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/f1/47d17a58fb3ab1da63bc4544b918d0/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/62e1db7ca6b483c5e64faa32f0f78c/tih_rna_sample_00668_B23MVV7LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/62e1db7ca6b483c5e64faa32f0f78c/tih_rna_sample_00668_B23MVV7LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/698b61632922f0e1c59a51e988f3dd/tih_rna_sample_00668_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/47d17a58fb3ab1da63bc4544b918d0/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/62e1db7ca6b483c5e64faa32f0f78c/tih_rna_sample_00668_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (7 inputs) 09:34:16 : INFO 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rate=13523076.92/min [5870000], rate=13546153.85/min [5880000], rate=13569230.77/min [5890000], rate=13592307.69/min [5900000], rate=13615384.62/min [5910000], rate=13638461.54/min [5920000], rate=13661538.46/min [5930000], rate=13684615.38/min [5940000], rate=13707692.31/min [5950000], rate=13730769.23/min [5960000], rate=13753846.15/min [5970000], rate=13776923.08/min [5980000], rate=13800000.00/min [5990000], rate=13823076.92/min [6000000], rate=13846153.85/min [6010000], rate=13355555.56/min [6020000], rate=13377777.78/min [6030000], rate=13400000.00/min [6040000], rate=13422222.22/min [6050000], rate=13444444.44/min [6060000], rate=13466666.67/min [6070000], rate=13488888.89/min [6080000], rate=13511111.11/min [6090000], rate=13533333.33/min [6100000], rate=13555555.56/min [6110000], rate=13577777.78/min [6120000], rate=13600000.00/min [6130000], rate=13622222.22/min [6140000], rate=13644444.44/min [6150000], rate=13666666.67/min [6160000], rate=13688888.89/min [6170000], rate=13711111.11/min [6180000], rate=13733333.33/min [6190000], rate=13755555.56/min [6200000], rate=13777777.78/min [6210000], rate=13800000.00/min [6220000], rate=13822222.22/min [6230000], rate=13844444.44/min [6240000], rate=13866666.67/min [6250000], rate=13888888.89/min [6260000], rate=13911111.11/min [6270000], rate=13933333.33/min [6280000], rate=13457142.86/min [6290000], rate=13478571.43/min [6300000], rate=13500000.00/min [6310000], rate=13521428.57/min [6320000], rate=13542857.14/min [6330000], rate=13564285.71/min [6340000], rate=13585714.29/min [6350000], rate=13607142.86/min [6360000], rate=13628571.43/min [6370000], rate=13650000.00/min [6380000], rate=13671428.57/min [6390000], rate=13692857.14/min [6400000], rate=13714285.71/min [6410000], rate=13735714.29/min [6420000], rate=13757142.86/min [6430000], rate=13778571.43/min [6440000], rate=13800000.00/min [6450000], rate=13821428.57/min [6460000], rate=13842857.14/min [6470000], rate=13864285.71/min [6480000], rate=13885714.29/min [6490000], rate=13907142.86/min [6500000], rate=13928571.43/min [6510000], rate=13950000.00/min [6520000], rate=13971428.57/min [6530000], rate=13510344.83/min [6540000], rate=13531034.48/min [6550000], rate=13551724.14/min [6560000], rate=13572413.79/min [6570000], rate=13593103.45/min [6580000], rate=13613793.10/min [6590000], rate=13634482.76/min [6600000], rate=13655172.41/min [6610000], rate=13675862.07/min [6620000], rate=13696551.72/min [6630000], rate=13717241.38/min [6640000], rate=13737931.03/min [6650000], rate=13758620.69/min [6660000], rate=13779310.34/min [6670000], rate=13800000.00/min [6680000], rate=13820689.66/min [6690000], rate=13841379.31/min [6700000], rate=13862068.97/min [6710000], rate=13882758.62/min [6720000], rate=13903448.28/min [6730000], rate=13924137.93/min [6740000], rate=13944827.59/min [6750000], rate=13965517.24/min [6760000], rate=13986206.90/min [6770000], rate=14006896.55/min [6780000], rate=14027586.21/min [6790000], rate=13580000.00/min [6800000], rate=13600000.00/min [6810000], rate=13620000.00/min [6820000], rate=13640000.00/min [6830000], rate=13660000.00/min [6840000], rate=13680000.00/min [6850000], rate=13700000.00/min [6860000], rate=13720000.00/min [6870000], rate=13740000.00/min [6880000], rate=13760000.00/min [6890000], rate=13780000.00/min [6900000], rate=13800000.00/min [6910000], rate=13820000.00/min [6920000], rate=13840000.00/min [6930000], rate=13860000.00/min [6940000], rate=13880000.00/min [6950000], rate=13900000.00/min [6960000], rate=13920000.00/min [6970000], rate=13940000.00/min [6980000], rate=13960000.00/min [6990000], rate=13980000.00/min [7000000], rate=14000000.00/min [7010000], rate=14020000.00/min [7020000], rate=14040000.00/min [7030000], rate=14060000.00/min [7040000], rate=13625806.45/min [7050000], rate=13645161.29/min [7060000], rate=13664516.13/min [7070000], rate=13683870.97/min [7080000], rate=13703225.81/min [7090000], rate=13722580.65/min [7100000], rate=13741935.48/min [7110000], rate=13761290.32/min [7120000], rate=13780645.16/min [7130000], rate=13800000.00/min [7140000], rate=13819354.84/min [7150000], rate=13838709.68/min [7160000], rate=13858064.52/min [7170000], rate=13877419.35/min [7180000], rate=13896774.19/min [7190000], rate=13916129.03/min [7200000], rate=13935483.87/min [7210000], rate=13954838.71/min [7220000], rate=13974193.55/min [7230000], rate=13993548.39/min [7240000], rate=14012903.23/min [7250000], rate=14032258.06/min [7260000], rate=14051612.90/min [7270000], rate=14070967.74/min [7280000], rate=14090322.58/min [7290000], rate=13668750.00/min [7300000], rate=13687500.00/min [7310000], rate=13706250.00/min [7320000], rate=13725000.00/min [7330000], rate=13743750.00/min [7340000], rate=13762500.00/min [7350000], rate=13781250.00/min [7360000], rate=13800000.00/min [7370000], rate=13818750.00/min [7380000], rate=13837500.00/min [7390000], rate=13856250.00/min [7400000], rate=13875000.00/min [7410000], rate=13893750.00/min [7420000], rate=13912500.00/min [7430000], rate=13931250.00/min [7440000], rate=13950000.00/min [7450000], rate=13968750.00/min [7460000], rate=13987500.00/min [7470000], rate=14006250.00/min [7480000], rate=14025000.00/min [7490000], rate=14043750.00/min [7500000], rate=14062500.00/min [7510000], rate=14081250.00/min [7520000], rate=14100000.00/min [7530000], rate=14118750.00/min [7540000], rate=13709090.91/min [7550000], rate=13727272.73/min [7560000], rate=13745454.55/min [7570000], rate=13763636.36/min [7580000], rate=13781818.18/min [7590000], rate=13800000.00/min [7600000], rate=13818181.82/min [7610000], rate=13836363.64/min [7620000], rate=13854545.45/min [7630000], rate=13872727.27/min [7640000], rate=13890909.09/min [7650000], rate=13909090.91/min [7660000], rate=13927272.73/min [7670000], rate=13945454.55/min [7680000], rate=13963636.36/min [7690000], rate=13981818.18/min [7700000], rate=14000000.00/min [7710000], rate=14018181.82/min [7720000], rate=14036363.64/min [7730000], rate=14054545.45/min [7740000], rate=14072727.27/min [7750000], rate=14090909.09/min [7760000], rate=14109090.91/min [7770000], rate=14127272.73/min [7780000], rate=14145454.55/min [7790000], rate=14163636.36/min [7800000], rate=13764705.88/min [7810000], rate=13782352.94/min [7820000], rate=13800000.00/min [7830000], rate=13817647.06/min [7840000], rate=13835294.12/min [7850000], rate=13852941.18/min [7860000], rate=13870588.24/min [7870000], rate=13888235.29/min [7880000], rate=13905882.35/min [7890000], rate=13923529.41/min [7900000], rate=13941176.47/min [7910000], rate=13958823.53/min [7920000], rate=13976470.59/min [7930000], rate=13994117.65/min [7940000], rate=14011764.71/min [7950000], rate=14029411.76/min [7960000], rate=14047058.82/min [7970000], rate=14064705.88/min [7980000], rate=14082352.94/min [7990000], rate=14100000.00/min [8000000], rate=14117647.06/min [8010000], rate=13731428.57/min [8020000], rate=13748571.43/min [8030000], rate=13765714.29/min [8040000], rate=13782857.14/min [8050000], rate=13800000.00/min [8060000], rate=13817142.86/min [8070000], rate=13834285.71/min [8080000], rate=13851428.57/min [8090000], rate=13868571.43/min [8100000], rate=13885714.29/min [8110000], rate=13902857.14/min [8120000], rate=13920000.00/min [8130000], rate=13937142.86/min [8140000], rate=13954285.71/min [8150000], rate=13971428.57/min [8160000], rate=13988571.43/min [8170000], rate=14005714.29/min [8180000], rate=14022857.14/min [8190000], rate=14040000.00/min [8200000], rate=14057142.86/min [8210000], rate=14074285.71/min [8220000], rate=14091428.57/min [8230000], rate=14108571.43/min [8240000], rate=14125714.29/min [8250000], rate=14142857.14/min [8260000], rate=13766666.67/min [8270000], rate=13783333.33/min [8280000], rate=13800000.00/min [8290000], rate=13816666.67/min [8300000], rate=13833333.33/min [8310000], rate=13850000.00/min [8320000], rate=13866666.67/min [8330000], rate=13883333.33/min [8340000], rate=13900000.00/min [8350000], rate=13916666.67/min [8360000], rate=13933333.33/min [8370000], rate=13950000.00/min [8380000], rate=13966666.67/min [8390000], rate=13983333.33/min [8400000], rate=14000000.00/min [8410000], rate=14016666.67/min [8420000], rate=14033333.33/min [8430000], rate=14050000.00/min [8440000], rate=14066666.67/min [8450000], rate=14083333.33/min [8460000], rate=14100000.00/min [8470000], rate=14116666.67/min [8480000], rate=14133333.33/min [8490000], rate=14150000.00/min [8500000], rate=14166666.67/min [8510000], rate=13800000.00/min [8520000], rate=13816216.22/min [8530000], rate=13832432.43/min [8540000], rate=13848648.65/min [8550000], rate=13864864.86/min [8560000], rate=13881081.08/min [8570000], rate=13897297.30/min [8580000], rate=13913513.51/min [8590000], rate=13929729.73/min [8600000], rate=13945945.95/min [8610000], rate=13962162.16/min [8620000], rate=13978378.38/min [8630000], rate=13994594.59/min [8640000], rate=14010810.81/min [8650000], rate=14027027.03/min [8660000], rate=14043243.24/min [8670000], rate=14059459.46/min [8680000], rate=14075675.68/min [8690000], rate=14091891.89/min [8700000], rate=14108108.11/min [8710000], rate=14124324.32/min [8720000], rate=14140540.54/min [8730000], rate=14156756.76/min [8740000], rate=14172972.97/min [8750000], rate=14189189.19/min [8760000], rate=13831578.95/min [8770000], rate=13847368.42/min [8780000], rate=13863157.89/min [8790000], rate=13878947.37/min [8800000], rate=13894736.84/min [8810000], rate=13910526.32/min [8820000], rate=13926315.79/min [8830000], rate=13942105.26/min [8840000], rate=13957894.74/min [8850000], rate=13973684.21/min [8860000], rate=13989473.68/min [8870000], rate=14005263.16/min [8880000], rate=14021052.63/min [8890000], rate=14036842.11/min [8900000], rate=14052631.58/min [8910000], rate=14068421.05/min [8920000], rate=14084210.53/min [8930000], rate=14100000.00/min [8940000], rate=14115789.47/min [8950000], rate=14131578.95/min [8960000], rate=14147368.42/min [8970000], rate=14163157.89/min 09:35:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00668_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00668_B23MVV7LT4_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. -tih_rna_sample_00668_B23MVV7LT4_1.introns: identified 7089 cancer introns 09:35:06 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00668_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00668_B23MVV7LT4_1.cancer.introns.prelim 09:35:06 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/prelim_introns.ok 09:35:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00668_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00668_B23MVV7LT4_1.cancer.introns 09:35:06 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00668_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00668_B23MVV7LT4_1.cancer.introns 09:35:06 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/introns_filtered.ok 09:35:06 : INFO : -found 2580 cancer introns 09:35:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00668_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00668_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00668_B23MVV7LT4_1.introns.for_IGV.bed 09:35:07 : INFO : Creating the BED File. 09:35:12 : INFO : Saving Bed File as tih_rna_sample_00668_B23MVV7LT4_1.introns.for_IGV.bed 09:35:12 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00668_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00668_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00668_B23MVV7LT4_1.introns.for_IGV.bed 09:35:12 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 09:35:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00668_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00668_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00668_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00668_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 10:02:34 : INFO : Execution Time = 27.36 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00668_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00668_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00668_B23MVV7LT4_1 10:02:34 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 10:02:34 : INFO : Running: samtools sort -o tih_rna_sample_00668_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00668_B23MVV7LT4_1.cancer_intron_reads.bam 10:02:34 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00668_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00668_B23MVV7LT4_1.cancer_intron_reads.bam 10:02:34 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 10:02:34 : INFO : Running: samtools sort -o tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 129 files and 1 in-memory blocks... 10:31:47 : INFO : Execution Time = 29.22 minutes. CMD: samtools sort -o tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.bam 10:31:47 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 10:31:48 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00668_B23MVV7LT4_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. Done with chr chrX. 10:40:23 : INFO : Execution Time = 8.58 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.bam 10:40:23 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:40:23 : INFO : Running: samtools sort -o tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:41:07 : INFO : Execution Time = 0.75 minutes. CMD: samtools sort -o tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 10:41:07 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:41:08 : INFO : Running: samtools index tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 10:41:13 : INFO : Execution Time = 0.09 minutes. CMD: samtools index tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 10:41:13 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/tih_rna_sample_00668_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:41:13 : INFO : Running: samtools index tih_rna_sample_00668_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 10:41:13 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00668_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 10:41:13 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/tih_rna_sample_00668_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:41:13 : INFO : Running: create_report tih_rna_sample_00668_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00668_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00668_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00668_B23MVV7LT4_1' [W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi 10:47:25 : INFO : Execution Time = 6.21 minutes. CMD: create_report tih_rna_sample_00668_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00668_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00668_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00668_B23MVV7LT4_1' 10:47:25 : INFO : Running: touch /tmp/nxf.bFpTkRn9Tu/tih_rna_sample_00668_B23MVV7LT4_1.chckpts/igv_create_html.ok 10:47:25 : INFO : done.