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/db/3d31afc13bb9b806ec78504a8d9354/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/27385695e43288cff28ebcd46dc4c9/659_bTo-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/27385695e43288cff28ebcd46dc4c9/659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/dfbb32fd89ba107e4305d79a2576c9/659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/27385695e43288cff28ebcd46dc4c9/659_bTo-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/3d31afc13bb9b806ec78504a8d9354/.command.run ==> STAGING COMPLETE (7 inputs) 08:42:04 : INFO : -reading 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rate=9645000.00/min [6440000], rate=9660000.00/min [6450000], rate=9675000.00/min [6460000], rate=9690000.00/min [6470000], rate=9705000.00/min [6480000], rate=9720000.00/min [6490000], rate=9735000.00/min [6500000], rate=9750000.00/min [6510000], rate=9765000.00/min [6520000], rate=9780000.00/min [6530000], rate=9556097.56/min [6540000], rate=9570731.71/min [6550000], rate=9585365.85/min [6560000], rate=9600000.00/min [6570000], rate=9614634.15/min [6580000], rate=9629268.29/min [6590000], rate=9643902.44/min [6600000], rate=9658536.59/min [6610000], rate=9673170.73/min [6620000], rate=9687804.88/min [6630000], rate=9702439.02/min [6640000], rate=9717073.17/min [6650000], rate=9731707.32/min [6660000], rate=9746341.46/min [6670000], rate=9760975.61/min [6680000], rate=9775609.76/min [6690000], rate=9790243.90/min [6700000], rate=9804878.05/min [6710000], rate=9819512.20/min [6720000], rate=9600000.00/min [6730000], rate=9614285.71/min [6740000], rate=9628571.43/min [6750000], rate=9642857.14/min [6760000], rate=9657142.86/min [6770000], rate=9671428.57/min [6780000], rate=9685714.29/min [6790000], rate=9700000.00/min [6800000], rate=9714285.71/min [6810000], rate=9728571.43/min [6820000], rate=9742857.14/min [6830000], rate=9757142.86/min [6840000], rate=9771428.57/min [6850000], rate=9785714.29/min [6860000], rate=9800000.00/min [6870000], rate=9814285.71/min [6880000], rate=9828571.43/min [6890000], rate=9842857.14/min [6900000], rate=9627906.98/min [6910000], rate=9641860.47/min [6920000], rate=9655813.95/min [6930000], rate=9669767.44/min [6940000], rate=9683720.93/min [6950000], rate=9697674.42/min [6960000], rate=9711627.91/min [6970000], rate=9725581.40/min [6980000], rate=9739534.88/min [6990000], rate=9753488.37/min [7000000], rate=9767441.86/min [7010000], rate=9781395.35/min [7020000], rate=9795348.84/min [7030000], rate=9809302.33/min [7040000], rate=9823255.81/min [7050000], rate=9837209.30/min [7060000], rate=9851162.79/min [7070000], rate=9640909.09/min [7080000], rate=9654545.45/min [7090000], rate=9668181.82/min [7100000], rate=9681818.18/min [7110000], rate=9695454.55/min [7120000], rate=9709090.91/min [7130000], rate=9722727.27/min [7140000], rate=9736363.64/min [7150000], rate=9750000.00/min [7160000], rate=9763636.36/min [7170000], rate=9777272.73/min [7180000], rate=9790909.09/min [7190000], rate=9804545.45/min [7200000], rate=9818181.82/min [7210000], rate=9831818.18/min [7220000], rate=9845454.55/min [7230000], rate=9859090.91/min [7240000], rate=9872727.27/min [7250000], rate=9666666.67/min [7260000], rate=9680000.00/min [7270000], rate=9693333.33/min [7280000], rate=9706666.67/min [7290000], rate=9720000.00/min [7300000], rate=9733333.33/min [7310000], rate=9746666.67/min [7320000], rate=9760000.00/min 08:43:02 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bTo-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_bTo-T1-TRNA-1_B23MHV2LT4_1.introns: identified 7808 cancer introns 08:43:03 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 08:43:03 : INFO : Running: touch /tmp/nxf.78hr1Hbt4H/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 08:43:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:43:03 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:43:03 : INFO : Running: touch /tmp/nxf.78hr1Hbt4H/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 08:43:03 : INFO : -found 3129 cancer introns 08:43:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:43:04 : INFO : Creating the BED File. 08:43:13 : INFO : Saving Bed File as 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:43:13 : INFO : Execution Time = 0.16 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:43:13 : INFO : Running: touch /tmp/nxf.78hr1Hbt4H/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 08:43:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:11:33 : INFO : Execution Time = 28.33 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1 09:11:33 : INFO : Running: touch /tmp/nxf.78hr1Hbt4H/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 09:11:33 : INFO : Running: samtools sort -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:11:33 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:11:33 : INFO : Running: touch /tmp/nxf.78hr1Hbt4H/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:11:33 : INFO : Running: samtools sort -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam