Problem with running PrepareAllPathsInputs.pl in Allpaths LG

[marrakesh]

I actually posted several months ago with another issue with PrepareAllPathsInputs.pl, 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//NaifDB.pm 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/CacheLibs.pl \
\
CACHE_DIR=/scratch/02985/emg2497/mouse_genome_project/all_paths_analysis/scotinomys/data//rea_cache \
ACTION=Add IN_LIBS_CSV=in_libs.csv OVERWRITE=0 DRY_RUN=0 VERBOSE=1
--------------------------------------------------------------------------------


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

Stack trace:
Shell command '/opt/apps/allpathslg/42179/bin/CacheLibs.pl 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//PerlRunTime.pm line 127
PerlRunTime::run_or_die('/opt/apps/allpathslg/42179/bin/CacheLibs.pl CACHE_DIR=/scratc...) called at /opt/apps/allpathslg/42179/bin/PrepareAllPathsInputs.pl 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 PrepareAllPathsInputs.pl up and running.

[Mathgon]

Same issue here, have you finally manage to solve your problem?

[RemitoAmigo]

possible solution

it was an encoding issue for me with the in_groups.csv and in_libs.csv file. If you test with this, ftp://ftp.broadinstitute.org/pub/crd...HS/Release-LG/
(see test.genome.tar.gz) and it works....encoding is more likely the culprit. Did everything in nano and then things started to work....