Mon Feb 20 15:29:27 PST 2017 /oasis/projects/nsf/lji100/mik/ncRNA/Ranzani_data/trinity_scripts /scratch/mik/7741707 Trinity version: __BLEEDING_EDGE__ Monday, February 20, 2017: 15:29:29 CMD: /home/mik/apps/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam ** NOTE: Latest version of Trinity is Trinity-v2.4.0, and can be obtained at: https://github.com/trinityrnaseq/trinityrnaseq/releases -appears to be a coordinate sorted bam file. ok. Monday, February 20, 2017: 15:29:29 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/mik/apps/trinityrnaseq/util/support_scripts/ExitTester.jar 0 Monday, February 20, 2017: 15:29:29 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/mik/apps/trinityrnaseq/util/support_scripts/ExitTester.jar 1 Monday, February 20, 2017: 15:29:29 CMD: mkdir -p /scratch/mik/7741707/trinity_ranzani_merged STARTING COLLECTL I'M THE PARENT, COLLECTL_PID=12155 I'M THE CHILD RUNNING TRINITY Running CMD: bash -c "set -eou pipefail && cd /scratch/mik/7741707/collectl && exec nohup /home/mik/apps/trinityrnaseq/trinity-plugins/COLLECTL/collectl/collectl --procopts w --procfilt u515756 --interval :60 -sZ -oD | egrep 'Trinity|trinityrnaseq|Inchworm|Chrysalis|Butterfly|jellyfish|samtools|sort|bowtie' | egrep -v 'egrep' > /scratch/mik/7741707/collectl/collectl.dat " ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- Monday, February 20, 2017: 15:29:29 CMD: samtools index /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam Monday, February 20, 2017: 15:36:05 CMD: /home/mik/apps/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam -I 100000 --sort_buffer 400G --CPU 24 CMD: /home/mik/apps/trinityrnaseq/util/support_scripts//SAM_to_frag_coords.pl --CPU 24 --sort_buffer 400G --sam /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam --min_insert_size 1 --max_insert_size 100000 -extracting read coordinates from /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam into /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.read_coords CMD: touch /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.read_coords.ok CMD: /bin/sort -S400G -T . -k1,1 -k2,2 -k4,4n /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.read_coords > /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.read_coords.sort_by_readname CMD: /bin/sort -S400G -T . -k1,1 -k3,3n /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.frag_coords > /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.frag_coords.coord_sorted CMD: /home/mik/apps/trinityrnaseq/util/support_scripts//fragment_coverage_writer.pl /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.frag_coords > /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.frag_coverage.wig CMD: /home/mik/apps/trinityrnaseq/util/support_scripts//define_coverage_partitions.pl /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.frag_coverage.wig 1 + > /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.minC1.gff CMD: touch /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.minC1.gff.ok CMD: /home/mik/apps/trinityrnaseq/util/support_scripts//extract_reads_per_partition.pl --partitions_gff /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.minC1.gff --coord_sorted_SAM /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam --parts_per_directory 100 --min_reads_per_partition 10 // parsing paritions. CMD: touch Dir_all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam.minC1.gff.ok ## Done ## Tuesday, February 21, 2017: 13:34:43 CMD: touch partitions.ok Tuesday, February 21, 2017: 13:34:43 CMD: find Dir_* -name '*reads' > read_files.list Tuesday, February 21, 2017: 13:34:43 CMD: touch read_files.list.ok Tuesday, February 21, 2017: 13:34:43 CMD: /home/mik/apps/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G --seqType fa --trinity_complete --full_cleanup > trinity_GG.cmds Tuesday, February 21, 2017: 13:34:44 CMD: touch trinity_GG.cmds.ok Tuesday, February 21, 2017: 13:34:44 CMD: touch trinity_GG.cmds.ok -------------------------------------------------------------------------------- ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- -------------------------------------------------------------------------------- Tuesday, February 21, 2017: 13:34:44 CMD: /home/mik/apps/trinityrnaseq/trinity-plugins/parafly/bin/ParaFly -c trinity_GG.cmds -CPU 24 -v -shuffle Number of Commands: 86533 All commands completed successfully. :-) Wednesday, February 22, 2017: 10:19:06 CMD: find Dir_* -name '*inity.fasta' | /home/mik/apps/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > Trinity-GG.fasta.tmp Finished. See Trinity-GG.fasta for reconstructed transcripts TERMINATING COLLECTL, PID = 12155 Wed Feb 22 10:45:15 PST 2017 #!/bin/bash ############################################################## #SBATCH --job-name="Trinity_R_all" #SBATCH --output="Trinity_R_all.%j.%N.out" #SBATCH --partition=large-shared #SBATCH --nodes=1 #SBATCH --mem=400G #SBATCH --export=ALL #SBATCH --ntasks-per-node=24 #SBATCH -t 48:00:00 date cd $PWD pwd cd /scratch/mik/$SLURM_JOBID pwd /home/mik/apps/trinityrnaseq/Trinity --monitoring --genome_guided_bam /oasis/scratch/comet/mik/temp_project/Ranzani_data/all_cell_types_vs_hg38_gencode_25.bamAligned.sortedByCoord.out.mapq2.sorted.bam --genome_guided_max_intron 100000 --max_memory 400G --CPU 24 --output /scratch/mik/$SLURM_JOBID/trinity_ranzani_merged cp -r /scratch/mik/$SLURM_JOBID /oasis/scratch/comet/mik/temp_project/$SLURM_JOBID date cat $0 ###############################################################