I got an error message from virsorter of dockerhub

[minsookim1983]

Hello,

I setup virsorter as described in "Docker-from Dockerhub" section. I did virsorter with my data, but I got an error message as follows:

Revision 1

Out : /usr/local/bin/Scripts/Step_0_make_new_clusters.pl r_1 /wdir/fasta/VIRSorter_prots.fasta r_0/db/Pool_unclustered.faa VIRSorter_new_prot_list.csv >> /wdir/log_out 2>> /wdir/log_err Step 1.1 new clusters and new database : Can't open 'r_1/db/Pool_clusters.hmm' for reading: 'No such file or directory' at /usr/local/bin/wrapper_phage_contigs_sorter_iPlant.pl line 292

rm VIRSorter_new_prot_list.csv ->

I have no idea of why "Pool_clusters.hmm" was not created in r_1/db/. I attached what was seen in my console. error.txt Please, let me know what is wrong with me, and what I can do to make it right. Thank you.

Min-Soo

[simroux]

Hi Min-Soo,

Unfortunately, this is not an error I've already seen. Could you send me the whole VirSorter output directory (in a zip file),so I can track down which file VirSorter generated and where the potential issue might be ?

Thanks,

Simon

[minsookim1983]

Thank you for your response. I am glad to hear that you have seen before the problem I have. Here I attached the whole VirSorter output directory below as a zip file.

One more thing I want to ask is that the sequence containing ambiguous calls (Ns) is excluded in analysis process? My input file is assembled contigs, so they contain several Ns in their sequences. I have seen the message below in log_out file: "we exclude VIRSorter_bin_357_MFP2_reassmbl_scaffold_16__-gene_41 because there is a pblm with the sequence -> too many succesive X, F, A, K or P"

Min-Soo ​ virsorter-specific501.zip https://drive.google.com/file/d/0B-02O4J9sOdkRnM3d0djek9PNms/view?usp=drive_web ​

On Wed, Oct 12, 2016 at 8:59 PM, simroux notifications@github.com wrote:

Hi Min-Soo,

Unfortunately, this is not an error I've already seen. Could you send me the whole VirSorter output directory (in a zip file),so I can track down which file VirSorter generated and where the potential issue might be ?

Thanks,

Simon

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/simroux/VirSorter/issues/9#issuecomment-253194201, or mute the thread https://github.com/notifications/unsubscribe-auth/AT2Aioc9qxqvYJCCynOkjy3EF-e57n9Tks5qzMuggaJpZM4KUkvh .

[simroux]

Hi Min-Soo,

I think I got what happened for your initial issue, and this should be fixed now in the github version of the scripts (not yet pushed to the Docker version though). Thanks for notifying us !

For your second questions (contigs with "Ns"), this is not a problem, the only thing is that sometimes ORfs are predicted that span this "N" region, and the corresponding predicted proteins will be absurdly long and low complexity (with stretches of X, F, A, K, or P), which will stall hmmsearch. So we exclude these proteins only (not the contigs) from the hmmsearch computations.

Best,

Simon

[minsookim1983]

Thank you for your kind response. It is good to hear you that my issue was helpful. I understood that the fixed version is update only on the github, but it is going to be fixed soon in the Docker version.

Best,

Min-Soo