Closed chadsmith123 closed 6 years ago
Hi, It looks like there is an issue is with the HMMER searches, you can see in the error log (logs/Virsorter_stderr_log): "Error: Unrecognized format, trying to open hmm file /data/PFAM_27/Pfam-A.hmm for reading.".
Could you double-check that you have all the correct files from the virsorter-data package ?
Thanks for your quick reply. I took the data files from
https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz
The file is present in the working directory. [chads@ip-172-31-2-81 virsorter]$ ls -l /home/chads/phage/virsorter/virsorter-data/PFAM_27/Pfam-A.hmm -rw-r--r-- 1 chads chads 1.2G Feb 6 23:15 /home/chads/phage/virsorter/virsorter-data/PFAM_27/Pfam-A.hmm
So what might happen is a version conflict between hmmsearch in docker and the files from this new data package. Did you try with the data package recommended for Docker: http://mirrors.iplantcollaborative.org/browse/iplant/home/shared/imicrobe/VirSorter/virsorter-data.tar.gz ?
I tried this three times in Firefox and the download stopped at exactly 1.1GB. Is it available at another location (preferable via wget)?
Unfortunately no, the only way I know to download these big files from CyVerse is using iCommands (https://pods.iplantcollaborative.org/wiki/display/DS/Setting+Up+iCommands). In the meantime, I will also try on my side to see if this is indeed a version conflict, and if so we may be able to release a new dockerfile.
I tried iCommand but got:
(virsorter) [chads@ip-172-31-2-81 ~]$ iget http://mirrors.iplantcollaborative.org/browse/iplant/home/shared/imicrobe/VirSorter/virsorter-data.tar.gz ERROR: resolveRodsTarget: srcPath /iplant/home/smith_cc/http:/mirrors.iplantcollaborative.org/browse/iplant/home/shared/imicrobe/VirSorter/virsorter-data.tar.gz does not exist ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR (virsorter) [chads@ip-172-31-2-81 ~]$
I just released a new version of the Docker container, which now run VirSorter v1.0.5 (so will work with the data package available at https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz). Instructions are in the readme (but very similar to the previous docker image), let me know if that helps you run VirSorter successfully !
Terrific. I will test it the week of April 8th.
[cid:image001.jpg@01D1AAC1.6FA947B0]http://assemblybio.com/
Chad C. Smith, Ph.D.
Senior Scientist I
Assembly Biosciences
csmith@assemblybio.commailto:csmith@assemblybio.com
(415) 316-0861 (office) (512) 954-2219 (cell)
From: simroux notifications@github.com Sent: Friday, March 30, 2018 5:49 PM To: simroux/VirSorter VirSorter@noreply.github.com Cc: Chad Smith csmith@assemblybio.com; Author author@noreply.github.com Subject: Re: [simroux/VirSorter] cat: r_0/Contigs_prots_vs_New_clusters.tab: No such file or directory (#27)
I just released a new version of the Docker container, which now run VirSorter v1.0.5 (so will work with the data package available at https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz). Instructions are in the readme (but very similar to the previous docker image), let me know if that helps you run VirSorter successfully !
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/simroux/VirSorter/issues/27#issuecomment-377653606, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJvS7kY6Uk9s_kWZZ59h8hdEFtGrmquNks5tjtJ_gaJpZM4TBCZt.
This e-mail is not a secured data transmission for Protected Health Information (PHI) as defined by the Health Insurance Portability and Accountability Act of 1996, as amended (HIPAA), and it is the responsibility of all parties involved to take all reasonable actions to protect this message from non-authorized disclosure. This e-mail is intended for the recipient only. If you receive this e-mail in error, you should notify the sender and destroy the e-mail immediately. Unauthorized use or disclosure of the information contained herein could subject discloser to civil or criminal penalties under state and federal privacy laws.
VirSorter v1.0.5 is producing output. The logs/err file is empty.
Hello! I trying to run the program on Docker but . Attached is the directory of the run. Included is 'virsorter.log' which captures the screen output, including the command I executed.
Interestingly r_0/Contigs_prots_vs_New_clusters.tab exists at the end of the run.
Thank you for your time! virsorter.tar.gz