Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/18adf10145133a025b2aacf835b23d/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/39ee7c5365d153ef7d612afc9e5fc7/.command.sh
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/4b/18adf10145133a025b2aacf835b23d/tih_rna_sample_00680_B23MVV7LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/39ee7c5365d153ef7d612afc9e5fc7/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/a1ef0c27e4f39cf4cdd4a6496c8982/tih_rna_sample_00680_B23MVV7LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00680_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00680_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/cytoBand.txt
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00680_B23MVV7LT4_1.star --out_dir /tmp/nxf.jJbViTbJ8s/fi_workdir --reads "/tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:52:52 ..... started STAR run
Jun 08 10:52:52 ..... loading genome
Jun 08 10:54:35 ... generating Suffix Array index
Jun 08 10:58:29 ... completed Suffix Array index
Jun 08 10:58:30 ..... processing annotations GTF
Jun 08 10:58:30 ..... inserting junctions into the genome indices
Jun 08 10:59:31 ..... started mapping
Jun 08 11:58:38 ..... finished mapping
Jun 08 11:58:40 ..... started sorting BAM
Jun 08 11:58:41 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 65.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00680_B23MVV7LT4_1.star --out_dir /tmp/nxf.jJbViTbJ8s/fi_workdir --reads "/tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:59:01 : INFO : Done.
Execution Time = 0.27 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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]
[1050000]
[1060000]
[1070000]
[1080000]
[1090000]
[1100000]
[1110000]
[1120000]
[1130000]
[1140000]
[1150000]
[1160000]
[1170000]
[1180000]
[1190000]
[1200000]
[1210000]
[1220000]
[1230000]
[1240000]
[1250000]
[1260000]
[1270000]
[1280000]
[1290000]
[1300000]
[1310000]
[1320000]
[1330000]
[1340000]
[1350000]
[1360000]
[1370000]
[1380000]
[1390000]
[1400000]
[1410000]
[1420000]
[1430000]
[1440000]
[1450000]
[1460000]
[1470000]
[1480000]
[1490000]
[1500000]
[1510000]
[1520000]
[1530000]
[1540000]
[1550000]
[1560000]
[1570000]
[1580000]
[1590000]
[1600000]
[1610000]
[1620000]
[1630000]
[1640000]
[1650000]
[1660000]
[1670000]
[1680000]
[1690000]
[1700000]
[1710000]
[1720000]
[1730000]
[1740000]
[1750000]
[1760000]
[1770000]
[1780000]
[1790000]
[1800000]
[1810000]
[1820000]
[1830000]
[1840000]
[1850000]
[1860000]
[1870000]
[1880000]
[1890000]
[1900000]
[1910000]
[1920000]
[1930000]
[1940000]
[1950000]
[1960000]
[1970000]
[1980000]
[1990000]
[2000000]
[2010000]
[2020000]
[2030000]
[2040000]
[2050000]
[2060000]
[2070000]
[2080000]
[2090000]
[2100000]
[2110000]
[2120000]
[2130000]
[2140000]
[2150000]
[2160000]
[2170000]
[2180000]
[2190000]
[2200000]
[2210000]
[2220000]
[2230000]
[2240000]
[2250000]
[2260000]
[2270000]
[2280000]
[2290000]
[2300000]
[2310000]
[2320000]
[2330000]
[2340000]
[2350000]
[2360000]
[2370000]
[2380000]
[2390000]
[2400000]
[2410000]
[2420000]
[2430000]
[2440000]
[2450000]
[2460000]
[2470000]
[2480000]
[2490000]
[2500000]
[2510000]
[2520000]
[2530000]
[2540000]
[2550000]
[2560000]
[2570000]
[2580000]
[2590000]
[2600000]
[2610000]
[2620000]
[2630000]
[2640000]
[2650000]
[2660000]
[2670000]
[2680000]
[2690000]
[2700000]
[2710000]
[2720000]
[2730000]
[2740000]
[2750000]
[2760000]
[2770000]
[2780000]
[2790000]
[2800000]
[2810000]
[2820000]
[2830000]
[2840000]
[2850000]
[2860000]
[2870000]
[2880000]
[2890000]
[2900000]
[2910000]
[2920000]
[2930000]
[2940000]
[2950000]
[2960000]
[2970000]
[2980000]
[2990000]
[3000000]
[3010000]
[3020000]
[3030000]
[3040000]
[3050000]
[3060000]
[3070000]
[3080000]
[3090000]
[3100000]
[3110000]
[3120000]
[3130000]
[3140000]
[3150000]
[3160000]
[3170000]
[3180000]
[3190000]
[3200000] -done parsing /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 24,
'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 160,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 395,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 84,
'num_hits: 9 != num_counted_on_fusion_contigs 1 ' => 11,
'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 18,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1285,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 4,
'num genes matched < 2' => 25,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 67,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 176,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 210,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 6,
'num_hits: 8 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 592,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 315,
' ** passed ** ' => 17371,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 216,
'excessive soft clipping' => 20757,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 13,
'per_id < 96' => 18849,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 66,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 264,
'num_hits: 10 != num_counted_on_fusion_contigs 1 ' => 6,
'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 20,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 4,
'small anchor length' => 507,
'num_hits: 10 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 20,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 33,
'num_hits: 10 != num_counted_on_fusion_contigs 4 ' => 20,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 9 != num_counted_on_fusion_contigs 4 ' => 4,
'seq-similar region overlap' => 218
};
-writing fusion junction support info.
