Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/6bb1f2137dafa7d1b2fade3211d055/aih-tih-sc-da460d-R1_A23WJ53LT4_1.SJ.out.tab 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/d8/5591d65dde28ed1936c5a5d270f077/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/6bb1f2137dafa7d1b2fade3211d055/aih-tih-sc-da460d-R1_A23WJ53LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/6bb1f2137dafa7d1b2fade3211d055/aih-tih-sc-da460d-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/5591d65dde28ed1936c5a5d270f077/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/b02b820888b75e0266362542d0c001/aih-tih-sc-da460d-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai ==> STAGING COMPLETE (7 inputs) 08:56:27 : INFO 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rate=8688888.89/min [7830000], rate=8700000.00/min [7840000], rate=8711111.11/min [7850000], rate=8722222.22/min [7860000], rate=8733333.33/min [7870000], rate=8744444.44/min [7880000], rate=8755555.56/min [7890000], rate=8766666.67/min [7900000], rate=8618181.82/min [7910000], rate=8629090.91/min [7920000], rate=8640000.00/min [7930000], rate=8650909.09/min [7940000], rate=8661818.18/min [7950000], rate=8672727.27/min [7960000], rate=8683636.36/min [7970000], rate=8694545.45/min [7980000], rate=8705454.55/min [7990000], rate=8716363.64/min [8000000], rate=8727272.73/min [8010000], rate=8738181.82/min [8020000], rate=8749090.91/min [8030000], rate=8760000.00/min [8040000], rate=8614285.71/min [8050000], rate=8625000.00/min [8060000], rate=8635714.29/min [8070000], rate=8646428.57/min [8080000], rate=8657142.86/min [8090000], rate=8667857.14/min [8100000], rate=8678571.43/min [8110000], rate=8689285.71/min [8120000], rate=8700000.00/min [8130000], rate=8710714.29/min [8140000], rate=8721428.57/min [8150000], rate=8732142.86/min [8160000], rate=8742857.14/min [8170000], rate=8753571.43/min [8180000], rate=8764285.71/min [8190000], rate=8621052.63/min [8200000], rate=8631578.95/min [8210000], rate=8642105.26/min [8220000], rate=8652631.58/min [8230000], rate=8663157.89/min [8240000], rate=8673684.21/min [8250000], rate=8684210.53/min [8260000], rate=8694736.84/min [8270000], rate=8705263.16/min [8280000], rate=8715789.47/min [8290000], rate=8726315.79/min [8300000], rate=8736842.11/min [8310000], rate=8747368.42/min [8320000], rate=8757894.74/min [8330000], rate=8768421.05/min [8340000], rate=8627586.21/min [8350000], rate=8637931.03/min [8360000], rate=8648275.86/min [8370000], rate=8658620.69/min [8380000], rate=8668965.52/min [8390000], rate=8679310.34/min [8400000], rate=8689655.17/min [8410000], rate=8700000.00/min [8420000], rate=8710344.83/min [8430000], rate=8720689.66/min [8440000], rate=8731034.48/min [8450000], rate=8741379.31/min [8460000], rate=8751724.14/min [8470000], rate=8613559.32/min [8480000], rate=8623728.81/min [8490000], rate=8633898.31/min [8500000], rate=8644067.80/min [8510000], rate=8654237.29/min [8520000], rate=8664406.78/min [8530000], rate=8674576.27/min [8540000], rate=8684745.76/min [8550000], rate=8694915.25/min [8560000], rate=8705084.75/min [8570000], rate=8715254.24/min [8580000], rate=8725423.73/min [8590000], rate=8735593.22/min [8600000], rate=8745762.71/min [8610000], rate=8610000.00/min [8620000], rate=8620000.00/min [8630000], rate=8630000.00/min [8640000], rate=8640000.00/min [8650000], rate=8650000.00/min [8660000], rate=8660000.00/min [8670000], rate=8670000.00/min [8680000], rate=8680000.00/min [8690000], rate=8690000.00/min [8700000], rate=8700000.00/min [8710000], rate=8710000.00/min [8720000], rate=8720000.00/min [8730000], rate=8730000.00/min [8740000], rate=8740000.00/min [8750000], rate=8750000.00/min [8760000], rate=8616393.44/min [8770000], rate=8626229.51/min [8780000], rate=8636065.57/min [8790000], rate=8645901.64/min [8800000], rate=8655737.70/min [8810000], rate=8665573.77/min [8820000], rate=8675409.84/min [8830000], rate=8685245.90/min [8840000], rate=8695081.97/min [8850000], rate=8704918.03/min 08:57:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-da460d-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-da460d-R1_A23WJ53LT4_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-da460d-R1_A23WJ53LT4_1.introns: identified 5898 cancer introns 08:57:42 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-da460d-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer.introns.prelim 08:57:42 : INFO : Running: touch /tmp/nxf.uhhEzq0aoQ/aih-tih-sc-da460d-R1_A23WJ53LT4_1.chckpts/prelim_introns.ok 08:57:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer.introns 08:57:42 : 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-da460d-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer.introns 08:57:42 : INFO : Running: touch /tmp/nxf.uhhEzq0aoQ/aih-tih-sc-da460d-R1_A23WJ53LT4_1.chckpts/introns_filtered.ok 08:57:42 : INFO : -found 2048 cancer introns 08:57:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-da460d-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-da460d-R1_A23WJ53LT4_1.introns.for_IGV.bed 08:57:43 : INFO : Creating the BED File. 08:57:48 : INFO : Saving Bed File as aih-tih-sc-da460d-R1_A23WJ53LT4_1.introns.for_IGV.bed 08:57:48 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-da460d-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-da460d-R1_A23WJ53LT4_1.introns.for_IGV.bed 08:57:48 : INFO : Running: touch /tmp/nxf.uhhEzq0aoQ/aih-tih-sc-da460d-R1_A23WJ53LT4_1.chckpts/intron_igv_bed.ok 08:57:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-da460d-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-da460d-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-da460d-R1_A23WJ53LT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-da460d-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai 09:20:24 : INFO : Execution Time = 22.59 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-da460d-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-da460d-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-da460d-R1_A23WJ53LT4_1 09:20:24 : INFO : Running: touch /tmp/nxf.uhhEzq0aoQ/aih-tih-sc-da460d-R1_A23WJ53LT4_1.chckpts/reads_alignments_extracted.ok 09:20:24 : INFO : Running: samtools sort -o aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer_intron_reads.bam 09:20:24 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-da460d-R1_A23WJ53LT4_1.cancer_intron_reads.bam 09:20:24 : INFO : Running: touch /tmp/nxf.uhhEzq0aoQ/aih-tih-sc-da460d-R1_A23WJ53LT4_1.chckpts/sort_cancer_intron_reads.ok 09:20:24 : INFO : Running: samtools sort -o aih-tih-sc-da460d-R1_A23WJ53LT4_1.gene_reads.sorted.bam aih-tih-sc-da460d-R1_A23WJ53LT4_1.gene_reads.bam