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/5f/581ba393ace8bbb2d9de177f562dae/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/f36b3f057f24a28819615a2798e32f/tih_rna_sample_00669_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/f36b3f057f24a28819615a2798e32f/tih_rna_sample_00669_B23MVV7LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/f36b3f057f24a28819615a2798e32f/tih_rna_sample_00669_B23MVV7LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/eaa91f4c3e91c6ff46743a70ef35ee/tih_rna_sample_00669_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/581ba393ace8bbb2d9de177f562dae/.command.run ==> STAGING COMPLETE (7 inputs) 08:47:57 : INFO 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rate=20815384.62/min [9030000], rate=20838461.54/min [9040000], rate=20861538.46/min [9050000], rate=20884615.38/min [9060000], rate=20907692.31/min [9070000], rate=20930769.23/min [9080000], rate=20953846.15/min [9090000], rate=20976923.08/min [9100000], rate=21000000.00/min [9110000], rate=21023076.92/min [9120000], rate=21046153.85/min [9130000], rate=21069230.77/min [9140000], rate=21092307.69/min [9150000], rate=21115384.62/min [9160000], rate=21138461.54/min [9170000], rate=21161538.46/min [9180000], rate=21184615.38/min [9190000], rate=21207692.31/min [9200000], rate=21230769.23/min [9210000], rate=21253846.15/min [9220000], rate=21276923.08/min [9230000], rate=21300000.00/min [9240000], rate=21323076.92/min [9250000], rate=21346153.85/min [9260000], rate=21369230.77/min [9270000], rate=20600000.00/min [9280000], rate=20622222.22/min [9290000], rate=20644444.44/min [9300000], rate=20666666.67/min [9310000], rate=20688888.89/min [9320000], rate=20711111.11/min [9330000], rate=20733333.33/min [9340000], rate=20755555.56/min [9350000], rate=20777777.78/min [9360000], rate=20800000.00/min [9370000], rate=20822222.22/min [9380000], rate=20844444.44/min [9390000], rate=20866666.67/min [9400000], rate=20888888.89/min [9410000], rate=20911111.11/min [9420000], rate=20933333.33/min [9430000], rate=20955555.56/min [9440000], rate=20977777.78/min [9450000], rate=21000000.00/min [9460000], rate=21022222.22/min [9470000], rate=21044444.44/min [9480000], rate=21066666.67/min [9490000], rate=21088888.89/min [9500000], rate=21111111.11/min [9510000], rate=21133333.33/min [9520000], rate=21155555.56/min [9530000], rate=21177777.78/min [9540000], rate=21200000.00/min [9550000], rate=21222222.22/min [9560000], rate=21244444.44/min [9570000], rate=21266666.67/min [9580000], rate=21288888.89/min [9590000], rate=21311111.11/min [9600000], rate=21333333.33/min [9610000], rate=21355555.56/min [9620000], rate=21377777.78/min [9630000], rate=21400000.00/min [9640000], rate=21422222.22/min [9650000], rate=21444444.44/min [9660000], rate=20700000.00/min [9670000], rate=20721428.57/min [9680000], rate=20742857.14/min [9690000], rate=20764285.71/min [9700000], rate=20785714.29/min [9710000], rate=20807142.86/min [9720000], rate=20828571.43/min [9730000], rate=20850000.00/min [9740000], rate=20871428.57/min [9750000], rate=20892857.14/min 08:48:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00669_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00669_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_00669_B23MVV7LT4_1.introns: identified 7190 cancer introns 08:48:32 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00669_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00669_B23MVV7LT4_1.cancer.introns.prelim 08:48:32 : INFO : Running: touch /tmp/nxf.g47Y9z1nSz/tih_rna_sample_00669_B23MVV7LT4_1.chckpts/prelim_introns.ok 08:48:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00669_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00669_B23MVV7LT4_1.cancer.introns 08:48:33 : 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_00669_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00669_B23MVV7LT4_1.cancer.introns 08:48:33 : INFO : Running: touch /tmp/nxf.g47Y9z1nSz/tih_rna_sample_00669_B23MVV7LT4_1.chckpts/introns_filtered.ok 08:48:33 : INFO : -found 3201 cancer introns 08:48:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00669_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00669_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00669_B23MVV7LT4_1.introns.for_IGV.bed 08:48:33 : INFO : Creating the BED File. 08:48:39 : INFO : Saving Bed File as tih_rna_sample_00669_B23MVV7LT4_1.introns.for_IGV.bed 08:48:39 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00669_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00669_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00669_B23MVV7LT4_1.introns.for_IGV.bed 08:48:39 : INFO : Running: touch /tmp/nxf.g47Y9z1nSz/tih_rna_sample_00669_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 08:48:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00669_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00669_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00669_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00669_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:06:57 : INFO : Execution Time = 18.29 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00669_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00669_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00669_B23MVV7LT4_1 09:06:57 : INFO : Running: touch /tmp/nxf.g47Y9z1nSz/tih_rna_sample_00669_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:06:57 : INFO : Running: samtools sort -o tih_rna_sample_00669_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00669_B23MVV7LT4_1.cancer_intron_reads.bam 09:06:58 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00669_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00669_B23MVV7LT4_1.cancer_intron_reads.bam 09:06:58 : INFO : Running: touch /tmp/nxf.g47Y9z1nSz/tih_rna_sample_00669_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:06:58 : INFO : Running: samtools sort -o tih_rna_sample_00669_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00669_B23MVV7LT4_1.gene_reads.bam