Execution Time = 1.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
[2000]
[3000]
[4000]
[5000]
[6000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
[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]
[587000]
[588000]
[589000]
[590000]
[591000]
[592000]
[593000]
[594000]
[595000]
[596000]
[597000]
[598000]
[599000]
[600000]
[601000]
[602000]
[603000]
[604000]
[605000]
[606000]
[607000]
[608000]
[609000]
[610000]
[611000]
[612000]
[613000]
[614000]
[615000]
[616000]
[617000]
[618000]
[619000]
[620000]
[621000]
[622000]
[623000]
[624000]
[625000]
[626000]
[627000]
[628000]
[629000]
[630000]
[631000]
[632000]
[633000]
[634000]
[635000]
[636000]
[637000]
[638000]
[639000]
[640000]
[641000]
[642000]
[643000]
[644000]
[645000]
[646000]
[647000]
[648000]
[649000]
[650000]
[651000]
[652000]
[653000]
[654000]
[655000]
[656000]
[657000]
[658000]
[659000]
[660000]
[661000]
[662000]
[663000]
[664000]
[665000]
[666000]
[667000]
[668000]
[669000]
[670000]
[671000]
[672000]
[673000]
[674000]
[675000]
[676000]
[677000]
[678000]
[679000]
[680000]
[681000]
[682000]
[683000]
[684000]
[685000]
[686000]
[687000]
[688000]
[689000]
[690000]
[691000]
[692000]
[693000]
[694000]
[695000]
[696000]
[697000]
[698000]
[699000]
[700000]
[701000]
[702000]
[703000]
[704000]
[705000]
[706000]
[707000]
[708000]
[709000]
[710000]
[711000]
[712000]
[713000]
[714000]
[715000]
[716000]
[717000]
[718000]
[719000]
[720000]
[721000]
[722000]
[723000]
[724000]
[725000]
[726000]
[727000]
[728000]
[729000]
[730000]
[731000]
[732000]
[733000]
[734000]
[735000]
[736000]
[737000]
[738000]
[739000]
[740000]
[741000]
[742000]
[743000]
[744000]
[745000]
[746000]
[747000]
[748000]
[749000]
[750000]
[751000]
[752000]
[753000]
[754000]
[755000]
[756000]
[757000]
[758000]
[759000]
[760000]
[761000]
[762000]
[763000]
[764000]
[765000]
[766000]
[767000]
[768000]
[769000]
[770000]
[771000]
[772000]
[773000]
[774000]
[775000]
[776000]
[777000]
[778000]
[779000]
[780000]
[781000]
[782000]
[783000]
[784000]
[785000]
[786000]
[787000]
[788000]
[789000]
[790000]
[791000]
[792000]
[793000]
[794000]
[795000]
[796000]
[797000]
[798000]
[799000]
[800000]
[801000]
[802000]
[803000]
[804000]
[805000]
[806000]
[807000]
[808000]
[809000]
[810000]
[811000]
[812000]
[813000]
[814000]
[815000]
[816000]
[817000]
[818000]
[819000]
[820000]
[821000]
[822000]
[823000]
[824000]
[825000]
[826000]
[827000]
[828000]
[829000]
[830000]
[831000]
[832000]
[833000]
[834000]
[835000]
[836000]
[837000] -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]
[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] -fusion SPANNING read extraction for scaff: ADAM9--SNTG1
[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] -fusion SPANNING read extraction for scaff: ADCY9--AC010601.1
[1000]
[2000]
[3000] -fusion SPANNING read extraction for scaff: C16orf96--SEPTIN12
[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] -fusion SPANNING read extraction for scaff: F13A1--NRN1
[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] -fusion SPANNING read extraction for scaff: GNB1--CFAP74
[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] -fusion SPANNING read extraction for scaff: GPATCH8--AL133464.1
[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] -fusion SPANNING read extraction for scaff: GPATCH8--LINC00261
[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] -fusion SPANNING read extraction for scaff: KATNIP--EPG5
[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] -fusion SPANNING read extraction for scaff: KIF3B--EFCAB8
[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] -fusion SPANNING read extraction for scaff: NPIPB12--AC009093.1
[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] -fusion SPANNING read extraction for scaff: PATJ--AC117464.1
[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] -fusion SPANNING read extraction for scaff: PATJ--LINC00971
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
[1000]
[2000]
[3000]
[4000]
[5000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
[1000]
[2000]
[3000]
[4000]
[5000]
[6000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
[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] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
