Left read files: $VAR1 = [ '/gscratch/srlab/graceac9/data/304428_S1_L001_R1_001.fastq', '/gscratch/srlab/graceac9/data/304428_S1_L002_R1_001.fastq' ]; Right read files: $VAR1 = [ '/gscratch/srlab/graceac9/data/304428_S1_L001_R2_001.fastq', '/gscratch/srlab/graceac9/data/304428_S1_L002_R2_001.fastq' ]; Trinity version: Trinity-v2.4.0 -ERROR: couldn't run the network check to confirm latest Trinity software version. Friday, October 26, 2018: 06:05:59 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /gscratch/srlab/programs/trinity/util/support_scripts/ExitTester.jar 0 Friday, October 26, 2018: 06:05:59 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /gscratch/srlab/programs/trinity/util/support_scripts/ExitTester.jar 1 Friday, October 26, 2018: 06:06:00 CMD: mkdir -p /gscratch/srlab/sr320/analyses/1026/trinity_out_dir Friday, October 26, 2018: 06:06:00 CMD: mkdir -p /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- --------------------------------------------------------------- ------ Quality Trimming Via Trimmomatic --------------------- << ILLUMINACLIP:/gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >> --------------------------------------------------------------- ## Running Trimmomatic on read files: /gscratch/srlab/graceac9/data/304428_S1_L001_R1_001.fastq, /gscratch/srlab/graceac9/data/304428_S1_L001_R2_001.fastq Friday, October 26, 2018: 06:06:00 CMD: java -jar /gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/trimmomatic.jar PE -threads 28 -phred33 /gscratch/srlab/graceac9/data/304428_S1_L001_R1_001.fastq /gscratch/srlab/graceac9/data/304428_S1_L001_R2_001.fastq 304428_S1_L001_R1_001.fastq.P.qtrim 304428_S1_L001_R1_001.fastq.U.qtrim 304428_S1_L001_R2_001.fastq.P.qtrim 304428_S1_L001_R2_001.fastq.U.qtrim ILLUMINACLIP:/gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 TrimmomaticPE: Started with arguments: -threads 28 -phred33 /gscratch/srlab/graceac9/data/304428_S1_L001_R1_001.fastq /gscratch/srlab/graceac9/data/304428_S1_L001_R2_001.fastq 304428_S1_L001_R1_001.fastq.P.qtrim 304428_S1_L001_R1_001.fastq.U.qtrim 304428_S1_L001_R2_001.fastq.P.qtrim 304428_S1_L001_R2_001.fastq.U.qtrim ILLUMINACLIP:/gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Read Pairs: 243 Both Surviving: 239 (98.35%) Forward Only Surviving: 4 (1.65%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully Friday, October 26, 2018: 06:06:00 CMD: cp 304428_S1_L001_R1_001.fastq.P.qtrim 304428_S1_L001_R1_001.fastq.PwU.qtrim.fq Friday, October 26, 2018: 06:06:00 CMD: cp 304428_S1_L001_R2_001.fastq.P.qtrim 304428_S1_L001_R2_001.fastq.PwU.qtrim.fq Friday, October 26, 2018: 06:06:00 CMD: touch trimmomatic.ok Friday, October 26, 2018: 06:06:00 CMD: gzip 304428_S1_L001_R1_001.fastq.P.qtrim 304428_S1_L001_R1_001.fastq.U.qtrim 304428_S1_L001_R2_001.fastq.P.qtrim 304428_S1_L001_R2_001.fastq.U.qtrim & ## Running Trimmomatic on read files: /gscratch/srlab/graceac9/data/304428_S1_L002_R1_001.fastq, /gscratch/srlab/graceac9/data/304428_S1_L002_R2_001.fastq Friday, October 26, 2018: 06:06:00 CMD: java -jar /gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/trimmomatic.jar PE -threads 28 -phred33 /gscratch/srlab/graceac9/data/304428_S1_L002_R1_001.fastq /gscratch/srlab/graceac9/data/304428_S1_L002_R2_001.fastq 304428_S1_L002_R1_001.fastq.P.qtrim 304428_S1_L002_R1_001.fastq.U.qtrim 304428_S1_L002_R2_001.fastq.P.qtrim 304428_S1_L002_R2_001.fastq.U.qtrim ILLUMINACLIP:/gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 TrimmomaticPE: Started with arguments: -threads 28 -phred33 /gscratch/srlab/graceac9/data/304428_S1_L002_R1_001.fastq /gscratch/srlab/graceac9/data/304428_S1_L002_R2_001.fastq 304428_S1_L002_R1_001.fastq.P.qtrim 304428_S1_L002_R1_001.fastq.U.qtrim 304428_S1_L002_R2_001.fastq.P.qtrim 304428_S1_L002_R2_001.fastq.U.qtrim ILLUMINACLIP:/gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Read Pairs: 243 Both Surviving: 237 (97.53%) Forward Only Surviving: 6 (2.47%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticPE: