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mvdbeek / usegalaxy-tests

Run tests against usegalaxy.org
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test trinity 2.9.1+galaxy2 #37

Closed jennaj closed 1 year ago

jennaj commented 2 years ago

Reported error about a job that looks like it finished (from the logs) but failed. Doesn't look like an input/param issue so far.

toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2

jennaj commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 6
Passed 6
Error 0
Failure 0
Skipped 0
Passed s *
✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ______ ____ ____ ____ ____ ______ __ __ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | |__| |__|\_||____||__|__||____| |__| |____/ Trinity-v2.9.1 Left read files: $VAR1 = [ 'left_input.fastqsanger' ]; Right read files: $VAR1 = [ 'right_input.fastqsanger' ]; Wednesday, May 4, 2022: 16:44:15 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:44:15 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:44:16 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir Wednesday, May 4, 2022: 16:44:16 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- --------------------------------------------------------------- ------------ In silico Read Normalization --------------------- -- (Removing Excess Reads Beyond 200 Coverage -- --------------------------------------------------------------- # running normalization on reads: $VAR1 = [ [ '/scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger' ], [ '/scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger' ] ]; Wednesday, May 4, 2022: 16:44:16 CMD: /usr/local/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 190G --max_cov 200 --min_cov 1 --CPU 56 --output /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --left /scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger --right /scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger --pairs_together --PARALLEL_STATS -prepping seqs Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 /scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger >> left.fa CMD: seqtk-trinity seq -A -R 2 /scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger >> 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 CMD finished (0 seconds) -kmer counting. ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- CMD: jellyfish count -t 56 -m 25 -s 100000000 both.fa CMD finished (0 seconds) CMD: jellyfish histo -t 56 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD finished (0 seconds) CMD: 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) -generating stats files CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 > left.fa.K25.stats CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 > right.fa.K25.stats -reading Kmer occurrences... -reading Kmer occurrences... done parsing 2541 Kmers, 2541 added, taking 0 seconds. done parsing 2541 Kmers, 2541 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 CMD finished (0 seconds) -sorting each stats file by read name. CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> left.fa.K25.stats.sort CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> 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) -defining normalized reads CMD: /usr/local/opt/trinity-2.9.1/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: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 100 / 100 = 100.00% reads selected during normalization. 0 / 100 = 0.00% reads discarded as likely aberrant based on coverage profiles. 0 / 100 = 0.00% reads discarded as below minimum coverage threshold=1 CMD finished (0 seconds) CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok CMD finished (0 seconds) -search and capture. -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger ... done prepping, now search and capture. -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger ... done prepping, now search and capture. -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq.ok CMD finished (0 seconds) CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq.ok CMD finished (0 seconds) CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq CMD finished (0 seconds) CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq CMD finished (0 seconds) -removing tmp dir /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads Normalization complete. See outputs: /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq Wednesday, May 4, 2022: 16:44:16 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/normalization.ok Converting input files. (in parallel)Wednesday, May 4, 2022: 16:44:16 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa Wednesday, May 4, 2022: 16:44:16 CMD: touch left.fa.ok Wednesday, May 4, 2022: 16:44:16 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa Wednesday, May 4, 2022: 16:44:16 CMD: touch right.fa.ok Wednesday, May 4, 2022: 16:44:16 CMD: touch left.fa.ok right.fa.ok Wednesday, May 4, 2022: 16:44:16 CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa Wednesday, May 4, 2022: 16:44:16 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa.ok ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer (25) catalog from reads) -- ------------------------------------------- * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf ---------------------------------------------- --------------- Inchworm (K=25, asm) --------------------- -- (Linear contig construction from k-mers) -- ---------------------------------------------- * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 6 --PARALLEL_IWORM -L 25 --no_prune_error_kmers > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa.tmp Kmer length set to: 25 Min assembly length set to: 25 Monitor turned on, set to: 1 setting number of threads to: 6 -setting parallel iworm mode. -reading Kmer occurrences... done parsing 5358 Kmers, 5358 added, taking 0 seconds. TIMING KMER_DB_BUILDING 0 s. -populating the kmer seed candidate list. Kcounter hash size: 5358 Processed 5358 non-zero abundance kmers in kcounter. -Not sorting list of kmers, given parallel mode in effect. -beginning inchworm contig assembly. Total kcounter hash size: 5358 vs. sorted list size: 5358 num threads set to: 6 Done opening file. tmp.iworm.fa.pid_75475.thread_0 Done opening file. tmp.iworm.fa.pid_75475.thread_1 Done opening file. tmp.iworm.fa.pid_75475.thread_2 Done opening file. tmp.iworm.fa.pid_75475.thread_3 Done opening file. tmp.iworm.fa.pid_75475.thread_4 Done opening file. tmp.iworm.fa.pid_75475.thread_5 Iworm contig assembly time: 0 seconds = 0 minutes. TIMING CONTIG_BUILDING 0 s. TIMING PROG_RUNTIME 0 s. * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa Wednesday, May 4, 2022: 16:44:16 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa.finished -------------------------------------------------------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -------------------------------------------------------- inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/inchworm.fa.min100 * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48 -strand -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000 -strand * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/readsToComponents.out.sort Wednesday, May 4, 2022: 16:44:19 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/read_partitions/Fb_0/CBin_0 Wednesday, May 4, 2022: 16:44:19 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/partitioned_reads.files.list.ok Wednesday, May 4, 2022: 16:44:19 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_version_check --min_contig_length 200 --min_kmer_cov 1 --bflyHeapSpaceMax 190G --bfly_opts "-V 10 --stderr" > recursive_trinity.cmds Wednesday, May 4, 2022: 16:44:19 CMD: touch recursive_trinity.cmds.ok Wednesday, May 4, 2022: 16:44:19 CMD: touch recursive_trinity.cmds.ok -------------------------------------------------------------------------------- ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- -------------------------------------------------------------------------------- Wednesday, May 4, 2022: 16:44:19 CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle Number of Commands: 8 succeeded(1) 12.5% completed. succeeded(2) 25% completed. ***** PairPath Counts ***** ***** PairPath Counts ***** Node: 197 has 1 pairpaths stored: PairPath [_paths=[[197], []]] has read support: 24 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 197 has 1 pairpaths stored: PairPath [_paths=[[197], []]] has read support: 24 ## Total number of pairpaths: 1 Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 496 has 1 pairpaths stored: PairPath [_paths=[[496], []]] has read support: 44 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 496 has 1 pairpaths stored: PairPath [_paths=[[496], []]] has read support: 44 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 339 has 1 pairpaths stored: PairPath [_paths=[[339], []]] has read support: 32 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 339 has 1 pairpaths stored: PairPath [_paths=[[339], []]] has read support: 32 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 873 has 2 pairpaths stored: PairPath [_paths=[[873], []]] has read support: 24 PairPath [_paths=[[873, 877], []]] has read support: 6 Node: 875 has 1 pairpaths stored: PairPath [_paths=[[875, 877], []]] has read support: 4 Node: 877 has 1 pairpaths stored: PairPath [_paths=[[877], []]] has read support: 68 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 873 has 2 pairpaths stored: PairPath [_paths=[[873], []]] has read support: 24 PairPath [_paths=[[873, 877], []]] has read support: 6 Node: 875 has 1 pairpaths stored: PairPath [_paths=[[875, 877], []]] has read support: 4 Node: 877 has 1 pairpaths stored: PairPath [_paths=[[877], []]] has read support: 68 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 558 has 1 pairpaths stored: PairPath [_paths=[[558], []]] has read support: 38 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 558 has 1 pairpaths stored: PairPath [_paths=[[558], []]] has read support: 38 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 559 has 1 pairpaths stored: PairPath [_paths=[[559], []]] has read support: 40 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 559 has 1 pairpaths stored: PairPath [_paths=[[559], []]] has read support: 40 ## Total number of pairpaths: 1 succeeded(3) 37.5% completed. succeeded(4) 50% completed. succeeded(5) 62.5% completed. succeeded(6) 75% completed. succeeded(7) 87.5% completed. succeeded(8) 100% completed. All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Wednesday, May 4, 2022: 16:44:21 CMD: find /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.tmp -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:44:21 CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:44:21 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta.gene_trans_map ################################################################### Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta ################################################################### ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pool | ` {"__current_case__": 1, "inputs": {"__current_case__": 1, "jaccard_clip": "false", "pair_input": {"values": [{"id": 1525648, "src": "hdca"}]}, "paired_or_single": "unmerged_paired_collection", "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "No"} ` | | norm | ` "true" ` | | additional\_params | ` {"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"} ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "fastqsanger" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test #2)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ______ ____ ____ ____ ____ ______ __ __ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | |__| |__|\_||____||__|__||____| |__| |____/ Trinity-v2.9.1 Left read files: $VAR1 = [ 'left_input.fastqsanger.gz' ]; Right read files: $VAR1 = [ 'right_input.fastqsanger.gz' ]; Wednesday, May 4, 2022: 16:45:15 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:45:15 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:45:16 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir Wednesday, May 4, 2022: 16:45:16 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- --------------------------------------------------------------- ------------ In silico Read Normalization --------------------- -- (Removing Excess Reads Beyond 200 Coverage -- --------------------------------------------------------------- # running normalization on reads: $VAR1 = [ [ '/scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz' ], [ '/scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz' ] ]; Wednesday, May 4, 2022: 16:45:16 CMD: /usr/local/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 190G --max_cov 200 --min_cov 1 --CPU 56 --output /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --left /scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz --right /scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz --pairs_together --PARALLEL_STATS -prepping seqs Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 <(gunzip -c /scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz) >> left.fa CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz) >> 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 CMD finished (0 seconds) -kmer counting. ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- CMD: jellyfish count -t 56 -m 25 -s 100000000 both.fa CMD finished (0 seconds) CMD: jellyfish histo -t 56 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD finished (0 seconds) CMD: 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) -generating stats files CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 > left.fa.K25.stats CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 > right.fa.K25.stats -reading Kmer occurrences... -reading Kmer occurrences... done parsing 2541 Kmers, 2541 added, taking 0 seconds. STATS_GENERATION_TIME: 0 done parsing seconds.2541 Kmers, 2541 added, taking 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 CMD finished (0 seconds) -sorting each stats file by read name. CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> left.fa.K25.stats.sort CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> 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) -defining normalized reads CMD: /usr/local/opt/trinity-2.9.1/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: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 100 / 100 = 100.00% reads selected during normalization. 0 / 100 = 0.00% reads discarded as likely aberrant based on coverage profiles. 