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/08/dcd61588d9dc3f6e8014e465bddbde/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/058b8b75143ffb98451c0921910eb5/659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/a7eda1020fd7404e23d2f434be6454/659_bua-T1-TRNA-1_B23WHTKLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/a7eda1020fd7404e23d2f434be6454/659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/dcd61588d9dc3f6e8014e465bddbde/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/a7eda1020fd7404e23d2f434be6454/659_bua-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
00:08:12 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
[230000], rate=13800000.00/min
[240000], rate=14400000.00/min
[250000], rate=15000000.00/min
[260000], rate=15600000.00/min
[270000], rate=16200000.00/min
[280000], rate=16800000.00/min
[290000], rate=17400000.00/min
[300000], rate=18000000.00/min
[310000], rate=18600000.00/min
[320000], rate=19200000.00/min
[330000], rate=19800000.00/min
[340000], rate=20400000.00/min
[350000], rate=21000000.00/min
[360000], rate=21600000.00/min
[370000], rate=22200000.00/min
[380000], rate=22800000.00/min
[390000], rate=23400000.00/min
[400000], rate=24000000.00/min
[410000], rate=24600000.00/min
[420000], rate=25200000.00/min
[430000], rate=25800000.00/min
[440000], rate=26400000.00/min
[450000], rate=27000000.00/min
[460000], rate=27600000.00/min
[470000], rate=28200000.00/min
[480000], rate=28800000.00/min
[490000], rate=29400000.00/min
[500000], rate=30000000.00/min
[510000], rate=30600000.00/min
[520000], rate=31200000.00/min
[530000], rate=31800000.00/min
[540000], rate=32400000.00/min
[550000], rate=33000000.00/min
[560000], rate=16800000.00/min
[570000], rate=17100000.00/min
[580000], rate=17400000.00/min
[590000], rate=17700000.00/min
[600000], rate=18000000.00/min
[610000], rate=18300000.00/min
[620000], rate=18600000.00/min
[630000], rate=18900000.00/min
[640000], rate=19200000.00/min
[650000], rate=19500000.00/min
[660000], rate=19800000.00/min
[670000], rate=20100000.00/min
[680000], rate=20400000.00/min
[690000], rate=20700000.00/min
[700000], rate=21000000.00/min
[710000], rate=21300000.00/min
[720000], rate=21600000.00/min
[730000], rate=21900000.00/min
[740000], rate=22200000.00/min
[750000], rate=22500000.00/min
[760000], rate=22800000.00/min
[770000], rate=23100000.00/min
[780000], rate=23400000.00/min
[790000], rate=23700000.00/min
[800000], rate=24000000.00/min
[810000], rate=24300000.00/min
[820000], rate=24600000.00/min
[830000], rate=24900000.00/min
[840000], rate=25200000.00/min
[850000], rate=25500000.00/min
[860000], rate=25800000.00/min
[870000], rate=26100000.00/min
[880000], rate=26400000.00/min
[890000], rate=26700000.00/min
[900000], rate=18000000.00/min
[910000], rate=18200000.00/min
[920000], rate=18400000.00/min
[930000], rate=18600000.00/min
[940000], rate=18800000.00/min
[950000], rate=19000000.00/min
[960000], rate=19200000.00/min
[970000], rate=19400000.00/min
[980000], rate=19600000.00/min
[990000], rate=19800000.00/min
[1000000], rate=20000000.00/min
[1010000], rate=20200000.00/min
[1020000], rate=20400000.00/min
[1030000], rate=20600000.00/min
[1040000], rate=20800000.00/min
[1050000], rate=21000000.00/min
[1060000], rate=21200000.00/min
[1070000], rate=21400000.00/min
[1080000], rate=21600000.00/min
[1090000], rate=21800000.00/min
[1100000], rate=22000000.00/min
[1110000], rate=22200000.00/min
[1120000], rate=22400000.00/min
[1130000], rate=22600000.00/min
[1140000], rate=22800000.00/min
[1150000], rate=23000000.00/min
[1160000], rate=23200000.00/min
[1170000], rate=23400000.00/min
[1180000], rate=23600000.00/min
[1190000], rate=23800000.00/min
[1200000], rate=24000000.00/min
[1210000], rate=24200000.00/min
[1220000], rate=18300000.00/min
[1230000], rate=18450000.00/min
[1240000], rate=18600000.00/min
[1250000], rate=18750000.00/min
[1260000], rate=18900000.00/min
[1270000], rate=19050000.00/min
[1280000], rate=19200000.00/min
[1290000], rate=19350000.00/min
[1300000], rate=19500000.00/min
[1310000], rate=19650000.00/min
[1320000], rate=19800000.00/min
[1330000], rate=19950000.00/min
[1340000], rate=20100000.00/min
[1350000], rate=20250000.00/min
[1360000], rate=20400000.00/min
[1370000], rate=20550000.00/min
[1380000], rate=20700000.00/min
[1390000], rate=20850000.00/min
[1400000], rate=21000000.00/min
[1410000], rate=21150000.00/min
