greetings ! I am trying to carry-out de-novo assembly of transcriptome for seven PE transcriptomes but everytime i try to run the job in galaxy trinity-rna seq it fails. the sequences were concationated using CAT tool and trimmed using trimmomatic. the error is as follows
LibCvmfs version 2.7, revision 28
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Trinity-v2.9.1
Left read files: $VAR1 = [ '/pylon5/mc48nsp/xcgalaxy/main/staging//29093926/inputs/dataset_42051971.dat' ]; Right read files: $VAR1 = [ '/pylon5/mc48nsp/xcgalaxy/main/staging//29093926/inputs/dataset_42051973.dat' ]; Saturday, June 27, 2020: 11:16:39 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /cvmfs/main.galaxyproject.org/deps/_conda/envs/__trinity@2.9.1/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Saturday, June 27, 2020: 11:16:41 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /cvmfs/main.galaxyproject.org/deps/_conda/envs/__trinity@2.9.1/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Saturday, June 27, 2020: 11:16:42 CMD: mkdir -p /pylon5/mc48nsp/xcgalaxy/main/staging/29093926/working/trinity_out_dir Saturday, June 27, 2020: 11:16:42 CMD: mkdir -p /pylon5/mc48nsp/xcgalaxy/main/staging/29093926/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 = [
[
'/pylon5/mc48nsp/xcgalaxy/main/staging//29093926/inputs/dataset_42051971.dat'
],
[
'/pylon5/mc48nsp/xcgalaxy/main/staging//29093926/inputs/dataset_42051973.dat'
]
];
Saturday, June 27, 2020: 11:16:43 CMD: /cvmfs/main.galaxyproject.org/deps/_conda/envs/__trinity@2.9.1/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 720G --max_cov 200 --min_cov 1 --CPU 16 --output /pylon5/mc48nsp/xcgalaxy/main/staging/29093926/working/trinity_out_dir/insilico_read_normalization --max_CV 10000 --SS_lib_type FR --left /pylon5/mc48nsp/xcgalaxy/main/staging//29093926/inputs/dataset_42051971.dat --right /pylon5/mc48nsp/xcgalaxy/main/staging//29093926/inputs/dataset_42051973.dat --pairs_together --PARALLEL_STATS
-prepping seqs
Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1 /pylon5/mc48nsp/xcgalaxy/main/staging//29093926/inputs/dataset_42051971.dat >> left.fa
CMD: seqtk-trinity seq -r -A -R 2 /pylon5/mc48nsp/xcgalaxy/main/staging//29093926/inputs/dataset_42051973.dat >> right.fa
CMD finished (1164 seconds)
CMD finished (1188 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 (169 seconds)
CMD: touch both.fa.ok
CMD finished (0 seconds)
-kmer counting.
----------- Jellyfish --------------------
-- (building a k-mer catalog from reads) --
CMD: jellyfish count -t 16 -m 25 -s 103245940669 both.fa CMD finished (2327 seconds) CMD: jellyfish histo -t 16 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD finished (231 seconds) CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa CMD finished (668 seconds) CMD: touch jellyfish.K25.min2.kmers.fa.success CMD finished (0 seconds) -generating stats files CMD: /cvmfs/main.galaxyproject.org/deps/_conda/envs/__trinity@2.9.1/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 8 > left.fa.K25.stats CMD: /cvmfs/main.galaxyproject.org/deps/_conda/envs/__trinity@2.9.1/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 8 > right.fa.K25.stats -reading Kmer occurrences... -reading Kmer occurrences...
