Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/ac8592b5c90b809658a0ad998a8b4f/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fusionreport.tsv
  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/96/be20de6bb2c097916c221385c5aac9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/be20de6bb2c097916c221385c5aac9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/c64f9385454ba9dcf8fdd0adcd1351/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/c64f9385454ba9dcf8fdd0adcd1351/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fusionreport.tsv --gtf /tmp/nxf.gPbN98xhBb/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.gPbN98xhBb/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fusionreport.tsv --gtf /tmp/nxf.gPbN98xhBb/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.gPbN98xhBb/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.gPbN98xhBb/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa /tmp/nxf.gPbN98xhBb/fi_workdir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa /tmp/nxf.gPbN98xhBb/fi_workdir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa
Running: touch /tmp/nxf.gPbN98xhBb/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf /tmp/nxf.gPbN98xhBb/fi_workdir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf /tmp/nxf.gPbN98xhBb/fi_workdir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf
Running: touch /tmp/nxf.gPbN98xhBb/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf > /tmp/nxf.gPbN98xhBb/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf > /tmp/nxf.gPbN98xhBb/cytoBand.txt
Running: touch /tmp/nxf.gPbN98xhBb/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf > /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed
-parsing GTF file: /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf > /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed
Running: touch /tmp/nxf.gPbN98xhBb/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed > /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed > /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.gPbN98xhBb/chckpts_dir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.gPbN98xhBb/chckpts_dir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.gPbN98xhBb/chckpts_dir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa
Running: touch /tmp/nxf.gPbN98xhBb/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.gPbN98xhBb/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.gPbN98xhBb/fi_workdir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.gPbN98xhBb/fi_workdir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.star --out_dir /tmp/nxf.gPbN98xhBb/fi_workdir --reads "/tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1_1.fastp.fastq.gz /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.gPbN98xhBb/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outSAMtype BAM SortedByCoordinate  --twopassMode None  --alignSJDBoverhangMin 10  --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705  --alignInsertionFlush Right   --alignMatesGapMax 100000  --alignIntronMax 100000  --outSAMattributes All  --readFilesIn /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1_1.fastp.fastq.gz /tmp/nxf.gPbN98xhBb/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.gPbN98xhBb/fi_workdir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.gPbN98xhBb/fi_workdir/aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:10:05 ..... started STAR run
Jun 08 09:10:05 ..... loading genome
Jun 08 09:11:49 ... generating Suffix Array index
Jun 08 09:16:37 ... completed Suffix Array index
Jun 08 09:16:37 ..... processing annotations GTF
Jun 08 09:16:37 ..... inserting junctions into the genome indices
Jun 08 09:17:39 ..... started mapping