Open ameetpinto opened 8 years ago
ameetpinto
commented
8 years ago The file in question (shotmap_db_nr_seqeunce_lengths.tab) is present in the folder where the shotmap database is present, but for some reason the "Calculating abundance.." step was looking for the file in the shotmap_output folder??
sharpton
commented
8 years ago Hi Ameet,
We recently stumbled across this bug and fixed it. You should be able to find a patched version in the most recent shotmap github repository. Can you please do the following:
If shotmap_tests_log.txt finishes without an error, then this bug should be fixed on your end.
That said, because I don't want you to have to rebuild your search database or rerun your homology search in shotmap (that was a lot of invested time, I'm sure), I'd request that you do the following:
Once I've been able to confirm that everything is properly configured, we'll use the --goto=P command to restart your failed run and jump straight to the parse results step.
Sorry for the trouble.
Best, Tom
On Mon, Mar 7, 2016 at 11:58 AM, ameetpinto notifications@github.com wrote:
The file in question (shotmap_db_nr_seqeunce_lengths.tab) is present in the folder where the shotmap database is present, but for some reason the "Calculating abundance.." step was looking for the file in the shotmap_output folder??
The command I used is: perl /home/opt/shotmap/scripts/shotmap.pl -i shotmap_input/ -d shotmap -o shotmap_output/ --nprocs 20 --class-score=35 --postrare-samps=69423326 --rarefaction-type=read
— Reply to this email directly or view it on GitHub https://github.com/sharpton/shotmap/issues/5#issuecomment-193423814.
Thomas J. Sharpton
Assistant Professor Department of Microbiology Department of Statistics Oregon State University
(541) 737-8623 thomas.sharpton@gmail.com @tjsharpton lab.sharpton.org
ameetpinto
commented
8 years ago Thanks Tom. This is very helpful!
I will give this a try and let you know how it goes.
Thanks again for being so responsive with this. Much appreciated. Ameet — Ameet J. Pinto, PhD. Assistant Professor Northeastern University Dept. Civil & Environmental Eng (primary) Dept. Bioengineering (affiliated) 269 SN, 360 Huntington Avenue, Boston, MA 02115. +1 (617) 373-5241 pintolab.com @watermicrobe —— www.mewe2016.org [cid:8A5E4DBD-7262-46F7-A208-0CF6AFCFCE9E]
From: Thomas Sharpton notifications@github.com<mailto:notifications@github.com> Reply-To: sharpton/shotmap reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday, March 8, 2016 at 4:59 PM To: sharpton/shotmap shotmap@noreply.github.com<mailto:shotmap@noreply.github.com> Cc: ameetpinto ameet.pinto@glasgow.ac.uk<mailto:ameet.pinto@glasgow.ac.uk> Subject: Re: [shotmap] error during shotmap.pl (#5)
Hi Ameet,
We recently stumbled across this bug and fixed it. You should be able to find a patched version in the most recent shotmap github repository. Can you please do the following:
If shotmap_tests_log.txt finishes without an error, then this bug should be fixed on your end.
That said, because I don't want you to have to rebuild your search database or rerun your homology search in shotmap (that was a lot of invested time, I'm sure), I'd request that you do the following:
Once I've been able to confirm that everything is properly configured, we'll use the --goto=P command to restart your failed run and jump straight to the parse results step.
Sorry for the trouble.
Best, Tom
On Mon, Mar 7, 2016 at 11:58 AM, ameetpinto notifications@github.com<mailto:notifications@github.com> wrote:
The file in question (shotmap_db_nr_seqeunce_lengths.tab) is present in the folder where the shotmap database is present, but for some reason the "Calculating abundance.." step was looking for the file in the shotmap_output folder??
The command I used is: perl /home/opt/shotmap/scripts/shotmap.pl -i shotmap_input/ -d shotmap -o shotmap_output/ --nprocs 20 --class-score=35 --postrare-samps=69423326 --rarefaction-type=read
— Reply to this email directly or view it on GitHub https://github.com/sharpton/shotmap/issues/5#issuecomment-193423814.
Thomas J. Sharpton
Assistant Professor Department of Microbiology Department of Statistics Oregon State University
(541) 737-8623 thomas.sharpton@gmail.commailto:thomas.sharpton@gmail.com @tjsharpton lab.sharpton.org
— Reply to this email directly or view it on GitHubhttps://github.com/sharpton/shotmap/issues/5#issuecomment-193867387.
sharpton
commented
8 years ago My pleasure, and apologies for the hiccup. Do let me know how I can help, and once you have the requested information, I should be able to promptly move you to the finish line.
