AAATAACACCGCTAATAATGAAAGTAATTATATTTTAGGCGGCGGTAATACAACTAAAAAAAAATATACTACAGTTGTTGGCAGAGGGAATAACTTAAACAGCCCAAAAATTGTTGCAGTCGGACACTATAATACATCAAGCGGTACTACGGATAACTCTACGTCTTTTGGTTATTCAAATAATAACCAACACTCAAATAGCCATTTGTTTGGGGTAGGCCTACAAAGCTATCAAGCAAAAGAGGTTGTAATAGGTAAACATAACGCCGCGCCGAGCAACCCAACTGGCGCAACCCCAAGGGGTGCAAATGTAATTATAGGCGTAGGGACTGGGCAGTATGCTGGTGCAAATATGAATGCGGTAGAGTATTACGGTTTTAATGACGGCAGTATGCAAGTTATACACAAGGCTTTATACAACTCTAGTAGTTACGCAAACGACAGTGCCGCGGCGTCTGGCGGTGTTCCGTTAGGTGGTTTATATAGGACTGGAAGCACGGTAAAAATAAGAATGACATAAATGTAGCTTAGTAAAAAAATACCAAAAACACGTAATACATATAATATACCGGCTCGGGATAGAGCAAACCAAATAGTAATAATTAAAACCAAAACCAATGACACTATTTTATTCGACTAATTCGTGGAGTAGTCAACCACAACCAAATGAAAAAACCGTAGAAACCTGGAAGCATGCGTCTACCAAATCCAACTGGCGCATTGTGCAGCTACCAAATGGATTCTACCAAACAGAAATTAAAGTACCAGACGAAGACTCCTGGAAAGATATTACAAGGAGAGAAACTATCGAGGGTGCAGAAGCAGCAATTGACGGATCTATACAGTATTATCAAAAAAAGCTTGATTTTATAAAAGGCCCTAAAGTTGTAAAGACTTTTGAAAAAGAGTAAGTAATTTAAAATTTAATTTAATGGAATTTAATAACCCTAGTGAGATAGTTAAAACTCTCACATTTGGCAATGAAGCCAAAGATCAAATTATGAAGGGCGTTGAAAAACTATCAAACGCAGTAAAGAGCACTCTAGGTGCGTCTGGAAAATGCGTGATATATGAGGACGCTCTTGGAAAACCGGTGATAACAAAAGATGGTGTAACCGTTGCGGAAAGCGTAGTCTTATTACATCCGGTTGAAAACATTGGTGCTACTTTAATAAAAGAAGCGGCAAGTAATACTGTAAAGGAGGCCGGGGACGGTACAACAACATCAACCGTCCTTGCGCATTCTTTGCTTAAAACAGTTAATGAAAATTTAGATGAAGAAAAAGTTAGAGAACTTAAAAGCGGCATTCTTAGTGGCGCTGAAAAAGTTATGGTTTATCTTGATAAAGCCAGTACTCAAATTAAAGGTGACATGCTTAAGCAAGTTGCTAGTATTTCATGCAACAACGACACAGAGCTTGGAGATAAAATTGGACAAGCTTACGAAAAAGTTGGAAAAAATGGAGTCGTTTTAATGGAGGAATCCGATACAAATGAAACTTATGTTGAGTTTGTTGACGGAGTACAATTTGATAGCGGTTTAAAATCACCGCATTTGGCTACAGACAAAAATAAAGGCTCGGCTACATTAGAAGATCCATATGTTCTTATAGTTTCTTCACCCATACCTAATATACGTAGAATACAAAATGTATTAGAGTTTGTAATTAAAAATAAGAAAAGCTTATTGATAGTTGCAGATGTTGAGCAGCAACCATACCAAACGTTACTGGCTAACAAAGTAAAAGGCAACATAAAAGTAAACATTGTTGATTTACCTGGCTTCGGCCCGACTAAGCAACAAACACTTGAAGACCTAGCGATACTAACTGGAGCTAAAATCATAAACGAAGAGTTAGGAGACGATTTAGATTTTATAGACCCTGACGTATTAGGAAAAGCGTTTAAAGCTGTTACAGACGATAAAAACACTGTTCTGCAAGTTGCTGAAGCAAACGAAGAGGTTGCATTAAGGATAATGGACGTTGAAAAGCAAATAGCTGAAGAATCAAATCCATTTTTTAAGAAACAACTAGAGCAAAGATTGTCAATGCTAACCGGTCAAGTTGGAATCATATATGTTGGTGCCGACAGTAAGGTTGAGCTTAAAGAAAAGAAAGATCGTGTTGAAGATGCGATTTATGCGACAAAAGCTGCTTATAAAGAAGGTATAGTTCCAGGTGGCGGTGTAGCGCTGTTAAATGCTTCTGTTTTAGTAAAAGCAAAAAACAAAGGCGAAGAAATATTACTTAAAGCAATCAAAGCGCCGTATAATACTATATTAGAAAACGCTAACCTAAATGCTAATCTGCAATCAGATAGAAAGGGTTGGGGTATTGACGTAACATCTGGGAAACCTGTTAATATGATTAAAGCAGGTATTATAGACCCGGTACTTGTTACAAAGACAGCTTTAAAGAATGCAGTAAGCGTTGTCAACACAATTATATCTGCCGATTGTATAATCAGTAATAAACGGTTGGCATGAAAGCAATAAATCATTTTGTAGTTGTAAACAAAATAAAAGAGGAACCTGCGAAAGTTGGTGGTCTTGAACTTACTGAAAAGCAGAATAAAGATGTTCGCTATTTAAAAGGCAAAGTAATCACTGTTGGCAATTTAGTAGAGGTAATAAAGAAAGGTGATATTGTCAGGTATGACAAACATGCTGGCCACGGAATTGAATGGGATGATTCCCTTTATTATGTGCTAAAGATCTCTGATATAGTACTTGTAGAATGAGATTAAGCCCATCTGACTTGCAAGAGATGAATTTGTTAAAGTATTACAGGCTCATAAGAAGGTGGGCCTGTAAAACTTATAACTTAAAAGATGCAGATTTAGAGCTGCTTATTTATCTAGATTGCAAAAAGCTTTTTACACGTAATGATTTTATAGAAGGTGTTTACACCTATAGCTGGGATAAAAACCGGTGGGAACGATTGCGAAGAGATGGGTGGATTGATGTTTTTAAAGAAAGAAACCGAACCACTTCTAAGTATGCAGTTTATAAAACGTCGTTTAAGTGTAAAACCTTAATTAAAAGAATATACAGAATAATGTTGGCAGAAGAAGATTTACCAACATCTGAACGAAGTACATTTTATAAAAACAAAACATATACCGATAAAGTCTTTAATAAGGCAATTGATGATATGATTAACGACAAAGAACGATGAGTTTTAAATTAAAGTCTAAAGGCGAACTTTTCGGTTACAACGAAGAATTATCTGAGTTTGGTACACCAGTGTTTGAAAAAGATTTAGGCGATAATATTATAGCAGAAGCTAATCGTGACTTTACTATATTTGTAAACAAAAATGCAAGCAAAGAGCAAAAGCGTGGTTCTATGAAAGAGGAAAATAATCACCTTGACCAAATGATGCAGGGCCGCTTGCAATACACAAATGAAGAAGTTATTTGGAAGAAAGATACAAAGTCACCAGCTAGAGTATACAAACGTATAGGTGGCAGGATAGTAAATAAAACAACAAATGAGCCAGAAGGCGGGAACCTTGAATGGGAAGCCGAGGCTAAAAAAGCAGACTAATTATGGCAAACCCAATTACAGCAATAGCGTCTCGCTCATGCGCGAAGAATTCAATGCTTAAGCAGACAGGTTCTACTGATGACGAAAAAGACGATATAACAACAAGTACCGGAGGTACAAAATCAGTGTCTACTATAGCGGATGTTCAACAAAATATTGGCGGCGGTCGTGCTATATCAGGTGATCAAACCGATACTACAATAACCGCACCGGGCTCAGAAGGCGGAACCGAAACTATTTACGATACAGGCAAAAGCCTTAAAGGTTTGACGCCAGAACAATTAGATTGGCGTGAAAAGGAAATTGAAAGGCTAGGTGGTATTGATGAATACCATAAAAAATATGGTGATCCTAAAAAAGGTAAAGCACGTGAAATAAAAACACCAGGTACTCCTCCTACATCTGATACTACTTCAGATTTTCAAATGGACCAAGCACAGGTCAAAGGAATGGAAAATCTTGATTTGAGAGCTGACATACGCCAAGAGAAAATACTAAATAGATTGGAAAGACAGGCTGAGCGCAGGCAAGATCGTTTTGAAAGAAAGGGTTTAAGCGGTAAAGAGAAACGGGCTCTTCGTAAAGCGCAAAGAAAAGACCGTAAAGCAAGCAATATAGAAAGACAGCAAAATATTCAGAATCTTATTGCTGATCGTAGAGCTTTAAGAGACCTGCAAAGAGATCAAGGCAGTTTTGGCGGTGAAAGCTACAACGTTGGCAAGGTTTCAGAAACCAAAGAAGGTGTTGTTAATAGAGTTGCAAAAGAATCTTTTACGCCCACACAAGTAACTGAAACGCCTAGTGGCAAAACAAAAGTGGGTGAAATTATAGAAGGTGTTGGGAATGTATTTGCAAAAAAAGAGGGAGGCACTGCTGTAGGTAATGCTTTAAGAGGTATTTTTAAACCAAAATCACCAGCGCCATTAAAGAAAAACTATTTTAATAAATAAGTTATGCCAGGATATATACAACCAGAGGTAAGTTCTGTGGTAAAAAAACTCCGCAAGACAACAAAAGGAAAAGGTAGGCATTTCTTAACAGCCAAAGAAGGCGCCGGAATGACTGAAGCTGGCAGAAGAGCTTATAATAAAGAAACCGGCGGCAATCTTAAAGCACCACAACCAGGCThis VirSorter run uses `diamond` (Buchfink et al., Nature Methods 2015) instead of `blastp`.

