c2997108/centos7:1-blast_2.9.0-nt_20190618-13 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/centos7:3-java centos:centos6 using docker + set -o pipefail + fasta=input_1/Trinity.demo.fa + '[' -e '' ']' + grep '^>' input_1/Trinity.demo.fa + awk '{a=substr($1,2); print a"\t"a}' + gene2trans=input.gene2trans + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 /usr/local/TransDecoder-TransDecoder-v5.5.0/TransDecoder.LongOrfs -t input_1/Trinity.demo.fa * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/compute_base_probs.pl input_1/Trinity.demo.fa 0 > /tmp/180/Trinity.demo.fa.transdecoder_dir/base_freqs.dat -first extracting base frequencies, we'll need them later. - extracting ORFs from transcripts. -total transcripts to examine: 14 CMD: touch /tmp/180/Trinity.demo.fa.transdecoder_dir.__checkpoints_longorfs/TD.longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: /tmp/180/Trinity.demo.fa.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 /usr/local/TransDecoder-TransDecoder-v5.5.0/TransDecoder.Predict -t input_1/Trinity.demo.fa --cpu 8 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/get_top_longest_fasta_entries.pl Trinity.demo.fa.transdecoder_dir/longest_orfs.cds 5000 5000 > Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/exclude_similar_proteins.pl Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000 > Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: TRINITY_DN2_c0_g1_i1.p1, not unique enough -skipping training candidate: TRINITY_DN8_c0_g1_i3.p1, not unique enough -skipping training candidate: TRINITY_DN8_c0_g1_i2.p1, not unique enough -skipping training candidate: TRINITY_DN2_c0_g1_i3.p1, not unique enough -skipping training candidate: TRINITY_DN2_c0_g2_i2.p1, not unique enough -skipping training candidate: TRINITY_DN1_c0_g1_i1.p1, not unique enough -skipping training candidate: TRINITY_DN1_c0_g1_i3.p1, not unique enough -skipping training candidate: TRINITY_DN8_c0_g1_i4.p1, not unique enough -skipping training candidate: TRINITY_DN2_c0_g1_i3.p2, not unique enough -redundancy-minimized set includes 7 / 16 = 43.75% * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/get_top_longest_fasta_entries.pl Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 42.6 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/seq_n_baseprobs_to_loglikelihood_vals.pl Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.top_500_longest Trinity.demo.fa.transdecoder_dir/base_freqs.dat > Trinity.demo.fa.transdecoder_dir/hexamer.scores * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/score_CDS_likelihood_all_6_frames.pl Trinity.demo.fa.transdecoder_dir/longest_orfs.cds Trinity.demo.fa.transdecoder_dir/hexamer.scores > Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.scores * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/select_best_ORFs_per_transcript.pl --gff3_file Trinity.demo.fa.transdecoder_dir/longest_orfs.gff3 --cds_scores Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 Selecting best orfs * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/train_start_PWM.pl --transcripts input_1/Trinity.demo.fa --selected_orfs Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Trinity.demo.fa.transdecoder_dir/start_refinement Training start codon pattern recognition* Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/build_atgPWM_+-.pl --transcripts input_1/Trinity.demo.fa --selected_orfs Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Trinity.demo.fa.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/feature_scoring.+-.pl --features_plus Trinity.demo.fa.transdecoder_dir/start_refinement.+.features --features_minus Trinity.demo.fa.transdecoder_dir/start_refinement.-.features --atg_position 20 > Trinity.demo.fa.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/feature_scores_to_ROC.pl Trinity.demo.fa.transdecoder_dir/start_refinement.feature.scores > Trinity.demo.fa.