[1420000], rate=21300000.00/min
[1430000], rate=21450000.00/min
[1440000], rate=21600000.00/min
[1450000], rate=21750000.00/min
[1460000], rate=21900000.00/min
[1470000], rate=22050000.00/min
[1480000], rate=22200000.00/min
[1490000], rate=22350000.00/min
[1500000], rate=22500000.00/min
[1510000], rate=22650000.00/min
[1520000], rate=22800000.00/min
[1530000], rate=22950000.00/min
[1540000], rate=23100000.00/min
[1550000], rate=18600000.00/min
[1560000], rate=18720000.00/min
[1570000], rate=18840000.00/min
[1580000], rate=18960000.00/min
[1590000], rate=19080000.00/min
[1600000], rate=19200000.00/min
[1610000], rate=19320000.00/min
[1620000], rate=19440000.00/min
[1630000], rate=19560000.00/min
[1640000], rate=19680000.00/min
[1650000], rate=19800000.00/min
[1660000], rate=19920000.00/min
[1670000], rate=20040000.00/min
[1680000], rate=20160000.00/min
[1690000], rate=20280000.00/min
[1700000], rate=20400000.00/min
[1710000], rate=20520000.00/min
[1720000], rate=20640000.00/min
[1730000], rate=20760000.00/min
[1740000], rate=20880000.00/min
[1750000], rate=21000000.00/min
[1760000], rate=21120000.00/min
[1770000], rate=21240000.00/min
[1780000], rate=21360000.00/min
[1790000], rate=21480000.00/min
[1800000], rate=21600000.00/min
[1810000], rate=21720000.00/min
[1820000], rate=21840000.00/min
[1830000], rate=18300000.00/min
[1840000], rate=18400000.00/min
[1850000], rate=18500000.00/min
[1860000], rate=18600000.00/min
[1870000], rate=18700000.00/min
[1880000], rate=18800000.00/min
[1890000], rate=18900000.00/min
[1900000], rate=19000000.00/min
[1910000], rate=19100000.00/min
[1920000], rate=19200000.00/min
[1930000], rate=19300000.00/min
[1940000], rate=19400000.00/min
[1950000], rate=19500000.00/min
[1960000], rate=19600000.00/min
[1970000], rate=19700000.00/min
[1980000], rate=19800000.00/min
[1990000], rate=19900000.00/min
[2000000], rate=20000000.00/min
[2010000], rate=20100000.00/min
[2020000], rate=20200000.00/min
[2030000], rate=20300000.00/min
[2040000], rate=20400000.00/min
[2050000], rate=20500000.00/min
[2060000], rate=20600000.00/min
[2070000], rate=20700000.00/min
[2080000], rate=20800000.00/min
[2090000], rate=20900000.00/min
[2100000], rate=21000000.00/min
[2110000], rate=21100000.00/min
[2120000], rate=21200000.00/min
[2130000], rate=21300000.00/min
[2140000], rate=21400000.00/min
[2150000], rate=21500000.00/min
[2160000], rate=21600000.00/min
[2170000], rate=21700000.00/min
[2180000], rate=18685714.29/min
[2190000], rate=18771428.57/min
[2200000], rate=18857142.86/min
[2210000], rate=18942857.14/min
[2220000], rate=19028571.43/min
[2230000], rate=19114285.71/min
[2240000], rate=19200000.00/min
[2250000], rate=19285714.29/min
[2260000], rate=19371428.57/min
[2270000], rate=19457142.86/min
[2280000], rate=19542857.14/min
[2290000], rate=19628571.43/min
[2300000], rate=19714285.71/min
[2310000], rate=19800000.00/min
[2320000], rate=19885714.29/min
[2330000], rate=19971428.57/min
[2340000], rate=20057142.86/min
[2350000], rate=20142857.14/min
[2360000], rate=20228571.43/min
[2370000], rate=20314285.71/min
[2380000], rate=20400000.00/min
[2390000], rate=20485714.29/min
[2400000], rate=20571428.57/min
[2410000], rate=20657142.86/min
[2420000], rate=20742857.14/min
[2430000], rate=20828571.43/min
[2440000], rate=20914285.71/min
[2450000], rate=21000000.00/min
[2460000], rate=21085714.29/min
[2470000], rate=21171428.57/min
[2480000], rate=21257142.86/min
[2490000], rate=21342857.14/min
[2500000], rate=21428571.43/min
[2510000], rate=21514285.71/min
[2520000], rate=21600000.00/min
[2530000], rate=21685714.29/min
[2540000], rate=21771428.57/min
[2550000], rate=19125000.00/min
[2560000], rate=19200000.00/min
[2570000], rate=19275000.00/min
[2580000], rate=19350000.00/min
[2590000], rate=19425000.00/min
[2600000], rate=19500000.00/min
[2610000], rate=19575000.00/min
[2620000], rate=19650000.00/min
[2630000], rate=19725000.00/min
[2640000], rate=19800000.00/min
[2650000], rate=19875000.00/min
[2660000], rate=19950000.00/min
[2670000], rate=20025000.00/min
[2680000], rate=20100000.00/min
[2690000], rate=20175000.00/min
[2700000], rate=20250000.00/min
[2710000], rate=20325000.00/min
[2720000], rate=20400000.00/min
[2730000], rate=20475000.00/min
[2740000], rate=20550000.00/min
[2750000], rate=20625000.00/min
[2760000], rate=20700000.00/min
[2770000], rate=20775000.00/min
[2780000], rate=20850000.00/min
