round [233] log likelihood: -2305.159695
EM: Round [234] log likelihood: -2305.159068
EM: Round [235] log likelihood: -2305.158448
EM: Round [236] log likelihood: -2305.157835
EM: Round [237] log likelihood: -2305.157228
EM: Round [238] log likelihood: -2305.156628
EM: Round [239] log likelihood: -2305.156034
EM: Round [240] log likelihood: -2305.155446
EM: Round [241] log likelihood: -2305.154865
EM: Round [242] log likelihood: -2305.154289
EM: Round [243] log likelihood: -2305.153720
EM: Round [244] log likelihood: -2305.153157
EM: Round [245] log likelihood: -2305.152600
EM: Round [246] log likelihood: -2305.152049
EM: Round [247] log likelihood: -2305.151503
EM: Round [248] log likelihood: -2305.150963
EM: Round [249] log likelihood: -2305.150429
EM: Round [250] log likelihood: -2305.149901
EM: Round [251] log likelihood: -2305.149378
EM: Round [252] log likelihood: -2305.148861
EM: Round [253] log likelihood: -2305.148349
EM: Round [254] log likelihood: -2305.147843
EM: Round [255] log likelihood: -2305.147342
EM: Round [256] log likelihood: -2305.146846
EM: Round [257] log likelihood: -2305.146355
EM: Round [258] log likelihood: -2305.145870
EM: Round [259] log likelihood: -2305.145390
EM: Round [260] log likelihood: -2305.144914
EM: Round [261] log likelihood: -2305.144444
EM: Round [262] log likelihood: -2305.143979
EM: Round [263] log likelihood: -2305.143519
EM: Round [264] log likelihood: -2305.143063
EM: Round [265] log likelihood: -2305.142613
EM: Round [266] log likelihood: -2305.142167
EM: Round [267] log likelihood: -2305.141726
EM: Round [268] log likelihood: -2305.141289
EM: Round [269] log likelihood: -2305.140857
EM: Round [270] log likelihood: -2305.140430
EM: Round [271] log likelihood: -2305.140007
EM: Round [272] log likelihood: -2305.139588
EM: Round [273] log likelihood: -2305.139174
EM: Round [274] log likelihood: -2305.138764
EM: Round [275] log likelihood: -2305.138359
EM: Round [276] log likelihood: -2305.137958
EM: Round [277] log likelihood: -2305.137561
EM: Round [278] log likelihood: -2305.137168
EM: Round [279] log likelihood: -2305.136779
EM: Round [280] log likelihood: -2305.136395
EM: Round [281] log likelihood: -2305.136014
EM: Round [282] log likelihood: -2305.135638
EM: Round [283] log likelihood: -2305.135265
EM: Round [284] log likelihood: -2305.134896
EM: Round [285] log likelihood: -2305.134532
EM: Round [286] log likelihood: -2305.134171
EM: Round [287] log likelihood: -2305.133813
EM: Round [288] log likelihood: -2305.133460
EM: Round [289] log likelihood: -2305.133110
EM: Round [290] log likelihood: -2305.132764
EM: Round [291] log likelihood: -2305.132422
EM: Round [292] log likelihood: -2305.132083
EM: Round [293] log likelihood: -2305.131747
EM: Round [294] log likelihood: -2305.131416
EM: Round [295] log likelihood: -2305.131087
EM: Round [296] log likelihood: -2305.130762
EM: Round [297] log likelihood: -2305.130441
EM: Round [298] log likelihood: -2305.130123
EM: Round [299] log likelihood: -2305.129808
EM: Round [300] log likelihood: -2305.129497
EM: Round [301] log likelihood: -2305.129188
EM: Round [302] log likelihood: -2305.128883
EM: Round [303] log likelihood: -2305.128581
EM: Round [304] log likelihood: -2305.128283
EM: Round [305] log likelihood: -2305.127987
EM: Round [306] log likelihood: -2305.127695
EM: Round [307] log likelihood: -2305.127405
EM: Round [308] log likelihood: -2305.127119
EM: Round [309] log likelihood: -2305.126836
EM: Round [310] log likelihood: -2305.126555
EM: Round [311] log likelihood: -2305.126278
EM: Round [312] log likelihood: -2305.126003
EM: Round [313] log likelihood: -2305.125731
EM: Round [314] log likelihood: -2305.125462
EM: Round [315] log likelihood: -2305.125196
EM: Round [316] log likelihood: -2305.124933
EM: Round [317] log likelihood: -2305.124672
EM: Round [318] log likelihood: -2305.124415
EM: Round [319] log likelihood: -2305.124159
EM: Round [320] log likelihood: -2305.123907
EM: Round [321] log likelihood: -2305.123657
EM: Round [322] log likelihood: -2305.123410
EM: Round [323] log likelihood: -2305.123165
EM: Round [324] log likelihood: -2305.122923
EM: Round [325] log likelihood: -2305.122684
EM: Round [326] log likelihood: -2305.122446
EM: Round [327] log likelihood: -2305.122212
EM: Round [328] log likelihood: -2305.121980
EM: Round [329] log likelihood: -2305.121750
EM: Round [330] log likelihood: -2305.121523
EM: Round [331] log likelihood: -2305.121298
EM: Round [332] log likelihood: -2305.121075
EM: Round [333] log likelihood: -2305.120855
EM: Round [334] log likelihood: -2305.120637
EM: Round [335] log likelihood: -2305.120421
EM: Round [336] log likelihood: -2305.120207
