+ Fri Dec 6 05:45:31 EST 2019 job testjob_02_run_virsorter started in sThC.q with jobID=3061231 on compute-43-09 + NSLOTS = 10 mkdir: cannot create directory ‘07_CLASSIFY_test/VIRSORTER/’: No such file or directory cp: cannot create regular file ‘02_FASTA/WATER/WATER-vir_contigs.fa’: Permission denied cp: cannot create regular file ‘02_FASTA/MAT/MAT-vir_contigs.fa’: Permission denied ~/miniconda3/envs/virsorter/bin/perl This VirSorter run uses `diamond` (Buchfink et al., Nature Methods 2015) instead of `blastp`. Bin : ~/miniconda3/envs/virsorter/bin Dataset : VIRSorter Input file : 02_FASTA/MAT/MAT-vir_contigs.fa Db : 2 Working dir : 07_CLASSIFY_test/VIRSORTER/MAT Custom phages : Data dir : /pool/genomics/stri_istmobiome/dbs/virsorter/virsorter-data Num CPUs : 10 blastp : diamond Started at Fri Dec 6 05:45:32 2019 Step 0.5 : ~/miniconda3/envs/virsorter/bin/Scripts/Step_1_contigs_cleaning_and_gene_prediction.pl VIRSorter 07_CLASSIFY_test/VIRSORTER/MAT/fasta 07_CLASSIFY_test/VIRSORTER/MAT/fasta/input_sequences.fna 2 >> 07_CLASSIFY_test/VIRSORTER/MAT/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/MAT/logs/err Started at Fri Dec 6 05:45:34 2019 Step 0.8 : ~/miniconda3/envs/virsorter/bin/hmmsearch --tblout 07_CLASSIFY_test/VIRSORTER/MAT/Contigs_prots_vs_PFAMa.tab --cpu 10 -o 07_CLASSIFY_test/VIRSORTER/MAT/Contigs_prots_vs_PFAMa.out --noali /pool/genomics/stri_istmobiome/dbs/virsorter/virsorter-data/PFAM_27/Pfam-A.hmm 07_CLASSIFY_test/VIRSORTER/MAT/fasta/VIRSorter_prots.fasta >> 07_CLASSIFY_test/VIRSORTER/MAT/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/MAT/logs/err Started at Fri Dec 6 05:46:21 2019 Step 0.9 : ~/miniconda3/envs/virsorter/bin/hmmsearch --tblout 07_CLASSIFY_test/VIRSORTER/MAT/Contigs_prots_vs_PFAMb.tab --cpu 10 -o 07_CLASSIFY_test/VIRSORTER/MAT/Contigs_prots_vs_PFAMb.out --noali /pool/genomics/stri_istmobiome/dbs/virsorter/virsorter-data/PFAM_27/Pfam-B.hmm 07_CLASSIFY_test/VIRSORTER/MAT/fasta/VIRSorter_prots.fasta >> 07_CLASSIFY_test/VIRSORTER/MAT/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/MAT/logs/err ### Revision 0 Started at Fri Dec 6 05:47:47 2019 Out : Started at Fri Dec 6 05:48:15 2019 Step 1.2 : ~/miniconda3/envs/virsorter/bin/hmmsearch --tblout 07_CLASSIFY_test/VIRSORTER/MAT/r_0/Contigs_prots_vs_New_clusters.tab --cpu 10 -o 07_CLASSIFY_test/VIRSORTER/MAT/r_0/Contigs_prots_vs_New_clusters.out --noali 07_CLASSIFY_test/VIRSORTER/MAT/r_0/db/Pool_clusters.hmm 07_CLASSIFY_test/VIRSORTER/MAT/fasta/VIRSorter_prots.fasta >> 07_CLASSIFY_test/VIRSORTER/MAT/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/MAT/logs/err Started at Fri Dec 6 05:49:09 2019 Step 1.3 : ~/miniconda3/envs/virsorter/bin/diamond blastp --query 07_CLASSIFY_test/VIRSORTER/MAT/fasta/VIRSorter_prots.fasta --db 07_CLASSIFY_test/VIRSORTER/MAT/r_0/db/Pool_new_unclustered --out 07_CLASSIFY_test/VIRSORTER/MAT/r_0/Contigs_prots_vs_New_unclustered.tab --threads 10 --outfmt 6 -b 1 --more-sensitive -k 500 --evalue 0.001 >> 07_CLASSIFY_test/VIRSORTER/MAT/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/MAT/logs/err Started at Fri Dec 6 05:49:11 2019 Step 2 : ~/miniconda3/envs/virsorter/bin/Scripts/Step_2_merge_contigs_annotation.pl 07_CLASSIFY_test/VIRSORTER/MAT/fasta/VIRSorter_mga_final.predict 07_CLASSIFY_test/VIRSORTER/MAT/Contigs_prots_vs_Phage_Gene_Catalog.tab 07_CLASSIFY_test/VIRSORTER/MAT/Contigs_prots_vs_Phage_Gene_unclustered.tab 07_CLASSIFY_test/VIRSORTER/MAT/Contigs_prots_vs_PFAMa.tab 07_CLASSIFY_test/VIRSORTER/MAT/Contigs_prots_vs_PFAMb.tab /pool/genomics/stri_istmobiome/dbs/virsorter/virsorter-data/Phage_gene_catalog_plus_viromes/Phage_Clusters_current.tab 07_CLASSIFY_test/VIRSORTER/MAT/VIRSorter_affi-contigs.csv >> 07_CLASSIFY_test/VIRSORTER/MAT/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/MAT/logs/err Started at Fri Dec 6 05:49:11 2019 Step 3 : ~/miniconda3/envs/virsorter/bin/Scripts/Step_3_highlight_phage_signal.pl -csv 07_CLASSIFY_test/VIRSORTER/MAT/VIRSorter_affi-contigs.csv -out 07_CLASSIFY_test/VIRSORTER/MAT/VIRSorter_phage-signal.csv -n_cpu 10 -no_c 0 >> 07_CLASSIFY_test/VIRSORTER/MAT/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/MAT/logs/err Setting up the final result file Started at Fri Dec 6 05:49:13 2019 Step 4 : ~/miniconda3/envs/virsorter/bin/Scripts/Step_4_summarize_phage_signal.pl 07_CLASSIFY_test/VIRSORTER/MAT/VIRSorter_affi-contigs.csv 07_CLASSIFY_test/VIRSORTER/MAT/VIRSorter_phage-signal.csv 07_CLASSIFY_test/VIRSORTER/MAT/VIRSorter_global-phage-signal.csv 07_CLASSIFY_test/VIRSORTER/MAT/VIRSorter_new_prot_list.csv >> 07_CLASSIFY_test/VIRSORTER/MAT/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/MAT/logs/err Started at Fri Dec 6 05:49:13 2019 Step 5 : VIRSorter 07_CLASSIFY_test/VIRSORTER/MAT >> 07_CLASSIFY_test/VIRSORTER/MAT/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/MAT/logs/err Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 1. Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 3. Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 5. Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 7. Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 9. Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 11. Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 13. Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 15. Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 17. Use of uninitialized value in addition (+) at ~/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 19. ## Verify if this should have been a virome decontamination mode based on 10kb+ contigs Cleaning the output directory rm -r 07_CLASSIFY_test/VIRSORTER/MAT/r_0/db :