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simroux / Inovirus

Set of scripts and data used to detect putative inovirus sequences and/or taxonomically classify them.
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No returning same results as example_files #1

Closed oseias-r-junior closed 5 years ago

oseias-r-junior commented 5 years ago

Hi simroux,

I'm trying to use your inovirus_detector with my data, but first I've applied your script to the example_file it come along with the script. But the returning files are not as the expected_results. Also, there is no gff file as output. Follows the output in terminal...

Real start = 29234 --- Real end = 90649 hmmsearch -o /dev/null --noali --tblout /home/oseias/Documents/Oseias/Programs/Inovirus_detector/input/2731957639_129103.assembled_frag_Ga0128599_102362_vs_Pfam_db.tsv --cpu 2 /home/oseias/Documents/Oseias/Programs/Inovirus_detector/Pfam-A.hmm /home/oseias/Documents/Oseias/Programs/Inovirus_detector/input/2731957639_129103.assembled_frag_Ga0128599_102362_prots.faa

hmmsearch -o /dev/null --noali --tblout /home/oseias/Documents/Oseias/Programs/Inovirus_detector/input/2731957639_129103.assembled_frag_Ga0128599_102362_vs_InoSuperPCs.tsv --cpu 2 /home/oseias/Documents/Oseias/Programs/Inovirus_detector/Inovirus_detector/Inovirus_db/Superclusters_db.hmm /home/oseias/Documents/Oseias/Programs/Inovirus_detector/input/2731957639_129103.assembled_frag_Ga0128599_102362_prots.faa

blastp -query /home/oseias/Documents/Oseias/Programs/Inovirus_detector/input/2731957639_129103.assembled_frag_Ga0128599_102362_prots.faa -db /home/oseias/Documents/Oseias/Programs/Inovirus_detector/Inovirus_detector/Inovirus_db/Inoviridae_singletons -out /home/oseias/Documents/Oseias/Programs/Inovirus_detector/input/2731957639_129103.assembled_frag_Ga0128599_102362_vs_singletons.tsv -num_threads 2 -outfmt 6 -evalue 0.001

./Predict_inovirus_coat_proteins.pl -f /home/oseias/Documents/Oseias/Programs/Inovirus_detector/input/2731957639_129103.assembled_frag_Ga0128599_102362_prots.faa -sp /home/oseias/Documents/Oseias/Programs/signalp-4.1/signalp -th /home/oseias/Documents/Oseias/Programs/tmhmm-2.0c/bin/tmhmm Seems like there was a problem with Predict_inovirus_coat_proteins.pl -> we didn't get any output file

I'll be glad with any response regarding this issue.

simroux commented 5 years ago

Hi,

Seems like this is only the end of the output (there should be some information before the "Real start = 29234 --- Real end = 90649"). It looks however as if the last step "Predict_inovirus_coat_proteins.pl" didn't work properly. Could you try running this command line separately (from the same folder from which you originally try to run "Identify_candidate_fragments_from_gbk.pl"), i.e.:

./Predict_inovirus_coat_proteins.pl -f /home/oseias/Documents/Oseias/Programs/Inovirus_detector/input/2731957639_129103.assembled_frag_Ga0128599_102362_prots.faa -sp /home/oseias/Documents/Oseias/Programs/signalp-4.1/signalp -th /home/oseias/Documents/Oseias/Programs/tmhmm-2.0c/bin/tmhmm

and check the output of this command specifically ?

oseias-r-junior commented 5 years ago

Hi simroux,

First of all, thank you very much for such a fast response to my issue.

So, I ran the code as suggested. The whole terminal output should be attached output_2.txt Plus a file "2731957639_129103.assembled_frag_Ga0128599_102362_prots.faa_inovirus_coat_prediction.csv" was created by running the code you (and terminal script output) suggested.

Also, I must tell you that in order to running the script "Identify_candidate_fragments_from_gbk.pl" (the same I sent you the terminal output) in first place, I had to change the file input (2731957639_129103.assembled.gbk, as it came along with the inovirus_detector). It seems that one of the gene were missing. So I edit the file. I'd erased this header-ok-but-missing-sequence gene and then a step for blast finally ran. But as I sent you I still had an issue predicting inovirus coat.

Now, it seems that running Predict_inovirus_coat_proteins.pl it was possible to detect inovirus coat from generated data (2731957639_129103.assembled_frag_Ga0128599_102362_prots.faa).

oseias-r-junior commented 5 years ago

Me again... I think I found one of the reasons why it was going something wrong. The tmhmm was with wrong path at the header "/local/bin/perl" instead of "/bin/perl". I fixed and finally worked. I'm sending also the output at the terminal as it seems to be ok. output_1_new.txt Thanks again simroux!

simroux commented 5 years ago

Sounds good, thanks for the update ! I will add this information to the Readme in case another user encounters the same issue.