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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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BLASTp error conda installation #39

Open jw51 opened 5 years ago

jw51 commented 5 years ago

I ran VirSorter (installed using conda) with following paramaters --db 2 --virome 1 It seemed to be working (I have a VIRSorter_global-phage-signal.csv file with some hits) ... But I got an error while running (Contigs_prots_vs_New_unclustered.tab: No such file or directory): 

Step 0.5 : /VirSorter/Scripts/Step_1_contigs_cleaning_and_gene_prediction.pl VIRSorter fasta fasta/input_sequences.fna 2 >> logs/out 2>> logs/err
Step 0.8 : /miniconda3/envs/virsorter/bin/hmmsearch --tblout ./Contigs_prots_vs_PFAMa.tab --cpu 36 -o ./Contigs_prots_vs_PFAMa.out --noali /virsorter-data/PFAM_27/Pfam-A.hmm fasta/VIRSorter_prots.fasta >> logs/out 2>> logs/err
Step 0.9 : /miniconda3/envs/virsorter/bin/hmmsearch --tblout ./Contigs_prots_vs_PFAMb.tab --cpu 36 -o ./Contigs_prots_vs_PFAMb.out --noali /virsorter-data/PFAM_27/Pfam-B.hmm fasta/VIRSorter_prots.fasta >> logs/out 2>> logs/err
### Revision 0
Step 1.2 : /miniconda3/envs/virsorter/bin/hmmsearch --tblout r_0/Contigs_prots_vs_New_clusters.tab --cpu 36 -o r_0/Contigs_prots_vs_New_clusters.out --noali r_0/db/Pool_clusters.hmm fasta/VIRSorter_prots.fasta >> logs/out 2>> logs/err
Step 1.3 : /miniconda3/envs/virsorter/bin/blastp -query fasta/VIRSorter_prots.fasta -db r_0/db/Pool_new_unclustered -out r_0/Contigs_prots_vs_New_unclustered.tab -num_threads 36 -outfmt 6 -evalue 0.001 >> logs/out 2>> logs/err
cat: r_0/Contigs_prots_vs_New_unclustered.tab: No such file or directory
Step 2 : /VirSorter/Scripts/Step_2_merge_contigs_annotation.pl fasta/VIRSorter_mga_final.predict ./Contigs_prots_vs_Phage_Gene_Catalog.tab ./Contigs_prots_vs_Phage_Gene_unclustered.tab ./Contigs_prots_vs_PFAMa.tab ./Contigs_prots_vs_PFAMb.tab /virsorter-data/Phage_gene_catalog_plus_viromes/Phage_Clusters_current.tab ./VIRSorter_affi-contigs.csv >> logs/out 2>> logs/err
Step 3 : /VirSorter/Scripts/Step_3_highlight_phage_signal.pl -csv ./VIRSorter_affi-contigs.csv -out ./VIRSorter_phage-signal.csv -n_cpu 36 -no_c 0 -ref virsorter-data/Generic_ref_file.refs >> logs/out 2>> logs/err
Step 4 : /VirSorter/Scripts/Step_4_summarize_phage_signal.pl ./VIRSorter_affi-contigs.csv ./VIRSorter_phage-signal.csv ./VIRSorter_global-phage-signal.csv ./VIRSorter_new_prot_list.csv >> logs/out 2>> logs/err
### Revision 1
Step 1.1 new clusters and new database : 
There are no clusters in the database, so skip the hmmsearch
Step 1.3 : /miniconda3/envs/virsorter/bin/blastp -query fasta/VIRSorter_prots.fasta -db r_1/db/Pool_new_unclustered -out r_1/Contigs_prots_vs_New_unclustered.tab -num_threads 36 -outfmt 6 -evalue 0.001 >> logs/out 2>> logs/err
cat: r_1/Contigs_prots_vs_New_unclustered.tab: No such file or directory
Step 2 : /VirSorter/Scripts/Step_2_merge_contigs_annotation.pl fasta/VIRSorter_mga_final.predict ./Contigs_prots_vs_Phage_Gene_Catalog.tab ./Contigs_prots_vs_Phage_Gene_unclustered.tab ./Contigs_prots_vs_PFAMa.tab ./Contigs_prots_vs_PFAMb.tab /virsorter-data/Phage_gene_catalog_plus_viromes/Phage_Clusters_current.tab ./VIRSorter_affi-contigs.csv >> logs/out 2>> logs/err
Step 3 : /VirSorter/Scripts/Step_3_highlight_phage_signal.pl -csv ./VIRSorter_affi-contigs.csv -out ./VIRSorter_phage-signal.csv -n_cpu 36 -no_c 0 -ref /virsorter-data/Generic_ref_file.refs >> logs/out 2>> logs/err
Step 4 : /VirSorter/Scripts/Step_4_summarize_phage_signal.pl ./VIRSorter_affi-contigs.csv ./VIRSorter_phage-signal.csv ./VIRSorter_global-phage-signal.csv ./VIRSorter_new_prot_list.csv >> logs/out 2>> logs/err
Step 5 : /VirSorter/Scripts/Step_5_get_phage_fasta-gb.pl VIRSorter . >> logs/out 2>> logs/err

The first few lines of the logs/err file:

/miniconda3/envs/virsorter/bin/blastp: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
/miniconda3/envs/virsorter/bin/makeblastdb: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
/miniconda3/envs/virsorter/bin/blastp: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

I compared the VIRSorter_global-phage-signal.csv with the one generated by CyVerse and the main difference is that one sequence is classified as cat2 by the locally installed VirSorter, while it classified as both cat5 and cat6 in the CyVerse version of VirSorter. Also the tab_files/Contigs_prots_vs_Phage_Gene_unclustered.tab file is empty when I run it myself.

So my question is: what should I do to fix this blast error? blastp was installed in the conda environment, which was loaded

simroux commented 5 years ago

This seems to be a common conda error without clear solution :-/ https://www.google.com/search?client=opera&q="error+while+loading+shared+libraries%3A+libssl.so.1.0.0"+conda&sourceid=opera&ie=UTF-8&oe=UTF-8

Looks like maybe trying to add manually the openssl package to the conda environment would work ? (conda install -c anaconda openssl / https://github.com/ENCODE-DCC/atac-seq-pipeline/issues/62).

Also, was VirSorter installed in a separate and "clean" conda environment ? If not, it may be worth trying (looks like this could be some version incompatibility between different tools installed in the same conda environment).