Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/70ea73390d494f815dab3a1fc5117d/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Chimeric.out.junction 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/d1/fe96c387cafb635901b9634689b8c1/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/70ea73390d494f815dab3a1fc5117d/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/5bf1f747d4063c4602e14db4154f4b/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/70ea73390d494f815dab3a1fc5117d/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/fe96c387cafb635901b9634689b8c1/.command.run ==> STAGING COMPLETE (7 inputs) 19:59:51 : INFO 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rate=8488524.59/min [8640000], rate=8498360.66/min [8650000], rate=8508196.72/min [8660000], rate=8518032.79/min [8670000], rate=8527868.85/min [8680000], rate=8537704.92/min [8690000], rate=8547540.98/min [8700000], rate=8419354.84/min [8710000], rate=8429032.26/min [8720000], rate=8438709.68/min [8730000], rate=8448387.10/min [8740000], rate=8458064.52/min [8750000], rate=8467741.94/min [8760000], rate=8477419.35/min [8770000], rate=8487096.77/min [8780000], rate=8496774.19/min [8790000], rate=8506451.61/min [8800000], rate=8516129.03/min [8810000], rate=8525806.45/min [8820000], rate=8535483.87/min [8830000], rate=8545161.29/min [8840000], rate=8419047.62/min [8850000], rate=8428571.43/min [8860000], rate=8438095.24/min [8870000], rate=8447619.05/min [8880000], rate=8457142.86/min [8890000], rate=8466666.67/min [8900000], rate=8476190.48/min [8910000], rate=8485714.29/min [8920000], rate=8495238.10/min [8930000], rate=8504761.90/min [8940000], rate=8514285.71/min [8950000], rate=8523809.52/min [8960000], rate=8533333.33/min [8970000], rate=8542857.14/min [8980000], rate=8418750.00/min [8990000], rate=8428125.00/min [9000000], rate=8437500.00/min [9010000], rate=8446875.00/min [9020000], rate=8456250.00/min [9030000], rate=8465625.00/min [9040000], rate=8475000.00/min [9050000], rate=8484375.00/min [9060000], rate=8493750.00/min [9070000], rate=8503125.00/min [9080000], rate=8512500.00/min [9090000], rate=8521875.00/min [9100000], rate=8531250.00/min [9110000], rate=8540625.00/min [9120000], rate=8550000.00/min [9130000], rate=8427692.31/min [9140000], rate=8436923.08/min [9150000], rate=8446153.85/min [9160000], rate=8455384.62/min [9170000], rate=8464615.38/min [9180000], rate=8473846.15/min [9190000], rate=8483076.92/min [9200000], rate=8492307.69/min [9210000], rate=8501538.46/min [9220000], rate=8510769.23/min [9230000], rate=8520000.00/min [9240000], rate=8529230.77/min [9250000], rate=8538461.54/min [9260000], rate=8547692.31/min [9270000], rate=8427272.73/min [9280000], rate=8436363.64/min [9290000], rate=8445454.55/min [9300000], rate=8454545.45/min [9310000], rate=8463636.36/min [9320000], rate=8472727.27/min [9330000], rate=8481818.18/min [9340000], rate=8490909.09/min [9350000], rate=8500000.00/min [9360000], rate=8509090.91/min [9370000], rate=8518181.82/min [9380000], rate=8527272.73/min [9390000], rate=8536363.64/min [9400000], rate=8545454.55/min [9410000], rate=8554545.45/min [9420000], rate=8563636.36/min [9430000], rate=8572727.27/min [9440000], rate=8581818.18/min [9450000], rate=8462686.57/min [9460000], rate=8471641.79/min [9470000], rate=8480597.01/min [9480000], rate=8489552.24/min [9490000], rate=8498507.46/min [9500000], rate=8507462.69/min [9510000], rate=8516417.91/min [9520000], rate=8525373.13/min [9530000], rate=8534328.36/min [9540000], rate=8543283.58/min 20:01:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3abdf4-R1_A23YTGFLT4_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. -aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns: identified 5705 cancer introns 20:01:11 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns.prelim 20:01:11 : INFO : Running: touch /tmp/nxf.nm2OsDLjRc/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 20:01:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns 20:01:12 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns 20:01:12 : INFO : Running: touch /tmp/nxf.nm2OsDLjRc/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 20:01:12 : INFO : -found 2598 cancer introns 20:01:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:01:12 : INFO : Creating the BED File. 20:01:28 : INFO : Saving Bed File as aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:01:28 : INFO : Execution Time = 0.27 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:01:28 : INFO : Running: touch /tmp/nxf.nm2OsDLjRc/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 20:01:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3abdf4-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 20:25:08 : INFO : Execution Time = 23.66 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3abdf4-R1_A23YTGFLT4_1 20:25:08 : INFO : Running: touch /tmp/nxf.nm2OsDLjRc/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 20:25:08 : INFO : Running: samtools sort -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.bam 20:25:08 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.bam 20:25:08 : INFO : Running: touch /tmp/nxf.nm2OsDLjRc/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 20:25:08 : INFO : Running: samtools sort -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 85 files and 1 in-memory blocks...