Completed successfully Friday, October 26, 2018: 06:06:00 CMD: cp 304428_S1_L002_R1_001.fastq.P.qtrim 304428_S1_L002_R1_001.fastq.PwU.qtrim.fq Friday, October 26, 2018: 06:06:00 CMD: cp 304428_S1_L002_R2_001.fastq.P.qtrim 304428_S1_L002_R2_001.fastq.PwU.qtrim.fq Friday, October 26, 2018: 06:06:00 CMD: touch trimmomatic.ok Friday, October 26, 2018: 06:06:00 CMD: gzip 304428_S1_L002_R1_001.fastq.P.qtrim 304428_S1_L002_R1_001.fastq.U.qtrim 304428_S1_L002_R2_001.fastq.P.qtrim 304428_S1_L002_R2_001.fastq.U.qtrim & --------------------------------------------------------------- ------------ In silico Read Normalization --------------------- -- (Removing Excess Reads Beyond 50 Coverage -- --------------------------------------------------------------- # running normalization on reads: $VAR1 = [ [ '304428_S1_L001_R1_001.fastq.PwU.qtrim.fq', '304428_S1_L002_R1_001.fastq.PwU.qtrim.fq' ], [ '304428_S1_L001_R2_001.fastq.PwU.qtrim.fq', '304428_S1_L002_R2_001.fastq.PwU.qtrim.fq' ] ]; Friday, October 26, 2018: 06:06:00 CMD: /gscratch/srlab/programs/trinity/util/insilico_read_normalization.pl --seqType fq --JM 100G --max_cov 50 --CPU 28 --output /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization --max_pct_stdev 10000 --left 304428_S1_L001_R1_001.fastq.PwU.qtrim.fq,304428_S1_L002_R1_001.fastq.PwU.qtrim.fq --right 304428_S1_L001_R2_001.fastq.PwU.qtrim.fq,304428_S1_L002_R2_001.fastq.PwU.qtrim.fq --pairs_together --PARALLEL_STATS Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/304428_S1_L001_R1_001.fastq.PwU.qtrim.fq >> left.fa CMD: seqtk-trinity seq -A /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/304428_S1_L001_R2_001.fastq.PwU.qtrim.fq >> right.fa CMD finished (0 seconds) CMD: seqtk-trinity seq -A /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/304428_S1_L002_R1_001.fastq.PwU.qtrim.fq >> left.fa CMD finished (0 seconds) CMD: seqtk-trinity seq -A /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/304428_S1_L002_R2_001.fastq.PwU.qtrim.fq >> right.fa CMD finished (0 seconds) CMD finished (0 seconds) CMD: touch left.fa.ok CMD finished (0 seconds) CMD: touch right.fa.ok CMD finished (0 seconds) Done converting input files.CMD: cat left.fa right.fa > both.fa CMD finished (0 seconds) CMD: touch both.fa.ok ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- CMD finished (0 seconds) CMD: /gscratch/srlab/programs/trinity/util/..//trinity-plugins/jellyfish/bin/jellyfish count -t 28 -m 25 -s 100000000 --canonical both.fa CMD finished (0 seconds) CMD: /gscratch/srlab/programs/trinity/util/..//trinity-plugins/jellyfish/bin/jellyfish histo -t 28 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD finished (0 seconds) CMD: /gscratch/srlab/programs/trinity/util/..//trinity-plugins/jellyfish/bin/jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa CMD finished (0 seconds) CMD: touch jellyfish.K25.min2.kmers.fa.success CMD finished (0 seconds) CMD: /gscratch/srlab/programs/trinity/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 --DS > left.fa.K25.stats CMD: /gscratch/srlab/programs/trinity/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 --DS > right.fa.K25.stats -reading Kmer occurrences... -reading Kmer occurrences... done parsing 10842 Kmers, 10842 added, taking 0 seconds. done parsing 10842 Kmers, 10842 added, taking 0 seconds. STATS_GENERATION_TIME: 0 seconds. CMD finished (0 seconds) STATS_GENERATION_TIME: 0 seconds. CMD finished (0 seconds) CMD: touch left.fa.K25.stats.ok CMD finished (0 seconds) CMD: touch right.fa.K25.stats.ok -sorting each stats file by read name. CMD finished (0 seconds) CMD: /usr/bin/sort --parallel=28 -k5,5 -T . -S 50G left.fa.K25.stats > left.fa.K25.stats.sort CMD: /usr/bin/sort --parallel=28 -k5,5 -T . -S 50G right.fa.K25.stats > right.fa.K25.stats.sort CMD finished (0 seconds) CMD finished (0 seconds) CMD: touch left.fa.K25.stats.sort.ok CMD finished (0 seconds) CMD: touch right.fa.K25.stats.sort.ok CMD finished (0 seconds) CMD: /gscratch/srlab/programs/trinity/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats -opening left.fa.K25.stats.sort -opening right.fa.K25.stats.sort -done opening files. CMD finished (0 seconds) CMD: touch pairs.K25.stats.ok CMD finished (0 seconds) CMD: /gscratch/srlab/programs/trinity/util/..