Bin            : /home/scottjj/miniconda3/envs/virsorter/bin
Dataset        : VIRSorter
Input file     : 02_FASTA/WATER/WATER-vir_contigs.fa
Db             : 2
Working dir    : 07_CLASSIFY_test/VIRSORTER/WATER
Custom phages  : 
Data dir       : /pool/genomics/stri_istmobiome/dbs/virsorter/virsorter-data
Num CPUs       : 10
blastp         : diamond

Started at Fri Dec  6 05:49:14 2019
Step 0.5 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_1_contigs_cleaning_and_gene_prediction.pl VIRSorter 07_CLASSIFY_test/VIRSORTER/WATER/fasta 07_CLASSIFY_test/VIRSORTER/WATER/fasta/input_sequences.fna 2 >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
Started at Fri Dec  6 05:50:05 2019
Step 0.8 : /home/scottjj/miniconda3/envs/virsorter/bin/hmmsearch --tblout 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_PFAMa.tab --cpu 10 -o 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_PFAMa.out --noali /pool/genomics/stri_istmobiome/dbs/virsorter/virsorter-data/PFAM_27/Pfam-A.hmm 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_prots.fasta >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
Started at Fri Dec  6 05:58:22 2019
Step 0.9 : /home/scottjj/miniconda3/envs/virsorter/bin/hmmsearch --tblout 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_PFAMb.tab --cpu 10 -o 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_PFAMb.out --noali /pool/genomics/stri_istmobiome/dbs/virsorter/virsorter-data/PFAM_27/Pfam-B.hmm 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_prots.fasta >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
### Revision 0
Started at Fri Dec  6 06:12:48 2019
Out : 

