Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/d672a47a266010b96e49181ec6830a/aih-tih-sc-01c779-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/74/62419a0361dad2b687ee1c93ac689b/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/3522bf601c26992c2b67a12656ce68/aih-tih-sc-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/d672a47a266010b96e49181ec6830a/aih-tih-sc-01c779-R1_A23YTGFLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/62419a0361dad2b687ee1c93ac689b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/d672a47a266010b96e49181ec6830a/aih-tih-sc-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (7 inputs) 20:05:32 : INFO 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rate=12028571.43/min [8430000], rate=12042857.14/min [8440000], rate=12057142.86/min [8450000], rate=12071428.57/min [8460000], rate=12085714.29/min [8470000], rate=12100000.00/min [8480000], rate=12114285.71/min [8490000], rate=12128571.43/min [8500000], rate=12142857.14/min [8510000], rate=12157142.86/min [8520000], rate=12171428.57/min [8530000], rate=12185714.29/min [8540000], rate=12200000.00/min [8550000], rate=12214285.71/min [8560000], rate=11944186.05/min [8570000], rate=11958139.53/min [8580000], rate=11972093.02/min [8590000], rate=11986046.51/min [8600000], rate=12000000.00/min [8610000], rate=12013953.49/min [8620000], rate=12027906.98/min [8630000], rate=12041860.47/min [8640000], rate=12055813.95/min [8650000], rate=12069767.44/min [8660000], rate=12083720.93/min [8670000], rate=12097674.42/min [8680000], rate=12111627.91/min [8690000], rate=12125581.40/min [8700000], rate=12139534.88/min [8710000], rate=12153488.37/min [8720000], rate=12167441.86/min [8730000], rate=12181395.35/min [8740000], rate=11918181.82/min [8750000], rate=11931818.18/min [8760000], rate=11945454.55/min [8770000], rate=11959090.91/min [8780000], rate=11972727.27/min [8790000], rate=11986363.64/min [8800000], rate=12000000.00/min [8810000], rate=12013636.36/min [8820000], rate=12027272.73/min [8830000], rate=12040909.09/min [8840000], rate=12054545.45/min [8850000], rate=12068181.82/min [8860000], rate=12081818.18/min [8870000], rate=12095454.55/min [8880000], rate=12109090.91/min [8890000], rate=12122727.27/min [8900000], rate=12136363.64/min [8910000], rate=12150000.00/min [8920000], rate=12163636.36/min [8930000], rate=12177272.73/min [8940000], rate=12190909.09/min [8950000], rate=12204545.45/min [8960000], rate=12218181.82/min [8970000], rate=12231818.18/min [8980000], rate=12245454.55/min [8990000], rate=11986666.67/min [9000000], rate=12000000.00/min [9010000], rate=12013333.33/min [9020000], rate=12026666.67/min [9030000], rate=12040000.00/min [9040000], rate=12053333.33/min [9050000], rate=12066666.67/min [9060000], rate=12080000.00/min [9070000], rate=12093333.33/min [9080000], rate=12106666.67/min [9090000], rate=12120000.00/min [9100000], rate=12133333.33/min [9110000], rate=12146666.67/min [9120000], rate=12160000.00/min [9130000], rate=12173333.33/min [9140000], rate=12186666.67/min [9150000], rate=12200000.00/min [9160000], rate=12213333.33/min [9170000], rate=12226666.67/min [9180000], rate=12240000.00/min [9190000], rate=12253333.33/min [9200000], rate=12266666.67/min [9210000], rate=12280000.00/min [9220000], rate=12293333.33/min [9230000], rate=12306666.67/min [9240000], rate=12320000.00/min [9250000], rate=12333333.33/min [9260000], rate=12346666.67/min [9270000], rate=12360000.00/min [9280000], rate=12104347.83/min [9290000], rate=12117391.30/min [9300000], rate=12130434.78/min [9310000], rate=12143478.26/min [9320000], rate=12156521.74/min [9330000], rate=12169565.22/min [9340000], rate=12182608.70/min [9350000], rate=12195652.17/min [9360000], rate=12208695.65/min [9370000], rate=12221739.13/min [9380000], rate=12234782.61/min [9390000], rate=12247826.09/min 20:06:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-01c779-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.introns: identified 6188 cancer introns 20:06:29 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-01c779-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer.introns.prelim 20:06:29 : INFO : Running: touch /tmp/nxf.AlIi0q3OLC/aih-tih-sc-01c779-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 20:06:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer.introns 20:06:30 : 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-01c779-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer.introns 20:06:30 : INFO : Running: touch /tmp/nxf.AlIi0q3OLC/aih-tih-sc-01c779-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 20:06:30 : INFO : -found 2345 cancer introns 20:06:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-01c779-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-01c779-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:06:30 : INFO : Creating the BED File. 20:06:37 : INFO : Saving Bed File as aih-tih-sc-01c779-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:06:38 : INFO : Execution Time = 0.13 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-01c779-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-01c779-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:06:38 : INFO : Running: touch /tmp/nxf.AlIi0q3OLC/aih-tih-sc-01c779-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 20:06:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-01c779-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-01c779-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 20:27:07 : INFO : Execution Time = 20.49 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-01c779-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-01c779-R1_A23YTGFLT4_1 20:27:07 : INFO : Running: touch /tmp/nxf.AlIi0q3OLC/aih-tih-sc-01c779-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 20:27:07 : INFO : Running: samtools sort -o aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer_intron_reads.bam 20:27:07 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-01c779-R1_A23YTGFLT4_1.cancer_intron_reads.bam 20:27:07 : INFO : Running: touch /tmp/nxf.AlIi0q3OLC/aih-tih-sc-01c779-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 20:27:07 : INFO : Running: samtools sort -o aih-tih-sc-01c779-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-01c779-R1_A23YTGFLT4_1.gene_reads.bam