[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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
[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: PIK3C3--RIT2
[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] -fusion SPANNING read extraction for scaff: PRSS27--TPSB2
[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] -fusion SPANNING read extraction for scaff: RIOK3--AC016074.2
[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: SMURF2P1--LRRC37B
[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] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[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: STX4--C16orf96
[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: TLK2--AC240565.1
[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] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
[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]
[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] -fusion SPANNING read extraction for scaff: TMEM123--MMP20
[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] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[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] -fusion SPANNING read extraction for scaff: USP22--C21orf62
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 22010,
'seq similar region alignment' => 62798
};
Execution Time = 4.56 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -7717.778134
EM: Round [1] log likelihood: -7717.189182
EM: Round [2] log likelihood: -7716.888387
EM: Round [3] log likelihood: -7716.624805
EM: Round [4] log likelihood: -7716.392920
EM: Round [5] log likelihood: -7716.188303
EM: Round [6] log likelihood: -7716.007244
EM: Round [7] log likelihood: -7715.846616
EM: Round [8] log likelihood: -7715.703769
EM: Round [9] log likelihood: -7715.576444
EM: Round [10] log likelihood: -7715.462705
EM: Round [11] log likelihood: -7715.360889
EM: Round [12] log likelihood: -7715.269561
EM: Round [13] log likelihood: -7715.187479
EM: Round [14] log likelihood: -7715.113565
EM: Round [15] log likelihood: -7715.046882
EM: Round [16] log likelihood: -7714.986609
EM: Round [17] log likelihood: -7714.932033
EM: Round [18] log likelihood: -7714.882526
EM: Round [19] log likelihood: -7714.837538
EM: Round [20] log likelihood: -7714.796585
EM: Round [21] log likelihood: -7714.759242
EM: Round [22] log likelihood: -7714.725132
EM: Round [23] log likelihood: -7714.693925
EM: Round [24] log likelihood: -7714.665325
EM: Round [25] log likelihood: -7714.639074
EM: Round [26] log likelihood: -7714.614941
EM: Round [27] log likelihood: -7714.592719
EM: Round [28] log likelihood: -7714.572228
EM: Round [29] log likelihood: -7714.553305
EM: Round [30] log likelihood: -7714.535803
EM: Round [31] log likelihood: -7714.519595
EM: Round [32] log likelihood: -7714.504564
EM: Round [33] log likelihood: -7714.490607
EM: Round [34] log likelihood: -7714.477630
EM: Round [35] log likelihood: -7714.465550
EM: Round [36] log likelihood: -7714.454292
EM: Round [37] log likelihood: -7714.443788
EM: Round [38] log likelihood: -7714.433976
EM: Round [39] log likelihood: -7714.424802
EM: Round [40] log likelihood: -7714.416216
EM: Round [41] log likelihood: -7714.408172
EM: Round [42] log likelihood: -7714.400629
EM: Round [43] log likelihood: -7714.393551
EM: Round [44] log likelihood: -7714.386903
EM: Round [45] log likelihood: -7714.380653
EM: Round [46] log likelihood: -7714.374775
EM: Round [47] log likelihood: -7714.369241
EM: Round [48] log likelihood: -7714.364028
EM: Round [49] log likelihood: -7714.359116
EM: Round [50] log likelihood: -7714.354482
EM: Round [51] log likelihood: -7714.350110
EM: Round [52] log likelihood: -7714.345983
EM: Round [53] log likelihood: -7714.342084
EM: Round [54] log likelihood: -7714.338399
EM: Round [55] log likelihood: -7714.334916
EM: Round [56] log likelihood: -7714.331621
EM: Round [57] log likelihood: -7714.328504
EM: Round [58] log likelihood: -7714.325553
EM: Round [59] log likelihood: -7714.322759
EM: Round [60] log likelihood: -7714.320113
EM: Round [61] log likelihood: -7714.317606
EM: Round [62] log likelihood: -7714.315230
EM: Round [63] log likelihood: -7714.312978
EM: Round [64] log likelihood: -7714.310842
EM: Round [65] log likelihood: -7714.308817
EM: Round [66] log likelihood: -7714.306896
