error during shotmap.pl

[ameetpinto]

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

[ameetpinto]

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]

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:

1. cd $SHOTMAP_LOCAL
2. git pull origin master
3. cd scripts
4. 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:

1. 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.
2. Please provide me with the result of running the ls command on this
   directory.
3. Go into shotmap_output/parameters
4. 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
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
#5 (comment).

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]

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.commailto:notifications@github.com>
Reply-To: sharpton/shotmap <reply@reply.github.commailto:reply@reply.github.com>
Date: Tuesday, March 8, 2016 at 4:59 PM
To: sharpton/shotmap <shotmap@noreply.github.commailto:shotmap@noreply.github.com>
Cc: ameetpinto <ameet.pinto@glasgow.ac.ukmailto: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:

1. cd $SHOTMAP_LOCAL
2. git pull origin master
3. cd scripts
4. 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:

1. 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.
2. Please provide me with the result of running the ls command on this
   directory.
3. Go into shotmap_output/parameters
4. 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.commailto: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
#5 (comment).

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//issues/5#issuecomment-193867387.

[sharpton]

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.ukmailto: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:

1. cd $SHOTMAP_LOCAL
2. git pull origin master
3. cd scripts
4. 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:

1. 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.
2. Please provide me with the result of running the ls command on this
   directory.
3. Go into shotmap_output/parameters
4. 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
#5 (comment).

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
#5 (comment).

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