Started at Fri Dec  6 06:12:59 2019
Step 1.2 : /home/scottjj/miniconda3/envs/virsorter/bin/hmmsearch --tblout 07_CLASSIFY_test/VIRSORTER/WATER/r_0/Contigs_prots_vs_New_clusters.tab --cpu 10 -o 07_CLASSIFY_test/VIRSORTER/WATER/r_0/Contigs_prots_vs_New_clusters.out --noali 07_CLASSIFY_test/VIRSORTER/WATER/r_0/db/Pool_clusters.hmm 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_prots.fasta >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
	

Started at Fri Dec  6 06:22:33 2019

Step 1.3 : /home/scottjj/miniconda3/envs/virsorter/bin/diamond blastp --query 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_prots.fasta --db 07_CLASSIFY_test/VIRSORTER/WATER/r_0/db/Pool_new_unclustered --out 07_CLASSIFY_test/VIRSORTER/WATER/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/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
	
Started at Fri Dec  6 06:22:37 2019
Step 2 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_2_merge_contigs_annotation.pl 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_mga_final.predict 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_Phage_Gene_Catalog.tab 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_Phage_Gene_unclustered.tab 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_PFAMa.tab 07_CLASSIFY_test/VIRSORTER/WATER/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/WATER/VIRSorter_affi-contigs.csv >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
Started at Fri Dec  6 06:22:39 2019
Step 3 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_3_highlight_phage_signal.pl -csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_affi-contigs.csv -out 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_phage-signal.csv -n_cpu 10 -no_c 0 >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
Setting up the final result file
Started at Fri Dec  6 06:22:43 2019
Step 4 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_4_summarize_phage_signal.pl 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_affi-contigs.csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_phage-signal.csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_global-phage-signal.csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_new_prot_list.csv >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
### Revision 1
Started at Fri Dec  6 06:22:43 2019
Out : 
/home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_0_make_new_clusters.pl 07_CLASSIFY_test/VIRSORTER/WATER/r_1 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_prots.fasta 07_CLASSIFY_test/VIRSORTER/WATER/r_0/db/Pool_unclustered.faa 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_new_prot_list.csv 10 diamond >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err

Step 1.1 new clusters and new database : 

Started at Fri Dec  6 06:22:49 2019
Step 1.2 : /home/scottjj/miniconda3/envs/virsorter/bin/hmmsearch --tblout 07_CLASSIFY_test/VIRSORTER/WATER/r_1/Contigs_prots_vs_New_clusters.tab --cpu 10 -o 07_CLASSIFY_test/VIRSORTER/WATER/r_1/Contigs_prots_vs_New_clusters.out --noali 07_CLASSIFY_test/VIRSORTER/WATER/r_1/db/Pool_clusters.hmm 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_prots.fasta >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
	

Started at Fri Dec  6 06:22:49 2019

Step 1.3 : /home/scottjj/miniconda3/envs/virsorter/bin/diamond blastp --query 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_prots.fasta --db 07_CLASSIFY_test/VIRSORTER/WATER/r_1/db/Pool_new_unclustered --out 07_CLASSIFY_test/VIRSORTER/WATER/r_1/Contigs_prots_vs_New_unclustered.tab --threads 10 --outfmt 6 -b 1 --more-sensitive -k 500 --evalue 0.001 >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
	
Started at Fri Dec  6 06:22:51 2019
Step 2 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_2_merge_contigs_annotation.pl 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_mga_final.predict 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_Phage_Gene_Catalog.tab 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_Phage_Gene_unclustered.tab 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_PFAMa.tab 07_CLASSIFY_test/VIRSORTER/WATER/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/WATER/VIRSorter_affi-contigs.csv >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
Started at Fri Dec  6 06:22:53 2019
Step 3 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_3_highlight_phage_signal.pl -csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_affi-contigs.csv -out 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_phage-signal.csv -n_cpu 10 -no_c 0 -ref 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_affi-contigs.refs >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
Setting up the final result file
Started at Fri Dec  6 06:22:57 2019
Step 4 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_4_summarize_phage_signal.pl 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_affi-contigs.csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_phage-signal.csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_global-phage-signal.csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_new_prot_list.csv >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
### Revision 2
Started at Fri Dec  6 06:22:57 2019
Out : 
/home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_0_make_new_clusters.pl 07_CLASSIFY_test/VIRSORTER/WATER/r_2 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_prots.fasta 07_CLASSIFY_test/VIRSORTER/WATER/r_1/db/Pool_unclustered.faa 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_new_prot_list.csv 10 diamond >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err

Step 1.1 new clusters and new database : 
There are no clusters in the database, so skip the hmmsearch

Started at Fri Dec  6 06:23:03 2019

Step 1.3 : /home/scottjj/miniconda3/envs/virsorter/bin/diamond blastp --query 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_prots.fasta --db 07_CLASSIFY_test/VIRSORTER/WATER/r_2/db/Pool_new_unclustered --out 07_CLASSIFY_test/VIRSORTER/WATER/r_2/Contigs_prots_vs_New_unclustered.tab --threads 10 --outfmt 6 -b 1 --more-sensitive -k 500 --evalue 0.001 >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
	
Started at Fri Dec  6 06:23:04 2019
Step 2 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_2_merge_contigs_annotation.pl 07_CLASSIFY_test/VIRSORTER/WATER/fasta/VIRSorter_mga_final.predict 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_Phage_Gene_Catalog.tab 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_Phage_Gene_unclustered.tab 07_CLASSIFY_test/VIRSORTER/WATER/Contigs_prots_vs_PFAMa.tab 07_CLASSIFY_test/VIRSORTER/WATER/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/WATER/VIRSorter_affi-contigs.csv >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
Started at Fri Dec  6 06:23:06 2019
Step 3 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_3_highlight_phage_signal.pl -csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_affi-contigs.csv -out 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_phage-signal.csv -n_cpu 10 -no_c 0 -ref 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_affi-contigs.refs >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
Setting up the final result file
Started at Fri Dec  6 06:23:10 2019
Step 4 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_4_summarize_phage_signal.pl 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_affi-contigs.csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_phage-signal.csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_global-phage-signal.csv 07_CLASSIFY_test/VIRSORTER/WATER/VIRSorter_new_prot_list.csv >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	

Started at Fri Dec  6 06:23:10 2019

Step 5 : /home/scottjj/miniconda3/envs/virsorter/bin/Scripts/Step_5_get_phage_fasta-gb.pl VIRSorter 07_CLASSIFY_test/VIRSORTER/WATER >> 07_CLASSIFY_test/VIRSORTER/WATER/logs/out 2>> 07_CLASSIFY_test/VIRSORTER/WATER/logs/err
	
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 19.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 21.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 23.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 25.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 27.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 29.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 31.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 33.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 35.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 37.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 39.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 41.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 43.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 45.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 47.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 49.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 51.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 53.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 55.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 57.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 59.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 61.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 63.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 65.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 67.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 69.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 71.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 131.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 133.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 135.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 137.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 139.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 141.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 143.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 145.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 147.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 149.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 151.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 153.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 155.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 157.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 159.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 161.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 163.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 165.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 167.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 169.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 171.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 173.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 175.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 177.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 179.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 181.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 183.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 185.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 187.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 189.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 191.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 193.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 195.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 197.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 199.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 201.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 203.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 205.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 207.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 209.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 211.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 213.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 215.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 217.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 219.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 221.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 223.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 225.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 227.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 229.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 231.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 233.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 235.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 237.
## Verify if this should have been a virome decontamination mode based on 10kb+ contigs
#!#!#!#!#!#!#!#!#!#!#!#!#!#!#!#!##!#!#!#!#!#!#!#!##!#!#!#!#!#!#!#!#
More than 25% of the bp in contigs >= 10kb were predicted as viral (estimated ratio: 43.67%
You may want to use the virome decontamination mode on this dataset, as it seems to have lot of viruses
#!#!#!#!#!#!#!#!#!#!#!#!#!#!#!#!##!#!#!#!#!#!#!#!##!#!#!#!#!#!#!#!#
Cleaning the output directory
rm -r 07_CLASSIFY_test/VIRSORTER/WATER/r_0/db : 
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
= Fri Dec 6 06:23:13 EST 2019 job testjob_02_run_virsorter don