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Old 12-04-2014, 10:15 AM   #1
Junior Member
Location: Austin

Join Date: Jul 2014
Posts: 8
Default Problem with running in Allpaths LG

I actually posted several months ago with another issue with, but the answer provided then gave me all the information I needed to solve that particular problem. At the time, I had the script working just fine.

Then I left the Allpaths assembly data alone while I ran a different de novo assembly of some of my other fragment data on Velvet. Unfortunately, the server I left it on was one that will periodically delete files if you don't touch them for long enough, and while I'd backed up my batch scripts and the resulting assembly, I definitely needed to run the assembly again from scratch. Now when I do that, I get this error almost immediately:
---- 2014-12-04 12:56:44 (PAPI): Using cache directory '/scratch/02985/emg2497/mouse_genome_projet/all_paths_analysis/scotinomys/data//read_cache'
---- 2014-12-04 12:56:44 (PAPI): Running on '/scratch/02985/emg2497/mouse_genome_project/all_path_analysis/scotinomys/data'.
**** line 2 has wrong number of values at /opt/apps/allpathslg/42179/bin// line 780.
Dec 4 12:56:44 2014 run on localhost (pid=31093), last modified Jul 6 11:34:09 2012
/opt/apps/allpathslg/42179/bin/ \
CACHE_DIR=/scratch/02985/emg2497/mouse_genome_project/all_paths_analysis/scotinomys/data//rea_cache \

Thu Dec 4 12:56:44 2014 - /opt/apps/allpathslg/42179/bin/
A shell command returned exit value -1.
Exiting Perl.

Stack trace:
Shell command '/opt/apps/allpathslg/42179/bin/ CACHE_DIR=/scratch/02985/emg247/mouse_genome_project/all_paths_analysis/scotinomys/data//read_cache ACTION=Add IN_LIBS_CSV=in_lbs.csv OVERWRITE=0 DRY_RUN=0 VERBOSE=1'
at /opt/apps/allpathslg/42179/bin// line 127
PerlRunTime::run_or_die('/opt/apps/allpathslg/42179/bin/ CACHE_DIR=/scratc...) called at /opt/apps/allpathslg/42179/bin/ line 207
Does anyone by chance know what might be causing this problem and how I can fix it? I don't think I've changed anything since I had successfully run the assembly the first time. What I would eventually like to do is run an AllPaths assembly using the Velvet assembly as a reference, but I can't do that until I get up and running.
marrakesh is offline   Reply With Quote
Old 08-06-2015, 07:28 AM   #2
Junior Member
Location: France

Join Date: Jun 2010
Posts: 8

Same issue here, have you finally manage to solve your problem?
Mathgon is offline   Reply With Quote
Old 12-20-2016, 05:20 PM   #3
Location: Ottawa, Canada

Join Date: Apr 2012
Posts: 22
Default possible solution

it was an encoding issue for me with the in_groups.csv and in_libs.csv file. If you test with this,
(see test.genome.tar.gz) and it works....encoding is more likely the culprit. Did everything in nano and then things started to work....
RemitoAmigo is offline   Reply With Quote

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