0 / 100 = 0.00% reads discarded as below minimum coverage threshold=1 CMD finished (0 seconds) CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok CMD finished (0 seconds) -search and capture. -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz ... done prepping, now search and capture. -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz ... done prepping, now search and capture. -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok CMD finished (0 seconds) CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok CMD finished (0 seconds) CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq CMD finished (0 seconds) CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq CMD finished (0 seconds) -removing tmp dir /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads Normalization complete. See outputs: /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq Wednesday, May 4, 2022: 16:45:16 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/normalization.ok Converting input files. (in parallel)Wednesday, May 4, 2022: 16:45:16 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa Wednesday, May 4, 2022: 16:45:16 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa Wednesday, May 4, 2022: 16:45:16 CMD: touch left.fa.ok Wednesday, May 4, 2022: 16:45:16 CMD: touch right.fa.ok Wednesday, May 4, 2022: 16:45:16 CMD: touch left.fa.ok right.fa.ok Wednesday, May 4, 2022: 16:45:16 CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa Wednesday, May 4, 2022: 16:45:16 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa.ok ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer (25) catalog from reads) -- ------------------------------------------- * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf ---------------------------------------------- --------------- Inchworm (K=25, asm) --------------------- -- (Linear contig construction from k-mers) -- ---------------------------------------------- * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 6 --PARALLEL_IWORM -L 25 --no_prune_error_kmers > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa.tmp Kmer length set to: 25 Min assembly length set to: 25 Monitor turned on, set to: 1 setting number of threads to: 6 -setting parallel iworm mode. -reading Kmer occurrences... done parsing 5358 Kmers, 5358 added, taking 0 seconds. TIMING KMER_DB_BUILDING 0 s. -populating the kmer seed candidate list. Kcounter hash size: 5358 Processed 5358 non-zero abundance kmers in kcounter. -Not sorting list of kmers, given parallel mode in effect. -beginning inchworm contig assembly. Total kcounter hash size: 5358 vs. sorted list size: 5358 num threads set to: 6 Done opening file. tmp.iworm.fa.pid_189063.thread_0 Done opening file. tmp.iworm.fa.pid_189063.thread_1 Done opening file. tmp.iworm.fa.pid_189063.thread_2 Done opening file. tmp.iworm.fa.pid_189063.thread_3 Done opening file. tmp.iworm.fa.pid_189063.thread_4 Done opening file. tmp.iworm.fa.pid_189063.thread_5 Iworm contig assembly time: 0 seconds = 0 minutes. TIMING CONTIG_BUILDING 0 s. TIMING PROG_RUNTIME 0 s. * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa Wednesday, May 4, 2022: 16:45:16 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa.finished -------------------------------------------------------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -------------------------------------------------------- inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/inchworm.fa.min100 * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48 -strand -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000 -strand * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/readsToComponents.out.sort Wednesday, May 4, 2022: 16:45:19 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/read_partitions/Fb_0/CBin_0 Wednesday, May 4, 2022: 16:45:19 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/partitioned_reads.files.list.ok Wednesday, May 4, 2022: 16:45:19 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_version_check --min_contig_length 200 --min_kmer_cov 1 --bflyHeapSpaceMax 190G --bfly_opts "-V 10 --stderr" > recursive_trinity.cmds Wednesday, May 4, 2022: 16:45:19 CMD: touch recursive_trinity.cmds.ok Wednesday, May 4, 2022: 16:45:19 CMD: touch recursive_trinity.cmds.ok -------------------------------------------------------------------------------- ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- -------------------------------------------------------------------------------- Wednesday, May 4, 2022: 16:45:19 CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle Number of Commands: 8 succeeded(1) 12.5% completed. ***** PairPath Counts ***** Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 257 has 1 pairpaths stored: PairPath [_paths=[[257], []]] has read support: 38 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 257 has 1 pairpaths stored: PairPath [_paths=[[257], []]] has read support: 38 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 873 has 2 pairpaths stored: PairPath [_paths=[[873], []]] has read support: 24 PairPath [_paths=[[873, 877], []]] has read support: 6 Node: 875 has 1 pairpaths stored: PairPath [_paths=[[875, 877], []]] has read support: 4 Node: 877 has 1 pairpaths stored: PairPath [_paths=[[877], []]] has read support: 68 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 873 has 2 pairpaths stored: PairPath [_paths=[[873], []]] has read support: 24 PairPath [_paths=[[873, 877], []]] has read support: 6 Node: 875 has 1 pairpaths stored: PairPath [_paths=[[875, 877], []]] has read support: 4 Node: 877 has 1 pairpaths stored: PairPath [_paths=[[877], []]] has read support: 68 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 339 has 1 pairpaths stored: PairPath [_paths=[[339], []]] has read support: 32 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 339 has 1 pairpaths stored: PairPath [_paths=[[339], []]] has read support: 32 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 197 has 1 pairpaths stored: PairPath [_paths=[[197], []]] has read support: 24 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 197 has 1 pairpaths stored: PairPath [_paths=[[197], []]] has read support: 24 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 218 has 1 pairpaths stored: PairPath [_paths=[[218], []]] has read support: 40 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 218 has 1 pairpaths stored: PairPath [_paths=[[218], []]] has read support: 40 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 593 has 1 pairpaths stored: PairPath [_paths=[[593], []]] has read support: 50 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 593 has 1 pairpaths stored: PairPath [_paths=[[593], []]] has read support: 50 ## Total number of pairpaths: 1 succeeded(2) 25% completed. succeeded(3) 37.5% completed. succeeded(4) 50% completed. succeeded(5) 62.5% completed. succeeded(6) 75% completed. succeeded(7) 87.5% completed. succeeded(8) 100% completed. All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Wednesday, May 4, 2022: 16:45:21 CMD: find /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.tmp -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:45:21 CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:45:21 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta.gene_trans_map ################################################################### Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta ################################################################### ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pool | ` {"__current_case__": 1, "inputs": {"__current_case__": 1, "jaccard_clip": "false", "pair_input": {"values": [{"id": 1525649, "src": "hdca"}]}, "paired_or_single": "unmerged_paired_collection", "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "No"} ` | | norm | ` "true" ` | | additional\_params | ` {"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"} ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "fastqsanger.gz" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test #3)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ______ ____ ____ ____ ____ ______ __ __ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | |__| |__|\_||____||__|__||____| |__| |____/ Trinity-v2.9.1 Single read files: $VAR1 = [ 'input.fastqsanger' ]; Wednesday, May 4, 2022: 16:02:33 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:02:34 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:02:34 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir Wednesday, May 4, 2022: 16:02:34 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- Wednesday, May 4, 2022: 16:02:34 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452562/working/input.fastqsanger | seqtk-trinity seq -A -R 1 - >> single.fa Wednesday, May 4, 2022: 16:02:34 CMD: touch single.fa.ok Wednesday, May 4, 2022: 16:02:35 CMD: touch single.fa.ok ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer (25) catalog from reads) -- ------------------------------------------- * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf ---------------------------------------------- --------------- Inchworm (K=25, asm) --------------------- -- (Linear contig construction from k-mers) -- ---------------------------------------------- * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 6 --PARALLEL_IWORM -L 25 --no_prune_error_kmers > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa.tmp Kmer length set to: 25 Min assembly length set to: 25 Monitor turned on, set to: 1 setting number of threads to: 6 -setting parallel iworm mode. -reading Kmer occurrences... done parsing 3044 Kmers, 3044 added, taking 0 seconds. TIMING KMER_DB_BUILDING 0 s. -populating the kmer seed candidate list. Kcounter hash size: 3044 Processed 3044 non-zero abundance kmers in kcounter. -Not sorting list of kmers, given parallel mode in effect. -beginning inchworm contig assembly. Total kcounter hash size: 3044 vs. sorted list size: 3044 num threads set to: 6 Done opening file. tmp.iworm.fa.pid_146740.thread_0 Done opening file. tmp.iworm.fa.pid_146740.thread_1 Done opening file. tmp.iworm.fa.pid_146740.thread_2 Done opening file. tmp.iworm.fa.pid_146740.thread_3 Done opening file. tmp.iworm.fa.pid_146740.thread_4 Done opening file. tmp.iworm.fa.pid_146740.thread_5 Iworm contig assembly time: 0 seconds = 0 minutes. TIMING CONTIG_BUILDING 0 s. TIMING PROG_RUNTIME 0 s. * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa Wednesday, May 4, 2022: 16:02:35 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa.finished -------------------------------------------------------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -------------------------------------------------------- inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48 -strand > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa -f /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000 -strand * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/readsToComponents.out.sort Wednesday, May 4, 2022: 16:02:35 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/read_partitions/Fb_0/CBin_0 Wednesday, May 4, 2022: 16:02:35 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/partitioned_reads.files.list.ok Wednesday, May 4, 2022: 16:02:35 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_version_check --min_contig_length 200 --min_kmer_cov 1 --bflyHeapSpaceMax 190G --bfly_opts "-V 10 --stderr" > recursive_trinity.cmds Wednesday, May 4, 2022: 16:02:35 CMD: touch recursive_trinity.cmds.ok Wednesday, May 4, 2022: 16:02:35 CMD: touch recursive_trinity.cmds.ok -------------------------------------------------------------------------------- ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- -------------------------------------------------------------------------------- Wednesday, May 4, 2022: 16:02:35 CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle Number of Commands: 3 succeeded(1) 33.3333% completed. succeeded(2) 66.6667% completed. ***** PairPath Counts ***** Node: 204 has 1 pairpaths stored: PairPath [_paths=[[204], []]] has read support: 32 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 204 has 1 pairpaths stored: PairPath [_paths=[[204], []]] has read support: 32 ## Total number of pairpaths: 1 succeeded(3) 100% completed. All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Wednesday, May 4, 2022: 16:02:38 CMD: find /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.tmp -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:02:38 CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:02:38 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta.gene_trans_map ################################################################### Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta ################################################################### ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pool | ` {"__current_case__": 1, "inputs": {"__current_case__": 0, "input": {"values": [{"id": 96572745, "src": "hda"}]}, "paired_or_single": "unmerged_single_collection", "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "F"}}, "pool_mode": "No"} ` | | norm | ` "false" ` | | additional\_params | ` {"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"} ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "fastqsanger" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test #4)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ______ ____ ____ ____ ____ ______ __ __ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | |__| |__|\_||____||__|__||____| |__| |____/ Trinity-v2.9.1 Left read files: $VAR1 = [ 'left_input0.fastqsanger' ]; Right read files: $VAR1 = [ 'right_input0.fastqsanger' ]; Wednesday, May 4, 2022: 16:06:47 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:06:47 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:06:47 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir Wednesday, May 4, 2022: 16:06:47 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- Converting input files. (in parallel)Wednesday, May 4, 2022: 16:06:47 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452572/working/left_input0.fastqsanger | seqtk-trinity seq -r -A -R 1 - >> left.fa Wednesday, May 4, 2022: 16:06:47 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452572/working/right_input0.fastqsanger | seqtk-trinity seq -A -R 2 - >> right.fa Wednesday, May 4, 2022: 16:06:47 CMD: touch right.fa.ok Wednesday, May 4, 2022: 16:06:47 CMD: touch left.fa.ok Wednesday, May 4, 2022: 16:06:47 CMD: touch left.fa.ok right.fa.ok Wednesday, May 4, 2022: 16:06:47 CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa Wednesday, May 4, 2022: 16:06:47 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa.ok ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer (25) catalog from reads) -- ------------------------------------------- * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf ---------------------------------------------- --------------- Inchworm (K=25, asm) --------------------- -- (Linear contig construction from k-mers) -- ---------------------------------------------- * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 6 --PARALLEL_IWORM -L 25 --no_prune_error_kmers > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa.tmp Kmer length set to: 25 Min assembly length set to: 25 Monitor turned on, set to: 1 setting number of threads to: 6 -setting parallel iworm mode. -reading Kmer occurrences... done parsing 5358 Kmers, 5358 added, taking 0 seconds. TIMING KMER_DB_BUILDING 0 s. -populating the kmer seed candidate list. Kcounter hash