[2790000], rate=20925000.00/min
[2800000], rate=21000000.00/min
[2810000], rate=21075000.00/min
[2820000], rate=21150000.00/min
[2830000], rate=21225000.00/min
[2840000], rate=21300000.00/min
[2850000], rate=21375000.00/min
[2860000], rate=21450000.00/min
[2870000], rate=21525000.00/min
[2880000], rate=21600000.00/min
[2890000], rate=21675000.00/min
[2900000], rate=21750000.00/min 00:08:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim
Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18.
-659_bua-T1-TRNA-1_B23WHTKLT4_1.introns: identified 3425 cancer introns
00:08:25 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim
00:08:25 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/prelim_introns.ok
00:08:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
00:08:26 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
00:08:26 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/introns_filtered.ok
00:08:26 : INFO : -found 1298 cancer introns
00:08:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
00:08:26 : INFO : Creating the BED File.
00:08:29 : INFO : Saving Bed File as 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
00:08:29 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
00:08:29 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
00:08:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bua-T1-TRNA-1_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
00:13:34 : INFO : Execution Time = 5.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bua-T1-TRNA-1_B23WHTKLT4_1
00:13:34 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
00:13:34 : INFO : Running: samtools sort -o 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
00:13:34 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
00:13:34 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
00:13:34 : INFO : Running: samtools sort -o 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
[bam_sort_core] merging from 27 files and 1 in-memory blocks...
00:19:26 : INFO : Execution Time = 5.87 minutes. CMD: samtools sort -o 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
00:19:26 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_gene_reads.ok
00:19:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
Done with chr chr1.
Done with chr chr2.
Done with chr chr3.
Done with chr chr4.
Done with chr chr5.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr9.
Done with chr chr10.
Done with chr chr11.
Done with chr chr12.
Done with chr chr13.
Done with chr chr14.
Done with chr chr15.
Done with chr chr16.
Done with chr chr17.
Done with chr chr18.
Done with chr chr19.
Done with chr chr20.
Done with chr chr21.
Done with chr chr22.
00:21:20 : INFO : Execution Time = 1.89 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
00:21:20 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
00:21:20 : INFO : Running: samtools sort -o 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
00:21:40 : INFO : Execution Time = 0.34 minutes. CMD: samtools sort -o 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
00:21:40 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
00:21:40 : INFO : Running: samtools index 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
00:21:43 : INFO : Execution Time = 0.04 minutes. CMD: samtools index 659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
00:21:43 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bua-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
00:21:43 : INFO : Running: samtools index 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
00:21:43 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
00:21:43 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bua-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
00:21:43 : INFO : Running: create_report 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bua-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bua-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bua-T1-TRNA-1_B23WHTKLT4_1'
00:25:35 : INFO : Execution Time = 3.88 minutes. CMD: create_report 659_bua-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bua-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bua-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bua-T1-TRNA-1_B23WHTKLT4_1'
00:25:35 : INFO : Running: touch /tmp/nxf.liqnWkb8CD/659_bua-T1-TRNA-1_B23WHTKLT4_1.chckpts/igv_create_html.ok
00:25:35 : INFO : done.