Best of luck, Tom
On Tue, Mar 8, 2016 at 11:24 AM, ameetpinto notifications@github.com wrote:
Thanks Tom. This is very helpful!
I will give this a try and let you know how it goes.
Thanks again for being so responsive with this. Much appreciated. Ameet — Ameet J. Pinto, PhD. Assistant Professor Northeastern University Dept. Civil & Environmental Eng (primary) Dept. Bioengineering (affiliated) 269 SN, 360 Huntington Avenue, Boston, MA 02115. +1 (617) 373-5241 pintolab.com @watermicrobe —— www.mewe2016.org [cid:8A5E4DBD-7262-46F7-A208-0CF6AFCFCE9E]
From: Thomas Sharpton <notifications@github.com<mailto: notifications@github.com>> Reply-To: sharpton/shotmap <reply@reply.github.com<mailto: reply@reply.github.com>> Date: Tuesday, March 8, 2016 at 4:59 PM To: sharpton/shotmap <shotmap@noreply.github.com<mailto: shotmap@noreply.github.com>> Cc: ameetpinto ameet.pinto@glasgow.ac.uk<mailto:ameet.pinto@glasgow.ac.uk>
Subject: Re: [shotmap] error during shotmap.pl (#5)
Hi Ameet,
We recently stumbled across this bug and fixed it. You should be able to find a patched version in the most recent shotmap github repository. Can you please do the following:
- cd $SHOTMAP_LOCAL
- git pull origin master
- cd scripts
- perl run_tests.pl &> shotmap_tests_log.txt
If shotmap_tests_log.txt finishes without an error, then this bug should be fixed on your end.
That said, because I don't want you to have to rebuild your search database or rerun your homology search in shotmap (that was a lot of invested time, I'm sure), I'd request that you do the following:
- Go into the directory that contains the shotmap search database that you formatted with build_shotmap_search_db.pl. According to your command, it looks like you named this shotmap.
- Please provide me with the result of running the ls command on this directory.
- Go into shotmap_output/parameters
- Please provide me with the result of running the ls command on this directory.
Once I've been able to confirm that everything is properly configured, we'll use the --goto=P command to restart your failed run and jump straight to the parse results step.
Sorry for the trouble.
Best, Tom
On Mon, Mar 7, 2016 at 11:58 AM, ameetpinto <notifications@github.com mailto:notifications@github.com> wrote:
The file in question (shotmap_db_nr_seqeunce_lengths.tab) is present in the folder where the shotmap database is present, but for some reason the "Calculating abundance.." step was looking for the file in the shotmap_output folder??
The command I used is: perl /home/opt/shotmap/scripts/shotmap.pl -i shotmap_input/ -d shotmap -o shotmap_output/ --nprocs 20 --class-score=35 --postrare-samps=69423326 --rarefaction-type=read
— Reply to this email directly or view it on GitHub https://github.com/sharpton/shotmap/issues/5#issuecomment-193423814.
Thomas J. Sharpton
Assistant Professor Department of Microbiology Department of Statistics Oregon State University
(541) 737-8623 thomas.sharpton@gmail.commailto:thomas.sharpton@gmail.com @tjsharpton lab.sharpton.org
— Reply to this email directly or view it on GitHub< https://github.com/sharpton/shotmap/issues/5#issuecomment-193867387>.
— Reply to this email directly or view it on GitHub https://github.com/sharpton/shotmap/issues/5#issuecomment-193930660.
Thomas J. Sharpton
Assistant Professor Department of Microbiology Department of Statistics Oregon State University
(541) 737-8623 thomas.sharpton@gmail.com @tjsharpton lab.sharpton.org
Hi,
I ran the following command and encountered an error. perl /home/opt/shotmap/scripts/shotmap.pl -i shotmap_input/ -d shotmap -o shotmap_output/ --nprocs 20 --class-score=35 --postrare-samps=69423326 --rarefaction-type=read
From what I can tell it successfully ran prodigal, rap search, and microbecensus on all four samples that I used for this analyses. It generated an error while "Calculating Abundances". The error was that it could not find the file: shotmap_db_nr_seqeunce_lengths.tab in the parameters folder. See attached snapshot of the error. Any suggestions on how to fix this issue?
Thanks again for your help, Ameet