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/plot_ROC.Rscript Trinity.demo.fa.transdecoder_dir/start_refinement.feature.scores.roc || : null device 1 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/compute_AUC.pl Trinity.demo.fa.transdecoder_dir/start_refinement.feature.scores.roc null device 1 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/make_seqLogo.Rscript Trinity.demo.fa.transdecoder_dir/start_refinement.+.pwm || : Error in library(seqLogo) : there is no package called 'seqLogo' Execution halted * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/make_seqLogo.Rscript Trinity.demo.fa.transdecoder_dir/start_refinement.-.pwm || : Error in library(seqLogo) : there is no package called 'seqLogo' Execution halted * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/deplete_feature_noise.pl --features_plus Trinity.demo.fa.transdecoder_dir/start_refinement.+.features --pwm_minus Trinity.demo.fa.transdecoder_dir/start_refinement.-.pwm --out_prefix Trinity.demo.fa.transdecoder_dir/start_refinement.enhanced num features: 7 num_incorporate: 2 -num feature swaps: 0 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/feature_scoring.+-.pl --features_plus Trinity.demo.fa.transdecoder_dir/start_refinement.enhanced.+.features --features_minus Trinity.demo.fa.transdecoder_dir/start_refinement.-.features --atg_position 20 > Trinity.demo.fa.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/feature_scores_to_ROC.pl Trinity.demo.fa.transdecoder_dir/start_refinement.enhanced.feature.scores > Trinity.demo.fa.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/plot_ROC.Rscript Trinity.demo.fa.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : null device 1 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/compute_AUC.pl Trinity.demo.fa.transdecoder_dir/start_refinement.enhanced.feature.scores.roc null device 1 * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/PWM/make_seqLogo.Rscript Trinity.demo.fa.transdecoder_dir/start_refinement.enhanced.+.pwm || : Error in library(seqLogo) : there is no package called 'seqLogo' Execution halted * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/start_codon_refinement.pl --transcripts input_1/Trinity.demo.fa --gff3_file Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir Trinity.demo.fa.transdecoder_dir > Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Refining start codon selections. -number of revised start positions: 0 * Running CMD: cp Trinity.demo.fa.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Trinity.demo.fa.transdecoder.gff3 copying output to final output file: Trinity.demo.fa.transdecoder.gff3* Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/gff3_file_to_bed.pl Trinity.demo.fa.transdecoder.gff3 > Trinity.demo.fa.transdecoder.bed Making bed file: Trinity.demo.fa.transdecoder.bed * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/gff3_file_to_proteins.pl --gff3 Trinity.demo.fa.transdecoder.gff3 --fasta input_1/Trinity.demo.fa --genetic_code Universal > Trinity.demo.fa.transdecoder.pep Making pep file: Trinity.demo.fa.transdecoder.pep * Running CMD: /usr/local/TransDecoder-TransDecoder-v5.5.0/util/gff3_file_to_proteins.pl --gff3 Trinity.demo.fa.transdecoder.gff3 --fasta input_1/Trinity.demo.fa --seqType CDS --genetic_code Universal > Trinity.demo.fa.transdecoder.cds Making cds file: Trinity.demo.fa.transdecoder.cds transdecoder is finished. See output files Trinity.demo.fa.transdecoder.* ++ basename input_1/Trinity.demo.fa + transfasta=Trinity.demo.fa + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 rm -rf Trinity.demo.fa.transdecoder_dir Trinity.demo.fa.transdecoder_dir.__checkpoints_longorfs Trinity.demo.fa.transdecoder_dir.