//util/support_scripts//nbkc_normalize.pl pairs.K25.stats 50 10000 > pairs.K25.stats.C50.pctSD10000.accs 476 / 476 = 100.00% reads selected during normalization. 0 / 476 = 0.00% reads discarded as likely aberrant based on coverage profiles. 0 / 476 = 0.00% reads missing kmer coverage (N chars included?). CMD finished (0 seconds) CMD: touch pairs.K25.stats.C50.pctSD10000.accs.ok CMD finished (0 seconds) CMD: touch /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/304428_S1_L001_R1_001.fastq.PwU.qtrim.fq_ext_all_reads.normalized_K25_C50_pctSD10000.fq.ok CMD finished (0 seconds) CMD: touch /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/304428_S1_L001_R2_001.fastq.PwU.qtrim.fq_ext_all_reads.normalized_K25_C50_pctSD10000.fq.ok CMD finished (0 seconds) CMD: ln -sf /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/304428_S1_L001_R1_001.fastq.PwU.qtrim.fq_ext_all_reads.normalized_K25_C50_pctSD10000.fq left.norm.fq CMD finished (0 seconds) CMD: ln -sf /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/304428_S1_L001_R2_001.fastq.PwU.qtrim.fq_ext_all_reads.normalized_K25_C50_pctSD10000.fq right.norm.fq -removing tmp dir /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads CMD finished (0 seconds) Normalization complete. See outputs: /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/304428_S1_L001_R1_001.fastq.PwU.qtrim.fq_ext_all_reads.normalized_K25_C50_pctSD10000.fq /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/304428_S1_L001_R2_001.fastq.PwU.qtrim.fq_ext_all_reads.normalized_K25_C50_pctSD10000.fq Friday, October 26, 2018: 06:06:02 CMD: touch /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/normalization.ok Converting input files. (in parallel)Friday, October 26, 2018: 06:06:02 CMD: cat /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A - >> left.fa Friday, October 26, 2018: 06:06:02 CMD: cat /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A - >> right.fa Friday, October 26, 2018: 06:06:02 CMD: touch left.fa.ok Friday, October 26, 2018: 06:06:02 CMD: touch right.fa.ok Friday, October 26, 2018: 06:06:02 CMD: touch left.fa.ok right.fa.ok Friday, October 26, 2018: 06:06:02 CMD: cat left.fa right.fa > /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/both.fa Friday, October 26, 2018: 06:06:02 CMD: touch /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/both.fa.ok ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- * Running CMD: /gscratch/srlab/programs/trinity/trinity-plugins/jellyfish/bin/jellyfish count -t 28 -m 25 -s 100000000 --canonical /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/both.fa * Running CMD: /gscratch/srlab/programs/trinity/trinity-plugins/jellyfish/bin/jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa * Running CMD: /gscratch/srlab/programs/trinity/trinity-plugins/jellyfish/bin/jellyfish histo -t 28 -o jellyfish.kmers.fa.histo mer_counts.jf ---------------------------------------------- --------------- Inchworm --------------------- -- (Linear contig construction from k-mers) -- ---------------------------------------------- * Running CMD: /gscratch/srlab/programs/trinity/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --num_threads 6 --PARALLEL_IWORM > /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp * Running CMD: mv /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/inchworm.K25.L25.DS.fa Friday, October 26, 2018: 06:06:02 CMD: touch /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/inchworm.K25.L25.DS.fa.finished -------------------------------------------------------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -------------------------------------------------------- inchworm_target: /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/both.fa