EM: Round [67] log likelihood: -7714.305073
EM: Round [68] log likelihood: -7714.303343
EM: Round [69] log likelihood: -7714.301701
EM: Round [70] log likelihood: -7714.300142
EM: Round [71] log likelihood: -7714.298662
EM: Round [72] log likelihood: -7714.297257
EM: Round [73] log likelihood: -7714.295923
EM: Round [74] log likelihood: -7714.294655
EM: Round [75] log likelihood: -7714.293451
EM: Round [76] log likelihood: -7714.292307
EM: Round [77] log likelihood: -7714.291219
EM: Round [78] log likelihood: -7714.290187
EM: Round [79] log likelihood: -7714.289205
EM: Round [80] log likelihood: -7714.288272
EM: Round [81] log likelihood: -7714.287385
EM: Round [82] log likelihood: -7714.286542
EM: Round [83] log likelihood: -7714.285741
EM: Round [84] log likelihood: -7714.284979
EM: Round [85] log likelihood: -7714.284255
EM: Round [86] log likelihood: -7714.283566
EM: Round [87] log likelihood: -7714.282911
EM: Round [88] log likelihood: -7714.282288
EM: Round [89] log likelihood: -7714.281696
EM: Round [90] log likelihood: -7714.281133
EM: Round [91] log likelihood: -7714.280598
EM: Round [92] log likelihood: -7714.280088
EM: Round [93] log likelihood: -7714.279604
EM: Round [94] log likelihood: -7714.279143
EM: Round [95] log likelihood: -7714.278705
EM: Round [96] log likelihood: -7714.278288
EM: Round [97] log likelihood: -7714.277891
EM: Round [98] log likelihood: -7714.277514
EM: Round [99] log likelihood: -7714.277156
EM: Round [100] log likelihood: -7714.276814
EM: Round [101] log likelihood: -7714.276489
EM: Round [102] log likelihood: -7714.276181
EM: Round [103] log likelihood: -7714.275887
EM: Round [104] log likelihood: -7714.275607
EM: Round [105] log likelihood: -7714.275341
EM: Round [106] log likelihood: -7714.275088
EM: Round [107] log likelihood: -7714.274847
EM: Round [108] log likelihood: -7714.274618
EM: Round [109] log likelihood: -7714.274400
EM: Round [110] log likelihood: -7714.274193
EM: Round [111] log likelihood: -7714.273996
EM: Round [112] log likelihood: -7714.273808
EM: Round [113] log likelihood: -7714.273630
EM: Round [114] log likelihood: -7714.273460
EM: Round [115] log likelihood: -7714.273298
EM: Round [116] log likelihood: -7714.273144
EM: Round [117] log likelihood: -7714.272998
EM: Round [118] log likelihood: -7714.272859
EM: Round [119] log likelihood: -7714.272726
EM: Round [120] log likelihood: -7714.272600
EM: Round [121] log likelihood: -7714.272480
EM: Round [122] log likelihood: -7714.272366
EM: Round [123] log likelihood: -7714.272257
EM: Round [124] log likelihood: -7714.272154
EM: Round [125] log likelihood: -7714.272055
EM: Stopping iterations at round 125 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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir
-done, see /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -6772.601260
EM: Round [1] log likelihood: -6772.403710
EM: Round [2] log likelihood: -6772.403416
EM: Round [3] log likelihood: -6772.403414
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz: 296091919
Execution Time = 5.65 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa --gtf /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa --gtf /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/fi_workdir/microH.dat
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.jJbViTbJ8s/fi_workdir/microH.dat /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/microH.dat /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.jJbViTbJ8s --json_outfile /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00680_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.jJbViTbJ8s --json_outfile /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00680_B23MVV7LT4_1
Running: touch /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00680_B23MVV7LT4_1 --html_output /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00680_B23MVV7LT4_1 --html_output /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000286122.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000259929.5]
WARNING, no entry stored in dbm for [ENSG00000259929.5]
WARNING, no entry stored in dbm for [ENSG00000259807.2]
WARNING, no entry stored in dbm for [ENSG00000259807.2]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory