about file conversion of AllPaths-LG

[biomichael]

I am using your softwar of AllPaths-LG, and encountered a problem when running the reads format conversion program "PrepareAllPathsInputs.pl". I have check all arguments and values according to the Manuel. However, I got the following error information with blue color:


**** line 2 has wrong number of values at /usr/local/bin//NaifDB.pm line 759.
Sat Jun 11 22:27:07 2011 - /usr/local/bin/PrepareAllPathsInputs.pl
A shell command returned exit value -1. Exiting Perl.
Stack trace:
Shell command '/usr/local/bin/CacheLibs.pl CACHE_DIR=/share/disk2/yangm/solexa/assembly_allpath/REFERENCE/MYDATA/read_cache ACTION=Add IN_LIBS_CSV=/share/disk2/yangm/solexa/assembly_allpath/in_libs.csv OVERWRITE=0 DRY_RUN=0 VERBOSE=1'
at /usr/local/bin//PerlRunTime.pm line 121
PerlRunTime::run_or_die('/usr/local/bin/CacheLibs.pl CACHE_DIR=/share/disk2/yangm/sole...') called at /usr/local/bin/PrepareAllPathsInputs.pl line 182

Can anyone help me solve the problem?
Thank you!!

[Narendra Kushwaha]

hi Did you got your answer if yes please tell me, I am getting same kind of problem..

[k821209]

.

Make sure that you put enough information in in_libs.csv including comma separated blanks

[sagarutturkar]

same problem

Anybody, any luck?

[Seth]

my suggestion

Anybody, any luck?

Hi,

I met this problem, I struggled and I fixed it.

Here's my suggestion:
1. check whether your PHRED_64 value is correct
2. check the arguments of HOSTS, cause the name of hosts should be a word to be recognized

[acgt]

Hello, I encountered a similar error when running PrepareAllPathsInputs.pl.

I finally realized that in addition to the correct number of commas in both of the input files (in_groups and in_libs), a space is required at the end of library lines where the "genomic end" value would be (since I did not have one). As soon as I added the spaces, the program worked fine.

Hope this helps someone out there!

[herstein]

To acgt, thanks for this pointer! I was banging my head against the wall until I read your suggestion to add a space at the end of the line if not using genome_end. This worked!