__checkpoints + tail -n+2 + head -n-1 + echo ' docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 ' blastx -db /usr/local/Trinotate-Trinotate-v3.1.1/db/uniprot_sprot.pep -query input_1/Trinity.demo.fa -num_threads 8 -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > swissprot.blastx.outfmt6 docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 ' blastp -query Trinity.demo.fa.transdecoder.pep -db /usr/local/Trinotate-Trinotate-v3.1.1/db/uniprot_sprot.pep -num_threads 8 -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > swissprot.blastp.outfmt6 docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 ' hmmscan --cpu 8 --domtblout TrinotatePFAM.out /usr/local/Trinotate-Trinotate-v3.1.1/db/Pfam-A.hmm Trinity.demo.fa.transdecoder.pep > pfam.log docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-blast_2.9.0-nt_20190618-13 ' blastn -db /usr/local/db/nt.2019-06-18/nt -query input_1/Trinity.demo.fa -num_threads 8 -max_target_seqs 1 -outfmt 6 | docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:3-java ' myuniq.pl 1 > input_1/Trinity.demo.fa.blastn ' + xargs -I '{}' -P 1 bash -c '{}' Warning: [blastx] Examining 5 or more matches is recommended Warning: [blastp] Examining 5 or more matches is recommended Warning: [blastn] Examining 5 or more matches is recommended + tail -n+2 + echo ' + head -n-1 docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 ' /usr/local/signalp-4.1/signalp -f short -n signalp.out Trinity.demo.fa.transdecoder.pep > sigP.log || true docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 ' /usr/local/tmhmm-2.0c/bin/tmhmm --short < Trinity.demo.fa.transdecoder.pep > tmhmm.out || true docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 ' /usr/local/Trinotate-Trinotate-v3.1.1/util/rnammer_support/RnammerTranscriptome.pl --transcriptome input_1/Trinity.demo.fa --path_to_rnammer /usr/local/rnammer-1.2/rnammer || true ' + xargs -I '{}' -P 8 bash -c '{}' CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/rnammer_support/util/superScaffoldGenerator.pl input_1/Trinity.demo.fa transcriptSuperScaffold 100 acc: TRINITY_DN2_c0_g1_i4 acc: TRINITY_DN2_c0_g1_i5 acc: TRINITY_DN2_c0_g1_i1 acc: TRINITY_DN2_c0_g1_i2 acc: TRINITY_DN2_c0_g1_i3 acc: TRINITY_DN2_c0_g2_i1 acc: TRINITY_DN2_c0_g2_i2 acc: TRINITY_DN8_c0_g1_i4 acc: TRINITY_DN8_c0_g1_i5 acc: TRINITY_DN8_c0_g1_i2 acc: TRINITY_DN8_c0_g1_i3 acc: TRINITY_DN1_c0_g1_i1 acc: TRINITY_DN1_c0_g1_i2 acc: TRINITY_DN1_c0_g1_i3 Done. CMD: perl /usr/local/rnammer-1.2/rnammer -S euk -m tsu,lsu,ssu -gff tmp.superscaff.rnammer.gff < transcriptSuperScaffold.fasta CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/rnammer_support/util/rnammer_supperscaffold_gff_to_indiv_transcripts.pl -R tmp.superscaff.rnammer.gff -T transcriptSuperScaffold.bed > Trinity.demo.fa.rnammer.gff WARNING: No RNAMMER features are described in file: tmp.superscaff.rnammer.gff at /usr/local/Trinotate-Trinotate-v3.1.1/util/rnammer_support/util/rnammer_supperscaffold_gff_to_indiv_transcripts.pl line 46. Error, cmd: /usr/local/Trinotate-Trinotate-v3.1.1/util/rnammer_support/util/rnammer_supperscaffold_gff_to_indiv_transcripts.pl -R tmp.superscaff.rnammer.gff -T transcriptSuperScaffold.bed > Trinity.demo.fa.rnammer.gff died with ret 65280 at /usr/local/Trinotate-Trinotate-v3.1.1/util/rnammer_support/RnammerTranscriptome.pl line 80. # No sequences predicted with a signal peptide + cat + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 bash run-trinotate-import.sh CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map input.gene2trans --transcript_fasta input_1/Trinity.demo.fa --transdecoder_pep Trinity.demo.fa.transdecoder.pep --bulk_load -parsing gene/trans map file.... done. -loading Transcripts. done. -loading ORFs. done. CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.Transcript.bulk_load Transcript" | sqlite3 Trinotate.sqlite memory CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.ORF.bulk_load ORF" | sqlite3 Trinotate.sqlite memory Loading