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/06/d8921bc046969e3bc2be9da1154f10/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/4d236ec70a548a0aeba345f9e0e72c/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/4d236ec70a548a0aeba345f9e0e72c/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/a5e90534942619c8a8751eda0bc6ea/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/d8921bc046969e3bc2be9da1154f10/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/4d236ec70a548a0aeba345f9e0e72c/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)

07:31:54 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

[140000], rate=8400000.00/min 
[150000], rate=9000000.00/min 
[160000], rate=9600000.00/min 
[170000], rate=10200000.00/min 
[180000], rate=10800000.00/min 
[190000], rate=11400000.00/min 
[200000], rate=12000000.00/min 07:32:02 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_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.
-1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 163 cancer introns
07:32:03 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim 
07:32:03 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok
07:32:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5  > 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 
07:32:03 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5  > 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 
07:32:03 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok
07:32:03 : INFO : -found 11 cancer introns
07:32:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns  --cancer_introns 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 
07:32:04 : INFO :  Creating the BED File.
07:32:04 : INFO : Saving Bed File as 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:32:04 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns  --cancer_introns 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 
07:32:04 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok
07:32:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed  --bam 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1 
[W::hts_idx_load3] The index file is older than the data file: 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
07:32:05 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed  --bam 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1 
07:32:05 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok
07:32:05 : INFO : Running: samtools sort -o 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
07:32:05 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
07:32:05 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok
07:32:05 : INFO : Running: samtools sort -o 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
07:32:05 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
07:32:05 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok
07:32:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 
Done with chr chr1.
Done with chr chr5.
Done with chr chr7.
Done with chr chr8.
Done with chr chr9.
Done with chr chr14.
07:32:05 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 
07:32:05 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:32:05 : INFO : Running: samtools sort -o 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
07:32:06 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
07:32:06 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:32:06 : INFO : Running: samtools index 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 
07:32:06 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 
07:32:06 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:32:06 : INFO : Running: samtools index 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 
07:32:06 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 
07:32:06 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:32:06 : INFO : Running: create_report 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html  --track-config 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1' 
07:32:08 : INFO : Execution Time = 0.03 minutes. CMD: create_report 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html  --track-config 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: 1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1' 
07:32:08 : INFO : Running: touch /tmp/nxf.Efq5LUU2ND/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok
07:32:08 : INFO : done.