Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/bc7ce2596a6859796c9212671b3e7e/tih_rna_sample_00434_B23WHTKLT4_1.Chimeric.out.junction 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/5c/bc7ce2596a6859796c9212671b3e7e/tih_rna_sample_00434_B23WHTKLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/9f4c6a00f739bd2ff08d34286c398e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/bc7ce2596a6859796c9212671b3e7e/tih_rna_sample_00434_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/25b8a1f3c48029e672e16ddf816b2f/tih_rna_sample_00434_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/9f4c6a00f739bd2ff08d34286c398e/.command.run ==> STAGING COMPLETE (7 inputs) 08:53:01 : INFO 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rate=22857142.86/min [8010000], rate=22885714.29/min [8020000], rate=22914285.71/min [8030000], rate=22942857.14/min [8040000], rate=21927272.73/min [8050000], rate=21954545.45/min [8060000], rate=21981818.18/min [8070000], rate=22009090.91/min [8080000], rate=22036363.64/min [8090000], rate=22063636.36/min [8100000], rate=22090909.09/min [8110000], rate=22118181.82/min [8120000], rate=22145454.55/min [8130000], rate=22172727.27/min [8140000], rate=22200000.00/min [8150000], rate=22227272.73/min [8160000], rate=22254545.45/min [8170000], rate=22281818.18/min [8180000], rate=22309090.91/min [8190000], rate=22336363.64/min [8200000], rate=22363636.36/min [8210000], rate=22390909.09/min [8220000], rate=22418181.82/min [8230000], rate=22445454.55/min [8240000], rate=22472727.27/min [8250000], rate=22500000.00/min [8260000], rate=22527272.73/min [8270000], rate=22554545.45/min [8280000], rate=22581818.18/min [8290000], rate=22609090.91/min [8300000], rate=22636363.64/min [8310000], rate=22663636.36/min [8320000], rate=22690909.09/min [8330000], rate=22718181.82/min [8340000], rate=22745454.55/min [8350000], rate=22772727.27/min [8360000], rate=22800000.00/min [8370000], rate=22827272.73/min [8380000], rate=22854545.45/min [8390000], rate=22881818.18/min [8400000], rate=22909090.91/min [8410000], rate=22936363.64/min [8420000], rate=22963636.36/min [8430000], rate=22990909.09/min [8440000], rate=23018181.82/min [8450000], rate=22043478.26/min [8460000], rate=22069565.22/min [8470000], rate=22095652.17/min [8480000], rate=22121739.13/min [8490000], rate=22147826.09/min [8500000], rate=22173913.04/min [8510000], rate=22200000.00/min [8520000], rate=22226086.96/min [8530000], rate=22252173.91/min [8540000], rate=22278260.87/min [8550000], rate=22304347.83/min [8560000], rate=22330434.78/min [8570000], rate=22356521.74/min [8580000], rate=22382608.70/min [8590000], rate=22408695.65/min [8600000], rate=22434782.61/min [8610000], rate=22460869.57/min [8620000], rate=22486956.52/min [8630000], rate=22513043.48/min [8640000], rate=22539130.43/min [8650000], rate=22565217.39/min [8660000], rate=22591304.35/min [8670000], rate=22617391.30/min [8680000], rate=22643478.26/min [8690000], rate=22669565.22/min [8700000], rate=22695652.17/min [8710000], rate=22721739.13/min [8720000], rate=22747826.09/min [8730000], rate=22773913.04/min [8740000], rate=22800000.00/min [8750000], rate=22826086.96/min [8760000], rate=22852173.91/min [8770000], rate=22878260.87/min [8780000], rate=22904347.83/min [8790000], rate=21975000.00/min [8800000], rate=22000000.00/min [8810000], rate=22025000.00/min [8820000], rate=22050000.00/min [8830000], rate=22075000.00/min [8840000], rate=22100000.00/min 08:53:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00434_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00434_B23WHTKLT4_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_00434_B23WHTKLT4_1.introns: identified 4609 cancer introns 08:53:32 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00434_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00434_B23WHTKLT4_1.cancer.introns.prelim 08:53:32 : INFO : Running: touch /tmp/nxf.xsqFs0lqsf/tih_rna_sample_00434_B23WHTKLT4_1.chckpts/prelim_introns.ok 08:53:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00434_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00434_B23WHTKLT4_1.cancer.introns 08:53:32 : 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_00434_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00434_B23WHTKLT4_1.cancer.introns 08:53:32 : INFO : Running: touch /tmp/nxf.xsqFs0lqsf/tih_rna_sample_00434_B23WHTKLT4_1.chckpts/introns_filtered.ok 08:53:32 : INFO : -found 2645 cancer introns 08:53:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00434_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00434_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00434_B23WHTKLT4_1.introns.for_IGV.bed 08:53:32 : INFO : Creating the BED File. 08:53:37 : INFO : Saving Bed File as tih_rna_sample_00434_B23WHTKLT4_1.introns.for_IGV.bed 08:53:37 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00434_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00434_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00434_B23WHTKLT4_1.introns.for_IGV.bed 08:53:37 : INFO : Running: touch /tmp/nxf.xsqFs0lqsf/tih_rna_sample_00434_B23WHTKLT4_1.chckpts/intron_igv_bed.ok 08:53:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00434_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00434_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00434_B23WHTKLT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00434_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai 09:07:54 : INFO : Execution Time = 14.28 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00434_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00434_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00434_B23WHTKLT4_1 09:07:54 : INFO : Running: touch /tmp/nxf.xsqFs0lqsf/tih_rna_sample_00434_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok 09:07:54 : INFO : Running: samtools sort -o tih_rna_sample_00434_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00434_B23WHTKLT4_1.cancer_intron_reads.bam 09:07:55 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00434_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00434_B23WHTKLT4_1.cancer_intron_reads.bam 09:07:55 : INFO : Running: touch /tmp/nxf.xsqFs0lqsf/tih_rna_sample_00434_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok 09:07:55 : INFO : Running: samtools sort -o tih_rna_sample_00434_B23WHTKLT4_1.gene_reads.sorted.bam tih_rna_sample_00434_B23WHTKLT4_1.gene_reads.bam