size: 5358 Processed 5358 non-zero abundance kmers in kcounter. -Not sorting list of kmers, given parallel mode in effect. -beginning inchworm contig assembly. Total kcounter hash size: 5358 vs. sorted list size: 5358 num threads set to: 6 Done opening file. tmp.iworm.fa.pid_271859.thread_0 Done opening file. tmp.iworm.fa.pid_271859.thread_1 Done opening file. tmp.iworm.fa.pid_271859.thread_2 Done opening file. tmp.iworm.fa.pid_271859.thread_3 Done opening file. tmp.iworm.fa.pid_271859.thread_4 Done opening file. tmp.iworm.fa.pid_271859.thread_5 Iworm contig assembly time: 0 seconds = 0 minutes. TIMING CONTIG_BUILDING 0 s. TIMING PROG_RUNTIME 0 s. * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa Wednesday, May 4, 2022: 16:06:48 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa.finished -------------------------------------------------------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -------------------------------------------------------- inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/inchworm.fa.min100 * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48 -strand -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000 -strand * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/readsToComponents.out.sort Wednesday, May 4, 2022: 16:06:51 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/read_partitions/Fb_0/CBin_0 Wednesday, May 4, 2022: 16:06:51 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/partitioned_reads.files.list.ok Wednesday, May 4, 2022: 16:06:51 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_version_check --min_contig_length 200 --min_kmer_cov 1 --bflyHeapSpaceMax 190G --bfly_opts "-V 10 --stderr" > recursive_trinity.cmds Wednesday, May 4, 2022: 16:06:51 CMD: touch recursive_trinity.cmds.ok Wednesday, May 4, 2022: 16:06:51 CMD: touch recursive_trinity.cmds.ok -------------------------------------------------------------------------------- ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- -------------------------------------------------------------------------------- Wednesday, May 4, 2022: 16:06:51 CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle Number of Commands: 6 succeeded(1) 16.6667% completed. ***** PairPath Counts ***** Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 339 has 1 pairpaths stored: PairPath [_paths=[[339], []]] has read support: 32 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 339 has 1 pairpaths stored: PairPath [_paths=[[339], []]] has read support: 32 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 593 has 1 pairpaths stored: PairPath [_paths=[[593], []]] has read support: 50 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 593 has 1 pairpaths stored: PairPath [_paths=[[593], []]] has read support: 50 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 754 has 1 pairpaths stored: PairPath [_paths=[[754], []]] has read support: 24 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 754 has 1 pairpaths stored: PairPath [_paths=[[754], []]] has read support: 24 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 755 has 1 pairpaths stored: PairPath [_paths=[[755], []]] has read support: 40 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 755 has 1 pairpaths stored: PairPath [_paths=[[755], []]] has read support: 40 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 756 has 1 pairpaths stored: PairPath [_paths=[[756], []]] has read support: 38 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 756 has 1 pairpaths stored: PairPath [_paths=[[756], []]] has read support: 38 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 873 has 2 pairpaths stored: PairPath [_paths=[[873], []]] has read support: 24 PairPath [_paths=[[873, 877], []]] has read support: 6 Node: 875 has 1 pairpaths stored: PairPath [_paths=[[875, 877], []]] has read support: 4 Node: 877 has 1 pairpaths stored: PairPath [_paths=[[877], []]] has read support: 68 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 873 has 2 pairpaths stored: PairPath [_paths=[[873], []]] has read support: 24 PairPath [_paths=[[873, 877], []]] has read support: 6 Node: 875 has 1 pairpaths stored: PairPath [_paths=[[875, 877], []]] has read support: 4 Node: 877 has 1 pairpaths stored: PairPath [_paths=[[877], []]] has read support: 68 ## Total number of pairpaths: 4 succeeded(2) 33.3333% completed. succeeded(3) 50% completed. succeeded(4) 66.6667% completed. succeeded(5) 83.3333% completed. succeeded(6) 100% completed. All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Wednesday, May 4, 2022: 16:06:53 CMD: find /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.tmp -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:06:53 CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:06:53 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta.gene_trans_map ################################################################### Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta ################################################################### ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pool | ` {"__current_case__": 0, "inputs": {"__current_case__": 1, "jaccard_clip": "false", "left_input": {"values": [{"id": 96572745, "src": "hda"}]}, "paired_or_single": "paired", "right_input": {"values": [{"id": 96572750, "src": "hda"}]}, "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "Yes"} ` | | norm | ` "false" ` | | additional\_params | ` {"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"} ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "fastqsanger" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test #5)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ______ ____ ____ ____ ____ ______ __ __ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | |__| |__|\_||____||__|__||____| |__| |____/ Trinity-v2.9.1 Left read files: $VAR1 = [ 'left_input0.fastqsanger' ]; Right read files: $VAR1 = [ 'right_input0.fastqsanger' ]; Wednesday, May 4, 2022: 16:05:00 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:05:01 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:05:01 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir Wednesday, May 4, 2022: 16:05:01 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- --------------------------------------------------------------- ------------ In silico Read Normalization --------------------- -- (Removing Excess Reads Beyond 200 Coverage -- --------------------------------------------------------------- # running normalization on reads: $VAR1 = [ [ '/scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger' ], [ '/scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger' ] ]; Wednesday, May 4, 2022: 16:05:01 CMD: /usr/local/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 190G --max_cov 200 --min_cov 1 --CPU 56 --output /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --left /scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger --right /scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger --pairs_together --PARALLEL_STATS -prepping seqs Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 /scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger >> left.fa CMD: seqtk-trinity seq -A -R 2 /scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger >> 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 CMD finished (0 seconds) -kmer counting. ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- CMD: jellyfish count -t 56 -m 25 -s 100000000 both.fa CMD finished (0 seconds) CMD: jellyfish histo -t 56 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD finished (0 seconds) CMD: 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) -generating stats files CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 > left.fa.K25.stats CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 > right.fa.K25.stats -reading Kmer occurrences... -reading Kmer occurrences... done parsing 2541 Kmers, 2541 added, taking 0 seconds. STATS_GENERATION_TIME: 0 seconds. done parsing 2541 Kmers, 2541 added, taking 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 CMD finished (0 seconds) -sorting each stats file by read name. CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> left.fa.K25.stats.sort CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> 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) -defining normalized reads CMD: /usr/local/opt/trinity-2.9.1/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: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 100 / 100 = 100.00% reads selected during normalization. 0 / 100 = 0.00% reads discarded as likely aberrant based on coverage profiles. 0 / 100 = 0.00% reads discarded as below minimum coverage threshold=1 CMD finished (0 seconds) CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok CMD finished (0 seconds) -search and capture. -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger ... done prepping, now search and capture. -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger ... done prepping, now search and capture. -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq.ok CMD finished (0 seconds) CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq.ok CMD finished (0 seconds) CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq CMD finished (0 seconds) CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq CMD finished (0 seconds) -removing tmp dir /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads Normalization complete. See outputs: /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq Wednesday, May 4, 2022: 16:05:01 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/normalization.ok Converting input files. (in parallel)Wednesday, May 4, 2022: 16:05:01 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa Wednesday, May 4, 2022: 16:05:01 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa Wednesday, May 4, 2022: 16:05:01 CMD: touch left.fa.ok Wednesday, May 4, 2022: 16:05:01 CMD: touch right.fa.ok Wednesday, May 4, 2022: 16:05:01 CMD: touch left.fa.ok right.fa.ok Wednesday, May 4, 2022: 16:05:01 CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa Wednesday, May 4, 2022: 16:05:01 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa.ok ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer (25) catalog from reads) -- ------------------------------------------- * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf ---------------------------------------------- --------------- Inchworm (K=25, asm) --------------------- -- (Linear contig construction from k-mers) -- ---------------------------------------------- * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 6 --PARALLEL_IWORM -L 25 --no_prune_error_kmers > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa.tmp Kmer length set to: 25 Min assembly length set to: 25 Monitor turned on, set to: 1 setting number of threads to: 6 -setting parallel iworm mode. -reading Kmer occurrences... done parsing 5358 Kmers, 5358 added, taking 0 seconds. TIMING KMER_DB_BUILDING 0 s. -populating the kmer seed candidate list. Kcounter hash size: 5358 Processed 5358 non-zero abundance kmers in kcounter. -Not sorting list of kmers, given parallel mode in effect. -beginning inchworm contig assembly. Total kcounter hash size: 5358 vs. sorted list size: 5358 num threads set to: 6 Done opening file. tmp.iworm.fa.pid_189047.thread_0 Done opening file. tmp.iworm.fa.pid_189047.thread_1 Done opening file. tmp.iworm.fa.pid_189047.thread_2 Done opening file. tmp.iworm.fa.pid_189047.thread_3 Done opening file. tmp.iworm.fa.pid_189047.thread_4 Done opening file. tmp.iworm.fa.pid_189047.thread_5 Iworm contig assembly time: 0 seconds = 0 minutes. TIMING CONTIG_BUILDING 0 s. TIMING PROG_RUNTIME 0 s. * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa Wednesday, May 4, 2022: 16:05:02 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa.finished -------------------------------------------------------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -------------------------------------------------------- inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/inchworm.fa.min100 * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48 -strand -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000 -strand * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/readsToComponents.out.sort Wednesday, May 4, 2022: 16:05:04 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/read_partitions/Fb_0/CBin_0 Wednesday, May 4, 2022: 16:05:04 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/partitioned_reads.files.list.ok Wednesday, May 4, 2022: 16:05:04 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_version_check --min_contig_length 200 --min_kmer_cov 1 --bflyHeapSpaceMax 190G --bfly_opts "-V 10 --stderr" > recursive_trinity.cmds Wednesday, May 4, 2022: 16:05:04 CMD: touch recursive_trinity.cmds.ok Wednesday, May 4, 2022: 16:05:04 CMD: touch recursive_trinity.cmds.ok -------------------------------------------------------------------------------- ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- -------------------------------------------------------------------------------- Wednesday, May 4, 2022: 16:05:04 CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle Number of Commands: 8 succeeded(1) 12.5% completed. succeeded(2) 25% completed. ***** PairPath Counts ***** Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 593 has 1 pairpaths stored: PairPath [_paths=[[593], []]] has read support: 50 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 593 has 1 pairpaths stored: PairPath [_paths=[[593], []]] has read support: 50 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 339 has 1 pairpaths stored: PairPath [_paths=[[339], []]] has read support: 32 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 339 has 1 pairpaths stored: PairPath [_paths=[[339], []]] has read support: 32 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 197 has 1 pairpaths stored: PairPath [_paths=[[197], []]] has read support: 24 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 197 has 1 pairpaths stored: PairPath [_paths=[[197], []]] has read support: 24 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 873 has 2 pairpaths stored: PairPath [_paths=[[873], []]] has read support: 24 PairPath [_paths=[[873, 877], []]] has read support: 6 Node: 875 has 1 pairpaths stored: PairPath [_paths=[[875, 877], []]] has read support: 4 Node: 877 has 1 pairpaths stored: PairPath [_paths=[[877], []]] has read support: 68 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 873 has 2 pairpaths stored: PairPath [_paths=[[873], []]] has read support: 24 PairPath [_paths=[[873, 877], []]] has read support: 6 Node: 875 has 1 pairpaths stored: PairPath [_paths=[[875, 877], []]] has read support: 4 Node: 877 has 1 pairpaths stored: PairPath [_paths=[[877], []]] has read support: 68 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 474 has 1 pairpaths stored: PairPath [_paths=[[474], []]] has read support: 38 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 474 has 1 pairpaths stored: PairPath [_paths=[[474], []]] has read support: 38 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 475 has 1 pairpaths stored: PairPath [_paths=[[475], []]] has read support: 40 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 475 has 1 pairpaths stored: PairPath [_paths=[[475], []]] has read support: 40 ## Total number of pairpaths: 1 succeeded(3) 37.5% completed. succeeded(4) 50% completed. succeeded(5) 62.5% completed. succeeded(6) 75% completed. succeeded(7) 87.5% completed. succeeded(8) 100% completed. All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Wednesday, May 4, 2022: 16:05:07 CMD: find /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.tmp -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:05:07 CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:05:07 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta.gene_trans_map ################################################################### Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta ################################################################### ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pool | ` {"__current_case__": 0, "inputs": {"__current_case__": 1, "jaccard_clip": "false", "left_input": {"values": [{"id": 96572745, "src": "hda"}]}, "paired_or_single": "paired", "right_input": {"values": [{"id": 96572750, "src": "hda"}]}, "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "Yes"} ` | | norm | ` "true" ` | | additional\_params | ` {"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"} ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "fastqsanger" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test #6)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ______ ____ ____ ____ ____ ______ __ __ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | |__| |__|\_||____||__|__||____| |__| |____/ Trinity-v2.9.1 Left read files: $VAR1 = [ 'left_input0.fastqsanger', 'left_input1.fastqsanger' ]; Right read files: $VAR1 = [ 'right_input0.fastqsanger', 'right_input1.fastqsanger' ]; Wednesday, May 4, 2022: 16:28:17 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:28:17 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m Wednesday, May 4, 2022: 16:28:17 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir Wednesday, May 4, 2022: 16:28:17 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- --------------------------------------------------------------- ------------ In silico Read Normalization --------------------- -- (Removing Excess Reads Beyond 200 Coverage -- --------------------------------------------------------------- # running normalization on reads: $VAR1 = [ [ '/scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger', '/scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger' ], [ '/scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger', '/scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger' ] ]; Wednesday, May 4, 2022: 16:28:18 CMD: /usr/local/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 190G --max_cov 200 --min_cov 1 --CPU 56 --output /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --left /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger,/scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger --right /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger,/scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger --pairs_together --PARALLEL_STATS -prepping seqs Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger >> left.fa CMD: seqtk-trinity seq -A -R 2 /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger >> right.fa CMD finished (0 seconds) CMD: seqtk-trinity seq -A -R 2 /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger >> right.fa CMD finished (0 seconds) CMD finished (0 seconds) CMD: seqtk-trinity seq -r -A -R 1 /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger >> left.fa 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 CMD finished (0 seconds) -kmer counting. ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- CMD: jellyfish count -t 56 -m 25 -s 100000000 both.fa CMD finished (0 seconds) CMD: jellyfish histo -t 56 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD finished (0 seconds) CMD: 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) -generating stats files CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 > left.fa.K25.stats CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 28 > right.fa.K25.stats -reading Kmer occurrences... -reading Kmer occurrences... done parsing 5358 Kmers, 5337 added, taking 0 seconds. done parsing 5358 Kmers, 5337 added, taking 0 seconds. STATS_GENERATION_TIME: 0 seconds. STATS_GENERATION_TIME: 0 seconds. CMD finished (0 seconds) CMD finished (0 seconds) CMD: touch left.fa.K25.stats.ok CMD finished (0 seconds) CMD: touch right.fa.K25.stats.ok CMD finished (0 seconds) -sorting each stats file by read name. CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> left.fa.K25.stats.sort CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> 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) -defining normalized reads CMD: /usr/local/opt/trinity-2.9.1/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: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 200 / 200 = 100.00% reads selected during normalization. 0 / 200 = 0.00% reads discarded as likely aberrant based on coverage profiles. 0 / 200 = 0.00% reads discarded as below minimum coverage threshold=1 CMD finished (0 seconds) CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok CMD finished (0 seconds) -search and capture. -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger ... done prepping, now search and capture. -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger ... done prepping, now search and capture. -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok CMD finished (0 seconds) CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok CMD finished (0 seconds) CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq CMD finished (0 seconds) CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq CMD finished (0 seconds) -removing tmp dir /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads Normalization complete. See outputs: /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq Wednesday, May 4, 2022: 16:28:18 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/normalization.ok Converting input files. (in parallel)Wednesday, May 4, 2022: 16:28:18 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa Wednesday, May 4, 2022: 16:28:18 CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa Wednesday, May 4, 2022: 16:28:18 CMD: touch left.fa.ok Wednesday, May 4, 2022: 16:28:18 CMD: touch right.fa.ok Wednesday, May 4, 2022: 16:28:18 CMD: touch left.fa.ok right.fa.ok Wednesday, May 4, 2022: 16:28:18 CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa Wednesday, May 4, 2022: 16:28:18 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa.ok ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer (25) catalog from reads) -- ------------------------------------------- * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf ---------------------------------------------- --------------- Inchworm (K=25, asm) --------------------- -- (Linear contig construction from k-mers) -- ---------------------------------------------- * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 6 --PARALLEL_IWORM -L 25 --no_prune_error_kmers > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa.tmp Kmer length set to: 25 Min assembly length set to: 25 Monitor