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/6c/c4ef7851a82a3b25256cda26f495bd/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/6745fa867f427c6cca145df2dfeb66/659_b4x-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0e82fd105c363c8146fbf9c779e01a/659_b4x-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/c4ef7851a82a3b25256cda26f495bd/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0e82fd105c363c8146fbf9c779e01a/659_b4x-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0e82fd105c363c8146fbf9c779e01a/659_b4x-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (7 inputs) 20:32:11 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=33600000.00/min [570000], rate=34200000.00/min [580000], rate=34800000.00/min [590000], rate=35400000.00/min [600000], rate=36000000.00/min [610000], rate=36600000.00/min [620000], rate=37200000.00/min [630000], rate=37800000.00/min [640000], rate=38400000.00/min [650000], rate=39000000.00/min [660000], rate=39600000.00/min [670000], rate=40200000.00/min [680000], rate=40800000.00/min [690000], rate=41400000.00/min [700000], rate=42000000.00/min [710000], rate=42600000.00/min [720000], rate=43200000.00/min [730000], rate=43800000.00/min [740000], rate=44400000.00/min [750000], rate=45000000.00/min [760000], rate=45600000.00/min [770000], rate=46200000.00/min [780000], rate=46800000.00/min [790000], rate=47400000.00/min [800000], rate=48000000.00/min [810000], rate=48600000.00/min [820000], rate=49200000.00/min [830000], rate=49800000.00/min [840000], rate=50400000.00/min [850000], rate=51000000.00/min [860000], rate=51600000.00/min [870000], rate=52200000.00/min [880000], rate=26400000.00/min [890000], rate=26700000.00/min [900000], rate=27000000.00/min [910000], rate=27300000.00/min [920000], rate=27600000.00/min [930000], rate=27900000.00/min [940000], rate=28200000.00/min [950000], rate=28500000.00/min [960000], rate=28800000.00/min [970000], rate=29100000.00/min [980000], rate=29400000.00/min [990000], rate=29700000.00/min [1000000], rate=30000000.00/min [1010000], rate=30300000.00/min [1020000], rate=30600000.00/min [1030000], rate=30900000.00/min [1040000], rate=31200000.00/min [1050000], rate=31500000.00/min [1060000], rate=31800000.00/min [1070000], rate=32100000.00/min [1080000], rate=32400000.00/min [1090000], rate=32700000.00/min [1100000], rate=33000000.00/min [1110000], rate=33300000.00/min [1120000], rate=33600000.00/min [1130000], rate=33900000.00/min [1140000], rate=34200000.00/min [1150000], rate=34500000.00/min [1160000], rate=34800000.00/min [1170000], rate=35100000.00/min [1180000], rate=35400000.00/min [1190000], rate=35700000.00/min [1200000], rate=36000000.00/min [1210000], rate=36300000.00/min [1220000], rate=36600000.00/min [1230000], rate=36900000.00/min [1240000], rate=37200000.00/min [1250000], rate=37500000.00/min [1260000], rate=37800000.00/min [1270000], rate=38100000.00/min [1280000], rate=38400000.00/min [1290000], rate=38700000.00/min [1300000], rate=39000000.00/min [1310000], rate=39300000.00/min [1320000], rate=39600000.00/min [1330000], rate=39900000.00/min [1340000], rate=40200000.00/min [1350000], rate=40500000.00/min [1360000], rate=40800000.00/min [1370000], rate=41100000.00/min [1380000], rate=41400000.00/min [1390000], rate=41700000.00/min [1400000], rate=28000000.00/min [1410000], rate=28200000.00/min [1420000], rate=28400000.00/min [1430000], rate=28600000.00/min [1440000], rate=28800000.00/min [1450000], rate=29000000.00/min [1460000], rate=29200000.00/min [1470000], rate=29400000.00/min [1480000], rate=29600000.00/min [1490000], rate=29800000.00/min [1500000], rate=30000000.00/min [1510000], rate=30200000.00/min [1520000], rate=30400000.00/min [1530000], rate=30600000.00/min [1540000], rate=30800000.00/min [1550000], rate=31000000.00/min [1560000], rate=31200000.00/min [1570000], rate=31400000.00/min [1580000], rate=31600000.00/min [1590000], rate=31800000.00/min [1600000], rate=32000000.00/min [1610000], rate=32200000.00/min [1620000], rate=32400000.00/min [1630000], rate=32600000.00/min [1640000], rate=32800000.00/min [1650000], rate=33000000.00/min [1660000], rate=33200000.00/min [1670000], rate=33400000.00/min [1680000], rate=33600000.00/min [1690000], rate=33800000.00/min [1700000], rate=34000000.00/min [1710000], rate=34200000.00/min [1720000], rate=34400000.00/min [1730000], rate=34600000.00/min [1740000], rate=34800000.00/min [1750000], rate=35000000.00/min [1760000], rate=35200000.00/min [1770000], rate=35400000.00/min [1780000], rate=35600000.00/min [1790000], rate=35800000.00/min [1800000], rate=36000000.00/min [1810000], rate=36200000.00/min [1820000], rate=36400000.00/min [1830000], rate=36600000.00/min [1840000], rate=36800000.00/min [1850000], rate=37000000.00/min [1860000], rate=37200000.00/min [1870000], rate=37400000.00/min [1880000], rate=37600000.00/min [1890000], rate=28350000.00/min [1900000], rate=28500000.00/min [1910000], rate=28650000.00/min [1920000], rate=28800000.00/min [1930000], rate=28950000.00/min [1940000], rate=29100000.00/min [1950000], rate=29250000.00/min [1960000], rate=29400000.00/min [1970000], rate=29550000.00/min [1980000], rate=29700000.00/min [1990000], rate=29850000.00/min [2000000], rate=30000000.00/min [2010000], rate=30150000.00/min [2020000], rate=30300000.00/min [2030000], rate=30450000.00/min [2040000], rate=30600000.00/min [2050000], rate=30750000.00/min [2060000], rate=30900000.00/min [2070000], rate=31050000.00/min [2080000], rate=31200000.00/min [2090000], rate=31350000.00/min [2100000], rate=31500000.00/min [2110000], rate=31650000.00/min [2120000], rate=31800000.00/min [2130000], rate=31950000.00/min [2140000], rate=32100000.00/min [2150000], rate=32250000.00/min [2160000], rate=32400000.00/min [2170000], rate=32550000.00/min [2180000], rate=32700000.00/min [2190000], rate=32850000.00/min [2200000], rate=33000000.00/min [2210000], rate=33150000.00/min [2220000], rate=33300000.00/min [2230000], rate=33450000.00/min [2240000], rate=33600000.00/min [2250000], rate=33750000.00/min [2260000], rate=33900000.00/min [2270000], rate=34050000.00/min [2280000], rate=34200000.00/min [2290000], rate=34350000.00/min [2300000], rate=34500000.00/min [2310000], rate=34650000.00/min [2320000], rate=34800000.00/min [2330000], rate=34950000.00/min [2340000], rate=35100000.00/min [2350000], rate=35250000.00/min [2360000], rate=35400000.00/min [2370000], rate=28440000.00/min [2380000], rate=28560000.00/min [2390000], rate=28680000.00/min [2400000], rate=28800000.00/min [2410000], rate=28920000.00/min [2420000], rate=29040000.00/min [2430000], rate=29160000.00/min [2440000], rate=29280000.00/min [2450000], rate=29400000.00/min [2460000], rate=29520000.00/min [2470000], rate=29640000.00/min [2480000], rate=29760000.00/min [2490000], rate=29880000.00/min [2500000], rate=30000000.00/min [2510000], rate=30120000.00/min [2520000], rate=30240000.00/min [2530000], rate=30360000.00/min [2540000], rate=30480000.00/min [2550000], rate=30600000.00/min [2560000], rate=30720000.00/min [2570000], rate=30840000.00/min [2580000], rate=30960000.00/min [2590000], rate=31080000.00/min [2600000], rate=31200000.00/min [2610000], rate=31320000.00/min [2620000], rate=31440000.00/min [2630000], rate=31560000.00/min [2640000], rate=31680000.00/min [2650000], rate=31800000.00/min [2660000], rate=31920000.00/min [2670000], rate=32040000.00/min [2680000], rate=32160000.00/min [2690000], rate=32280000.00/min [2700000], rate=32400000.00/min [2710000], rate=32520000.00/min [2720000], rate=32640000.00/min [2730000], rate=32760000.00/min [2740000], rate=32880000.00/min [2750000], rate=33000000.00/min [2760000], rate=33120000.00/min [2770000], rate=33240000.00/min [2780000], rate=33360000.00/min [2790000], rate=33480000.00/min [2800000], rate=33600000.00/min [2810000], rate=33720000.00/min [2820000], rate=33840000.00/min [2830000], rate=33960000.00/min [2840000], rate=34080000.00/min [2850000], rate=34200000.00/min [2860000], rate=34320000.00/min [2870000], rate=34440000.00/min [2880000], rate=34560000.00/min [2890000], rate=28900000.00/min [2900000], rate=29000000.00/min [2910000], rate=29100000.00/min [2920000], rate=29200000.00/min [2930000], rate=29300000.00/min [2940000], rate=29400000.00/min [2950000], rate=29500000.00/min [2960000], rate=29600000.00/min [2970000], rate=29700000.00/min [2980000], rate=29800000.00/min [2990000], rate=29900000.00/min [3000000], rate=30000000.00/min [3010000], rate=30100000.00/min [3020000], rate=30200000.00/min [3030000], rate=30300000.00/min [3040000], rate=30400000.00/min [3050000], rate=30500000.00/min [3060000], rate=30600000.00/min [3070000], rate=30700000.00/min [3080000], rate=30800000.00/min [3090000], rate=30900000.00/min [3100000], rate=31000000.00/min [3110000], rate=31100000.00/min [3120000], rate=31200000.00/min [3130000], rate=31300000.00/min [3140000], rate=31400000.00/min [3150000], rate=31500000.00/min [3160000], rate=31600000.00/min [3170000], rate=31700000.00/min [3180000], rate=31800000.00/min [3190000], rate=31900000.00/min [3200000], rate=32000000.00/min [3210000], rate=32100000.00/min [3220000], rate=32200000.00/min [3230000], rate=32300000.00/min [3240000], rate=32400000.00/min [3250000], rate=32500000.00/min [3260000], rate=32600000.00/min [3270000], rate=32700000.00/min [3280000], rate=32800000.00/min 20:32:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_b4x-T1-TRNA-1_B23MHV2LT4_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_b4x-T1-TRNA-1_B23MHV2LT4_1.introns: identified 755 cancer introns 20:32:21 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 20:32:21 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 20:32:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 20:32:21 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 20:32:21 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 20:32:21 : INFO : -found 507 cancer introns 20:32:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 20:32:21 : INFO : Creating the BED File. 20:32:23 : INFO : Saving Bed File as 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 20:32:23 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 20:32:23 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 20:32:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_b4x-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_b4x-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 20:33:13 : INFO : Execution Time = 0.85 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_b4x-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_b4x-T1-TRNA-1_B23MHV2LT4_1 20:33:13 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 20:33:13 : INFO : Running: samtools sort -o 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 20:33:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 20:33:14 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 20:33:14 : INFO : Running: samtools sort -o 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam [bam_sort_core] merging from 5 files and 1 in-memory blocks... 20:34:14 : INFO : Execution Time = 1.00 minutes. CMD: samtools sort -o 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam 20:34:14 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok 20:34:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_b4x-T1-TRNA-1_B23MHV2LT4_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. 20:34:29 : INFO : Execution Time = 0.25 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 20:34:29 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 20:34:29 : INFO : Running: samtools sort -o 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp 20:34:33 : INFO : Execution Time = 0.06 minutes. CMD: samtools sort -o 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp 20:34:33 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 20:34:33 : INFO : Running: samtools index 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 20:34:33 : INFO : Execution Time = 0.01 minutes. CMD: samtools index 659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 20:34:33 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_b4x-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 20:34:33 : INFO : Running: samtools index 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 20:34:33 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 20:34:33 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_b4x-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 20:34:33 : INFO : Running: create_report 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_b4x-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_b4x-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_b4x-T1-TRNA-1_B23MHV2LT4_1' 20:35:14 : INFO : Execution Time = 0.68 minutes. CMD: create_report 659_b4x-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_b4x-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_b4x-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_b4x-T1-TRNA-1_B23MHV2LT4_1' 20:35:14 : INFO : Running: touch /tmp/nxf.hZN7XJie3c/659_b4x-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok 20:35:14 : INFO : done.