bowite_reads_fa: /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/both.fa chrysalis_reads_fa: /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/both.fa * Running CMD: /gscratch/srlab/programs/trinity/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/inchworm.K25.L25.DS.fa 100 10 > /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 * Running CMD: bowtie2-build -o 3 /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null * Running CMD: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 28 -f --score-min G,46,0 -x /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/both.fa | samtools view -@ 28 -F4 -Sb - | samtools sort -m 1917396114 -@ 28 -no - - > /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" * Running CMD: /gscratch/srlab/programs/trinity/util/support_scripts/scaffold_iworm_contigs.pl /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/inchworm.K25.L25.DS.fa > /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/iworm_scaffolds.txt * Running CMD: /gscratch/srlab/programs/trinity/Chrysalis/GraphFromFasta -i /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/inchworm.K25.L25.DS.fa -r /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 28 -k 24 -kk 48 -scaffolding /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt * Running CMD: /gscratch/srlab/programs/trinity/Chrysalis/BubbleUpClustering -i /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/inchworm.K25.L25.DS.fa -weld_graph /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt -min_contig_length 200 > /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/GraphFromIwormFasta.out * Running CMD: /gscratch/srlab/programs/trinity/Chrysalis/CreateIwormFastaBundle -i /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 * Running CMD: /gscratch/srlab/programs/trinity/Chrysalis/ReadsToTranscripts -i /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/both.fa -f /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/readsToComponents.out -t 28 -max_mem_reads 50000000 * Running CMD: /usr/bin/sort --parallel=28 -T . -S 100G -k 1,1n /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/readsToComponents.out > /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/chrysalis/readsToComponents.out.sort Friday, October 26, 2018: 06:06:05 CMD: mkdir -p read_partitions/Fb_0/CBin_0 Friday, October 26, 2018: 06:06:05 CMD: touch partitioned_reads.files.list.ok Friday, October 26, 2018: 06:06:05 CMD: /gscratch/srlab/programs/trinity/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup > recursive_trinity.cmds Friday, October 26, 2018: 06:06:05 CMD: touch recursive_trinity.cmds.ok Friday, October 26, 2018: 06:06:05 CMD: touch recursive_trinity.cmds.ok -------------------------------------------------------------------------------- ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- -------------------------------------------------------------------------------- Friday, October 26, 2018: 06:06:05 CMD: /gscratch/srlab/programs/trinity/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 28 -v Number of Commands: 15 succeeded(1) 6.66667% completed. succeeded(2) 13.3333% completed. succeeded(3) 20% completed. succeeded(4) 26.6667% completed. succeeded(5) 33.3333% completed. succeeded(6) 40% completed. succeeded(7) 46.6667% completed. succeeded(8) 53.3333% completed. succeeded(9) 60% completed. succeeded(10) 66.6667% completed. succeeded(11) 73.3333% completed. succeeded(12) 80% completed. succeeded(13) 86.6667% completed. succeeded(14) 93.3333% completed. succeeded(15) 100% completed. All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Friday, October 26, 2018: 06:06:07 CMD: find read_partitions/ -name '*inity.fasta' | /gscratch/srlab/programs/trinity/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp ################################################################### Butterfly assemblies are written to /gscratch/srlab/sr320/analyses/1026/trinity_out_dir/Trinity.fasta ###################################################################