EM: Round [337] log likelihood: -2305.119996
EM: Round [338] log likelihood: -2305.119787
EM: Round [339] log likelihood: -2305.119580
EM: Round [340] log likelihood: -2305.119375
EM: Round [341] log likelihood: -2305.119173
EM: Round [342] log likelihood: -2305.118972
EM: Round [343] log likelihood: -2305.118774
EM: Round [344] log likelihood: -2305.118577
EM: Round [345] log likelihood: -2305.118383
EM: Round [346] log likelihood: -2305.118191
EM: Round [347] log likelihood: -2305.118000
EM: Round [348] log likelihood: -2305.117812
EM: Round [349] log likelihood: -2305.117626
EM: Round [350] log likelihood: -2305.117441
EM: Round [351] log likelihood: -2305.117259
EM: Round [352] log likelihood: -2305.117078
EM: Round [353] log likelihood: -2305.116899
EM: Round [354] log likelihood: -2305.116723
EM: Round [355] log likelihood: -2305.116548
EM: Round [356] log likelihood: -2305.116374
EM: Round [357] log likelihood: -2305.116203
EM: Round [358] log likelihood: -2305.116033
EM: Round [359] log likelihood: -2305.115865
EM: Round [360] log likelihood: -2305.115699
EM: Round [361] log likelihood: -2305.115535
EM: Round [362] log likelihood: -2305.115372
EM: Round [363] log likelihood: -2305.115211
EM: Round [364] log likelihood: -2305.115052
EM: Round [365] log likelihood: -2305.114894
EM: Round [366] log likelihood: -2305.114738
EM: Round [367] log likelihood: -2305.114584
EM: Round [368] log likelihood: -2305.114431
EM: Round [369] log likelihood: -2305.114280
EM: Round [370] log likelihood: -2305.114130
EM: Round [371] log likelihood: -2305.113982
EM: Round [372] log likelihood: -2305.113836
EM: Round [373] log likelihood: -2305.113690
EM: Round [374] log likelihood: -2305.113547
EM: Round [375] log likelihood: -2305.113405
EM: Round [376] log likelihood: -2305.113264
EM: Round [377] log likelihood: -2305.113125
EM: Round [378] log likelihood: -2305.112988
EM: Round [379] log likelihood: -2305.112851
EM: Round [380] log likelihood: -2305.112716
EM: Round [381] log likelihood: -2305.112583
EM: Round [382] log likelihood: -2305.112451
EM: Round [383] log likelihood: -2305.112320
EM: Round [384] log likelihood: -2305.112191
EM: Round [385] log likelihood: -2305.112063
EM: Round [386] log likelihood: -2305.111936
EM: Round [387] log likelihood: -2305.111811
EM: Round [388] log likelihood: -2305.111687
EM: Round [389] log likelihood: -2305.111564
EM: Round [390] log likelihood: -2305.111443
EM: Round [391] log likelihood: -2305.111323
EM: Round [392] log likelihood: -2305.111204
EM: Round [393] log likelihood: -2305.111086
EM: Round [394] log likelihood: -2305.110969
EM: Round [395] log likelihood: -2305.110854
EM: Round [396] log likelihood: -2305.110740
EM: Round [397] log likelihood: -2305.110627
EM: Round [398] log likelihood: -2305.110515
EM: Round [399] log likelihood: -2305.110405
EM: Round [400] log likelihood: -2305.110295
EM: Round [401] log likelihood: -2305.110187
EM: Round [402] log likelihood: -2305.110080
EM: Round [403] log likelihood: -2305.109974
EM: Round [404] log likelihood: -2305.109869
EM: Round [405] log likelihood: -2305.109765
EM: Round [406] log likelihood: -2305.109662
EM: Round [407] log likelihood: -2305.109560
EM: Round [408] log likelihood: -2305.109460
EM: Round [409] log likelihood: -2305.109360
EM: Stopping iterations at round 409 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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir
-done, see /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1682.840867
EM: Round [1] log likelihood: -1682.840867
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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 248185552
Execution Time = 4.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.U5nUa6x7eF/fi_workdir/microH.dat
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.U5nUa6x7eF/fi_workdir/microH.dat /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_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.U5nUa6x7eF/fi_workdir/microH.dat /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.U5nUa6x7eF --json_outfile /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_Lx-T1-TRNA-1_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.U5nUa6x7eF --json_outfile /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_Lx-T1-TRNA-1_B23WHTKLT4_1
Running: touch /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_Lx-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_Lx-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.U5nUa6x7eF/ctat_genome_lib_build_dir > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.U5nUa6x7eF/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory