Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/1285b252a8ed0b6ef804e8232d816d/tih_rna_sample_00261_23H5VFLT4_s06.Aligned.sortedByCoord.out.bam.bai
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/98/49b2f2ef019408597a1cce83c49871/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/51bd193d442ae86570083bea8ce863/tih_rna_sample_00261_23H5VFLT4_s06.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/51bd193d442ae86570083bea8ce863/tih_rna_sample_00261_23H5VFLT4_s06.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/49b2f2ef019408597a1cce83c49871/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/51bd193d442ae86570083bea8ce863/tih_rna_sample_00261_23H5VFLT4_s06.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
08:37:03 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10460000], rate=14595348.84/min
[10470000], rate=14609302.33/min
[10480000], rate=14623255.81/min
[10490000], rate=14637209.30/min
[10500000], rate=14318181.82/min
[10510000], rate=14331818.18/min
[10520000], rate=14345454.55/min
[10530000], rate=14359090.91/min
[10540000], rate=14372727.27/min
[10550000], rate=14386363.64/min
[10560000], rate=14400000.00/min
[10570000], rate=14413636.36/min
[10580000], rate=14427272.73/min
[10590000], rate=14440909.09/min
[10600000], rate=14454545.45/min
[10610000], rate=14468181.82/min
[10620000], rate=14481818.18/min
[10630000], rate=14495454.55/min
[10640000], rate=14509090.91/min
[10650000], rate=14522727.27/min
[10660000], rate=14536363.64/min
[10670000], rate=14550000.00/min
[10680000], rate=14563636.36/min
[10690000], rate=14577272.73/min
[10700000], rate=14590909.09/min
[10710000], rate=14280000.00/min
[10720000], rate=14293333.33/min
[10730000], rate=14306666.67/min
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[10750000], rate=14333333.33/min
[10760000], rate=14346666.67/min
[10770000], rate=14360000.00/min
[10780000], rate=14373333.33/min
[10790000], rate=14386666.67/min
[10800000], rate=14400000.00/min
[10810000], rate=14413333.33/min
[10820000], rate=14426666.67/min
[10830000], rate=14440000.00/min
[10840000], rate=14453333.33/min
[10850000], rate=14466666.67/min
[10860000], rate=14480000.00/min
[10870000], rate=14493333.33/min
[10880000], rate=14506666.67/min
[10890000], rate=14204347.83/min
[10900000], rate=14217391.30/min
[10910000], rate=14230434.78/min
[10920000], rate=14243478.26/min
[10930000], rate=14256521.74/min
[10940000], rate=14269565.22/min
[10950000], rate=14282608.70/min
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[10970000], rate=14308695.65/min
[10980000], rate=14321739.13/min
[10990000], rate=14334782.61/min
[11000000], rate=14347826.09/min
[11010000], rate=14360869.57/min
[11020000], rate=14373913.04/min
[11030000], rate=14080851.06/min
[11040000], rate=14093617.02/min
[11050000], rate=14106382.98/min
[11060000], rate=14119148.94/min
[11070000], rate=14131914.89/min
[11080000], rate=14144680.85/min
[11090000], rate=14157446.81/min
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[11110000], rate=14182978.72/min
[11120000], rate=14195744.68/min
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[11140000], rate=14221276.60/min
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[11160000], rate=14246808.51/min
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[11180000], rate=13975000.00/min
[11190000], rate=13987500.00/min
[11200000], rate=14000000.00/min 08:38:01 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00261_23H5VFLT4_s06.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00261_23H5VFLT4_s06.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_00261_23H5VFLT4_s06.introns: identified 5993 cancer introns
08:38:02 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00261_23H5VFLT4_s06.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00261_23H5VFLT4_s06.cancer.introns.prelim
08:38:02 : INFO : Running: touch /tmp/nxf.o0CdH3Sh3x/tih_rna_sample_00261_23H5VFLT4_s06.chckpts/prelim_introns.ok
08:38:02 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00261_23H5VFLT4_s06.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00261_23H5VFLT4_s06.cancer.introns
08:38:02 : 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_00261_23H5VFLT4_s06.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00261_23H5VFLT4_s06.cancer.introns
08:38:02 : INFO : Running: touch /tmp/nxf.o0CdH3Sh3x/tih_rna_sample_00261_23H5VFLT4_s06.chckpts/introns_filtered.ok
08:38:02 : INFO : -found 2915 cancer introns
08:38:02 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00261_23H5VFLT4_s06.introns --cancer_introns tih_rna_sample_00261_23H5VFLT4_s06.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00261_23H5VFLT4_s06.introns.for_IGV.bed
08:38:03 : INFO : Creating the BED File.
08:38:10 : INFO : Saving Bed File as tih_rna_sample_00261_23H5VFLT4_s06.introns.for_IGV.bed
08:38:11 : INFO : Execution Time = 0.13 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00261_23H5VFLT4_s06.introns --cancer_introns tih_rna_sample_00261_23H5VFLT4_s06.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00261_23H5VFLT4_s06.introns.for_IGV.bed
08:38:11 : INFO : Running: touch /tmp/nxf.o0CdH3Sh3x/tih_rna_sample_00261_23H5VFLT4_s06.chckpts/intron_igv_bed.ok
08:38:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00261_23H5VFLT4_s06.introns.for_IGV.bed --bam tih_rna_sample_00261_23H5VFLT4_s06.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00261_23H5VFLT4_s06
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00261_23H5VFLT4_s06.Aligned.sortedByCoord.out.bam.bai
09:03:27 : INFO : Execution Time = 25.27 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00261_23H5VFLT4_s06.introns.for_IGV.bed --bam tih_rna_sample_00261_23H5VFLT4_s06.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00261_23H5VFLT4_s06
09:03:27 : INFO : Running: touch /tmp/nxf.o0CdH3Sh3x/tih_rna_sample_00261_23H5VFLT4_s06.chckpts/reads_alignments_extracted.ok
09:03:27 : INFO : Running: samtools sort -o tih_rna_sample_00261_23H5VFLT4_s06.cancer_intron_reads.sorted.bam tih_rna_sample_00261_23H5VFLT4_s06.cancer_intron_reads.bam
09:03:28 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00261_23H5VFLT4_s06.cancer_intron_reads.sorted.bam tih_rna_sample_00261_23H5VFLT4_s06.cancer_intron_reads.bam
09:03:28 : INFO : Running: touch /tmp/nxf.o0CdH3Sh3x/tih_rna_sample_00261_23H5VFLT4_s06.chckpts/sort_cancer_intron_reads.ok
09:03:28 : INFO : Running: samtools sort -o tih_rna_sample_00261_23H5VFLT4_s06.gene_reads.sorted.bam tih_rna_sample_00261_23H5VFLT4_s06.gene_reads.bam