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.

[GenoMax]

If you need to make your post visible again there is no need to create a duplicate

You can just respond to your own original post and it will rise to the top again.

Sorry don't have specific advice on this problem. Has something been upgraded (perl, libraries) since you used this program last?