Hi! I'm posting after having read as many threads here as I can on similar problems, but I still can't get this script to run. I'm trying to run a de novo assembly of a mammalian genome for the first time and was instructed to use Allpaths LG on my data. Unfortunately, I'm having some difficulty getting PrepareAllPathsInputs.pl to run so that I can even try to figure out Allpaths. Googling hasn't yielded any solutions.
When I run the program, I get an output that starts having problems here:
Those repeat for a while, and then I get this:
There's a little more in here, but it either repeats previous things or doesn't appear to be an error message, and I'm cutting in the interests of brevity. Finally the error message ends:
This is my script:
I can also provide my all_groups and all_libs .csv files if that would be helpful. I've made sure that all fields are filled and that I have a space after the final comma on all of the entries.
Strangely, the Perl script seems to have worked fine on my Pac-Bio reads, but not my Illumina fragment and mate-pair libraries. I have no idea why this would be the case.
Does anyone have any insight at all? I am at my wits' end.
When I run the program, I get an output that starts having problems here:
Call to new failed, memory usage before call = 22473992k.
Here is the output of top:
/bin/sh: fork: Cannot allocate memory
Aborting.
Thu Jul 31 13:28:07 2014. Abort. Stopping.
Generating a backtrace...
Bummer. I can't run ps to determine the command name.
failed: ps -p 2309 -o command
Here's what happened:
Exiting.
Thu Jul 31 13:28:07 2014. Abort. Stopping.
Generating a backtrace...
Bummer. I can't run ps to determine the command name.
failed: ps -p 2309 -o command
Here's what happened:
Exiting.
Thu Jul 31 13:28:07 2014. Abort. Stopping.
Generating a backtrace...
Bummer. I can't run ps to determine the command name.
failed: ps -p 2309 -o command
Here's what happened:
Exiting.
Here is the output of top:
/bin/sh: fork: Cannot allocate memory
Aborting.
Thu Jul 31 13:28:07 2014. Abort. Stopping.
Generating a backtrace...
Bummer. I can't run ps to determine the command name.
failed: ps -p 2309 -o command
Here's what happened:
Exiting.
Thu Jul 31 13:28:07 2014. Abort. Stopping.
Generating a backtrace...
Bummer. I can't run ps to determine the command name.
failed: ps -p 2309 -o command
Here's what happened:
Exiting.
Thu Jul 31 13:28:07 2014. Abort. Stopping.
Generating a backtrace...
Bummer. I can't run ps to determine the command name.
failed: ps -p 2309 -o command
Here's what happened:
Exiting.
Those repeat for a while, and then I get this:
Generating a backtrace...
/bin/sh: /usr/bin/top: Argument list too long
Dump of stack:
0. std::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::~b asic_stringbuf( ... ), in ??:0
1. std::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::~b asic_stringbuf( ... ), in ??:0
(cut--this repeats all the way up to n=33)
/bin/sh: /usr/bin/top: Argument list too long
Dump of stack:
0. std::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::~b asic_stringbuf( ... ), in ??:0
1. std::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::~b asic_stringbuf( ... ), in ??:0
(cut--this repeats all the way up to n=33)
There's a little more in here, but it either repeats previous things or doesn't appear to be an error message, and I'm cutting in the interests of brevity. Finally the error message ends:
**** 2014-07-31 13:39:41 (CG): 2 errors occurred while converting groups. Aborting.
Thu Jul 31 13:39:41 2014 - /opt/apps/allpathslg/44837/bin/PrepareAllPathsInputs. pl
A shell command returned exit value 29.
Exiting Perl.
Thu Jul 31 13:39:41 2014 - /opt/apps/allpathslg/44837/bin/PrepareAllPathsInputs. pl
A shell command returned exit value 29.
Exiting Perl.
This is my script:
PrepareAllPathsInputs.pl DATA_DIR=/scratch/02985/emg2497/mouse_genome_project/al l_paths_analysis/S.teguina/data/ PICARD_TOOLS_DIR=/opt/picard/bin/ PLOIDY=2 PHRED_64=0
I can also provide my all_groups and all_libs .csv files if that would be helpful. I've made sure that all fields are filled and that I have a space after the final comma on all of the entries.
Strangely, the Perl script seems to have worked fine on my Pac-Bio reads, but not my Illumina fragment and mate-pair libraries. I have no idea why this would be the case.
Does anyone have any insight at all? I am at my wits' end.
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