turned on, set to: 1 setting number of threads to: 6 -setting parallel iworm mode. -reading Kmer occurrences... done parsing 5358 Kmers, 5358 added, taking 0 seconds. TIMING KMER_DB_BUILDING 0 s. -populating the kmer seed candidate list. Kcounter hash size: 5358 Processed 5358 non-zero abundance kmers in kcounter. -Not sorting list of kmers, given parallel mode in effect. -beginning inchworm contig assembly. Total kcounter hash size: 5358 vs. sorted list size: 5358 num threads set to: 6 Done opening file. tmp.iworm.fa.pid_107126.thread_0 Done opening file. tmp.iworm.fa.pid_107126.thread_1 Done opening file. tmp.iworm.fa.pid_107126.thread_2 Done opening file. tmp.iworm.fa.pid_107126.thread_3 Done opening file. tmp.iworm.fa.pid_107126.thread_4 Done opening file. tmp.iworm.fa.pid_107126.thread_5 Iworm contig assembly time: 0 seconds = 0 minutes. TIMING CONTIG_BUILDING 0 s. TIMING PROG_RUNTIME 0 s. * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa Wednesday, May 4, 2022: 16:28:18 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa.finished -------------------------------------------------------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -------------------------------------------------------- inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/inchworm.fa.min100 * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48 -strand -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000 -strand * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/readsToComponents.out.sort Wednesday, May 4, 2022: 16:28:21 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/read_partitions/Fb_0/CBin_0 Wednesday, May 4, 2022: 16:28:21 CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/partitioned_reads.files.list.ok Wednesday, May 4, 2022: 16:28:21 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_version_check --min_contig_length 200 --min_kmer_cov 1 --bflyHeapSpaceMax 190G --bfly_opts "-V 10 --stderr" > recursive_trinity.cmds Wednesday, May 4, 2022: 16:28:21 CMD: touch recursive_trinity.cmds.ok Wednesday, May 4, 2022: 16:28:21 CMD: touch recursive_trinity.cmds.ok -------------------------------------------------------------------------------- ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- -------------------------------------------------------------------------------- Wednesday, May 4, 2022: 16:28:21 CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle Number of Commands: 8 succeeded(1) 12.5% completed. succeeded(2) 25% completed. ***** PairPath Counts ***** Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 194 has 1 pairpaths stored: PairPath [_paths=[[194], []]] has read support: 30 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 282 has 3 pairpaths stored: PairPath [_paths=[[282], []]] has read support: 30 PairPath [_paths=[[282, 283, 284], []]] has read support: 6 PairPath [_paths=[[282, 283], []]] has read support: 2 ## Total number of pairpaths: 3 ***** PairPath Counts ***** Node: 282 has 3 pairpaths stored: PairPath [_paths=[[282], []]] has read support: 30 PairPath [_paths=[[282, 283, 284], []]] has read support: 6 PairPath [_paths=[[282, 283], []]] has read support: 2 ## Total number of pairpaths: 3 ***** PairPath Counts ***** Node: 522 has 2 pairpaths stored: PairPath [_paths=[[522], []]] has read support: 20 PairPath [_paths=[[522, 523], []]] has read support: 2 Node: 523 has 1 pairpaths stored: PairPath [_paths=[[523], []]] has read support: 16 ## Total number of pairpaths: 3 ***** PairPath Counts ***** Node: 522 has 2 pairpaths stored: PairPath [_paths=[[522], []]] has read support: 20 PairPath [_paths=[[522, 523], []]] has read support: 2 Node: 523 has 1 pairpaths stored: PairPath [_paths=[[523], []]] has read support: 16 ## Total number of pairpaths: 3 ***** PairPath Counts ***** Node: 243 has 2 pairpaths stored: PairPath [_paths=[[243], []]] has read support: 20 PairPath [_paths=[[243, 244, 245], []]] has read support: 4 Node: 244 has 1 pairpaths stored: PairPath [_paths=[[244, 245], []]] has read support: 2 Node: 245 has 1 pairpaths stored: PairPath [_paths=[[245], []]] has read support: 14 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 243 has 2 pairpaths stored: PairPath [_paths=[[243], []]] has read support: 20 PairPath [_paths=[[243, 244, 245], []]] has read support: 4 Node: 244 has 1 pairpaths stored: PairPath [_paths=[[244, 245], []]] has read support: 2 Node: 245 has 1 pairpaths stored: PairPath [_paths=[[245], []]] has read support: 14 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 658 has 1 pairpaths stored: PairPath [_paths=[[658], []]] has read support: 36 Node: 653 has 1 pairpaths stored: PairPath [_paths=[[653, 658], []]] has read support: 2 Node: 655 has 2 pairpaths stored: PairPath [_paths=[[655], []]] has read support: 8 PairPath [_paths=[[655, 656, 658], []]] has read support: 2 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 658 has 1 pairpaths stored: PairPath [_paths=[[658], []]] has read support: 36 Node: 653 has 1 pairpaths stored: PairPath [_paths=[[653, 658], []]] has read support: 2 Node: 655 has 2 pairpaths stored: PairPath [_paths=[[655], []]] has read support: 8 PairPath [_paths=[[655, 656, 658], []]] has read support: 2 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 946 has 1 pairpaths stored: PairPath [_paths=[[946], []]] has read support: 24 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 946 has 1 pairpaths stored: PairPath [_paths=[[946], []]] has read support: 24 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 945 has 1 pairpaths stored: PairPath [_paths=[[945], []]] has read support: 8 Node: 949 has 3 pairpaths stored: PairPath [_paths=[[949], []]] has read support: 64 PairPath [_paths=[[949, 945], []]] has read support: 4 PairPath [_paths=[[949, 948], []]] has read support: 2 ## Total number of pairpaths: 4 ***** PairPath Counts ***** Node: 945 has 1 pairpaths stored: PairPath [_paths=[[945], []]] has read support: 8 Node: 949 has 3 pairpaths stored: PairPath [_paths=[[949], []]] has read support: 64 PairPath [_paths=[[949, 945], []]] has read support: 4 PairPath [_paths=[[949, 948], []]] has read support: 2 ## Total number of pairpaths: 4 succeeded(3) 37.5% completed. succeeded(4) 50% completed. succeeded(5) 62.5% completed. succeeded(6) 75% completed. succeeded(7) 87.5% completed. succeeded(8) 100% completed. All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Wednesday, May 4, 2022: 16:28:23 CMD: find /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.tmp -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:28:23 CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta Wednesday, May 4, 2022: 16:28:23 CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta.gene_trans_map ################################################################### Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta ################################################################### ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pool | ` {"__current_case__": 0, "inputs": {"__current_case__": 2, "jaccard_clip": "false", "pair_input": {"values": [{"id": 1525647, "src": "hdca"}]}, "paired_or_single": "paired_collection", "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "Yes"} ` | | norm | ` "true" ` | | additional\_params | ` {"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"} ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "fastqsanger" ` |

jennaj commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2

jennaj commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2