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/ec/46d6be99fcda8e23d0e22f984645be/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/33bed37e769455eccf1349050b417f/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/33bed37e769455eccf1349050b417f/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/cb1a8165fb0443d527b62710da32fb/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/33bed37e769455eccf1349050b417f/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/46d6be99fcda8e23d0e22f984645be/.command.run ==> STAGING COMPLETE (7 inputs) 08:50:13 : INFO 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[8020000], rate=8020000.00/min [8030000], rate=8030000.00/min [8040000], rate=8040000.00/min [8050000], rate=8050000.00/min [8060000], rate=8060000.00/min [8070000], rate=8070000.00/min [8080000], rate=8080000.00/min [8090000], rate=8090000.00/min [8100000], rate=7967213.11/min [8110000], rate=7977049.18/min [8120000], rate=7986885.25/min [8130000], rate=7996721.31/min [8140000], rate=8006557.38/min [8150000], rate=8016393.44/min [8160000], rate=8026229.51/min [8170000], rate=8036065.57/min [8180000], rate=8045901.64/min [8190000], rate=8055737.70/min [8200000], rate=8065573.77/min [8210000], rate=8075409.84/min [8220000], rate=8085245.90/min [8230000], rate=8095081.97/min [8240000], rate=8104918.03/min [8250000], rate=8114754.10/min [8260000], rate=8124590.16/min [8270000], rate=8134426.23/min [8280000], rate=8012903.23/min [8290000], rate=8022580.65/min [8300000], rate=8032258.06/min [8310000], rate=8041935.48/min [8320000], rate=8051612.90/min [8330000], rate=8061290.32/min [8340000], rate=8070967.74/min [8350000], rate=8080645.16/min [8360000], rate=8090322.58/min [8370000], rate=8100000.00/min [8380000], rate=8109677.42/min [8390000], rate=8119354.84/min [8400000], rate=8129032.26/min [8410000], rate=8138709.68/min [8420000], rate=8148387.10/min [8430000], rate=8158064.52/min [8440000], rate=8167741.94/min [8450000], rate=8177419.35/min [8460000], rate=8187096.77/min [8470000], rate=8066666.67/min [8480000], rate=8076190.48/min [8490000], rate=8085714.29/min [8500000], rate=8095238.10/min [8510000], rate=8104761.90/min [8520000], rate=8114285.71/min [8530000], rate=8123809.52/min [8540000], rate=8133333.33/min [8550000], rate=8142857.14/min [8560000], rate=8152380.95/min 08:51:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1.introns: identified 7955 cancer introns 08:51:28 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer.introns.prelim 08:51:28 : INFO : Running: touch /tmp/nxf.1hLEApIuzq/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 08:51:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer.introns 08:51:29 : 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-f6bb6f-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer.introns 08:51:29 : INFO : Running: touch /tmp/nxf.1hLEApIuzq/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 08:51:29 : INFO : -found 3336 cancer introns 08:51:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:51:29 : INFO : Creating the BED File. 08:51:40 : INFO : Saving Bed File as aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:51:40 : INFO : Execution Time = 0.18 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:51:40 : INFO : Running: touch /tmp/nxf.1hLEApIuzq/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 08:51:40 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 09:25:51 : INFO : Execution Time = 34.19 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1 09:25:51 : INFO : Running: touch /tmp/nxf.1hLEApIuzq/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 09:25:51 : INFO : Running: samtools sort -o aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:25:53 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:25:53 : INFO : Running: touch /tmp/nxf.1hLEApIuzq/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 09:25:53 : INFO : Running: samtools sort -o aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.gene_reads.bam