done parsing 429493222 Kmers, 332051587 added, taking 19712 seconds. Sequence: ATTCTTCCNis smaller than 25 base pairs, skipping Sequence: TTTGTGSequence: is smaller than ATCGCCACGCGCACCGCCGis smaller than 25Sequence: base pairs, skippingCCGCAGTCGAGCGCCGis smaller than 25Sequence: CGGATACAGAGAAGGTCTGCG is smaller than 25Sequence: GCAAGCTTTGGTTCCCCTGGCC25is smaller than 25 base pairs, skipping base pairs, skippingSequence:
Sequence: base pairs, skippingGACCGCCGis smaller than 25 base pairs, skipping base pairs, skipping
Sequence: AGAAAGCGTCGGASequence: is smaller than 25GGGGGTTGGAGCCAAGCAGGAGTTTACGCGis smaller than is smaller than 2525 base pairs, skipping Sequence: ATGAGACAATTTCATCGCAG base pairs, skippingSequence: base pairs, skipping is smaller than GTACCGCTCTCGC25 base pairs, skippingSequence: Sequence: CACCACGGGCGGCGGAis smaller than is smaller than 25is smaller than base pairs, skippingSequence: 25TGGG is smaller than 2525 base pairs, skipping base pairs, skipping base pairs, skipping
Sequence: Sequence: GCTCCATCACGGAGGGCGGCGAGGAGGGACGCGis smaller than is smaller than 25 base pairs, skipping25 Sequence: base pairs, skippingAGGAAGG is smaller than Sequence: Sequence: Sequence: 25GCTTTCCTGAAGGTGGSequence: Sequence: CGTCCATCATCCCATGCCis smaller than is smaller than 25GATAGAGAGis smaller than 25 base pairs, skipping base pairs, skippingSequence: AGAGGGACACATGGTGAGAGis smaller than 25 base pairs, skipping TACCCCAACGGTTCACGGis smaller than Sequence: ATCCTCCAGGTGGAGCCCA25 base pairs, skipping base pairs, skippingCCTCGTGCGATATCCAAAG25 base pairs, skipping
is smaller than 25 base pairs, skipping is smaller than 25 base pairs, skipping
Sequence: Sequence: CCTCTTTCGAATCCTCGSequence: AAATTGGGis smaller than is smaller than 2525Sequence: is smaller than 25 base pairs, skippingGCGG base pairs, skipping base pairs, skippingSequence: is smaller than 25 base pairs, skippingTTTC
is smaller than 25 base pairs, skipping Sequence: TGATCCCCTCCGATCTCGis smaller than 25 base pairs, skipping Sequence: GATGCGis smaller than 25Sequence: CGTCTCCGCGGAGGTATGCASequence: base pairs, skippingis smaller than Sequence: CGGATTTACATTTAGGAAAGSequence: is smaller than 25CTTTCGCCGCC25Sequence: Sequence: CGGGCGAAGAAGAGGAAGA base pairs, skipping GTGTTCAAGGCGGATCTGCCCGis smaller than base pairs, skipping is smaller than 25is smaller than TTAGAGAACACCGAG25 base pairs, skipping25 Sequence: AGCGis smaller than is smaller than base pairs, skipping25 base pairs, skipping base pairs, skipping Sequence: 25AAATGCTGAAT is smaller than Sequence: GAGGTG25is smaller than 25 base pairs, skipping base pairs, skipping base pairs, skipping
Sequence: Sequence: AACCTCGTCAGGTCAAGGSequence: is smaller than TGGACAAGACCAAGis smaller than Sequence: 2525is smaller than GTACATATTAAC base pairs, skipping25 base pairs, skipping base pairs, skippingis smaller than Sequence: GGACGAAGGATGAGGGACCTTATis smaller than 2525 base pairs, skipping base pairs, skipping Sequence: Sequence: ACAGTCATCACGCGTGGGCGTTAGAGCATTGAGis smaller than Sequence: 25Sequence: base pairs, skipping GTGCGCCTGATis smaller than is smaller than CGATTGTAT25is smaller than base pairs, skipping25 Sequence: CGCCTGATTCTTCGCG base pairs, skipping25 base pairs, skippingis smaller than 25 base pairs, skipping Sequence: Sequence: GAAATGGTGTTGCAAGGATGTCTTCAACCGCGis smaller than is smaller than 2525 base pairs, skipping base pairs, skippingSequence: Sequence:
CTCCAGGCGCTTGCSequence: Sequence: GTGACAGGTGCACTATACCACGTAAATGACCGGGis smaller than is smaller than 2525 base pairs, skippingis smaller than Sequence: base pairs, skippingSequence: is smaller than AGTAGCATTTTCAAGCTCGG25 base pairs, skippingis smaller than Sequence: AATAAAGAAGGG25is smaller than 25 base pairs, skippingSequence: 25GTGGGCG base pairs, skippingSequence: is smaller than ATCATCCCCAAGTGAAGAC25CTTGCACCG base pairs, skipping base pairs, skipping is smaller than is smaller than 2525 base pairs, skipping base pairs, skipping Sequence: AGGTCAACCCCGAGSequence: GCGTCGCCCGCCGAAGAAGCis smaller than is smaller than 2525 base pairs, skipping base pairs, skippingSequence:
and so on any help is greatly appriciated