complete.. CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 swissprot.blastx.outfmt6 --prog blastx --dbtype Swissprot CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.blast_bulk_load.16 BlastDbase" | sqlite3 Trinotate.sqlite memory BlastDbase loading complete.. CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 swissprot.blastp.outfmt6 --prog blastp --dbtype Swissprot CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.blast_bulk_load.21 BlastDbase" | sqlite3 Trinotate.sqlite memory BlastDbase loading complete.. CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_PFAM_loader.pl --sqlite Trinotate.sqlite --pfam TrinotatePFAM.out CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.pfam_bulk_load.26 HMMERDbase" | sqlite3 Trinotate.sqlite memory Loading complete.. CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_RNAMMER_loader.pl --sqlite Trinotate.sqlite --rnammer input_1/Trinity.demo.fa.rnammer.gff No such file or directory at /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_RNAMMER_loader.pl line 81. Error, cmd: /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_RNAMMER_loader.pl --sqlite Trinotate.sqlite --rnammer input_1/Trinity.demo.fa.rnammer.gff died with ret 512 at /usr/local/Trinotate-Trinotate-v3.1.1/Trinotate line 126. CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_TMHMM_loader.pl --sqlite Trinotate.sqlite --tmhmm tmhmm.out CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.tmhmm_bulk_load.33 tmhmm" | sqlite3 Trinotate.sqlite memory Loading complete.. CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_SIGNALP_loader.pl --sqlite Trinotate.sqlite --signalp signalp.out No such file or directory at /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_SIGNALP_loader.pl line 69. Error, cmd: /usr/local/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_SIGNALP_loader.pl --sqlite Trinotate.sqlite --signalp signalp.out died with ret 512 at /usr/local/Trinotate-Trinotate-v3.1.1/Trinotate line 126. CMD: /usr/local/Trinotate-Trinotate-v3.1.1/util/Trinotate_report_writer.pl --sqlite Trinotate.sqlite --incl_pep --incl_trans Total transcript entries: 15 -including ancestral terms in report. -init GO_DAG Found obo: /usr/local/Trinotate-Trinotate-v3.1.1/util/../PerlLib/obo/go-basic.obo.gz Done processing, writing output. Finished. + cat + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 bash run-kegg.sh + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-blast_2.9.0-nt_20190618-13 zcat /usr/local/db/nt.2019-06-18/nt.name.gz + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 awk '-F\t' 'FILENAME==ARGV[1]{id[$1]=$2; sim[$1]=$3; len[$1]=$4; eval[$1]=$11; flagname[$2]=1} FILENAME==ARGV[2]{if(flagname[$1]==1){name[$1]=$2}else{delete flagname[$1]}} FILENAME==ARGV[3]{if(FNR==1){print $0"\tNCBI NT top hit\te-value\tsimilarity\thit length"}else{if(name[id[$2]]==""){name[id[$2]]=id[$2]}; print $0"\t"name[id[$2]]"\t"eval[$2]"\t"sim[$2]"\t"len[$2]}}' input_1/Trinity.demo.fa.blastn /dev/stdin Trinotate.xls2 + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 awk '-F\t' '{ORS=""; print $2"\t"$1; for(i=3;i<=NF;i++){print "\t"$i}; print "\n"}' Trinotate.xls3 + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 rm -rf TMHMM_1 + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 rm -f transcriptSuperScaffold.fasta transcriptSuperScaffold.bed tmp.superscaff.rnammer.gff Trinotate.sqlite run-trinotate-import.sh + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 rm -f Trinotate.xls.gene_ontology run-kegg.sh Trinotate.xls2 + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 rm -f pipeliner.1.cmds pipeliner.25.cmds tmp.rnammer_bulk_load.31 tmp.signalp_bulk_load.38 + post_processing + '[' 1 = 1 ']' + '[' 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']' + docker run -v /tmp/180:/tmp/180 -w /tmp/180 -u root -i --rm centos:centos6 chmod -R a=rXw . + echo 0 + exit