I was trying to perform error correction with ALLPATHS-LG, using paired-end R1 and R2 read files, that had already undergone Trimmomatic based processing.
The STDOUT of the ALLPATHS-LG's ErrorCorrectReads.pl run, all 600+ lines of it, are available at http://textuploader.com/d64wm, indicates a missing Perl module ? PerlRunTime.pm? Could someone please advice me how to fix this so I can get my run going? Thanks much! Excerpt from this STDOUT, with the error messages alone, are copy / pasted below.
I am not so much interested in using ALLPATHS-LG for my EC step, towards genome assemblies. However, I need to compare my current genome assembly pipeline (BBTools + SPAdes) to one used by a colleague (Trimmomatic + ALLPATHS-LG + A5), and I am merely replicating the bioinformatics steps of my colleague.
Running SplitReadsByLibrary. Can't exec "/share/apps/allpathslg-52488/bin/SplitReadsByLibrary": No such file or directory at /share/apps/allpathslg-52488/bin/PerlRunTime.pm line 66. Use of uninitialized value $signal in hash element at /share/apps/allpathslg-52488/bin/PerlRunTime.pm line 101. Sun Aug 27 03:25:36 2017 - /share/apps/allpathslg-52488/bin/ErrorCorrectReads.pl A shell command Use of uninitialized value $signal in concatenation (.) or string at /share/apps/allpathslg-52488/bin/PerlRunTime.pm line 117. Use of uninitialized value $signal in hash element at /share/apps/allpathslg-52488/bin/PerlRunTime.pm line 117. Use of uninitialized value in concatenation (.) or string at /share/apps/allpathslg-52488/bin/PerlRunTime.pm line 117. detected signal SIG (). Exiting Perl. Stack trace: Shell command '/share/apps/allpathslg-52488/bin/SplitReadsByLibrary READS_IN=./EthFoc11_PC_Trimmomatic_ALLPATHS-EC.fq.allpaths-lg/data/run/frag_reads_corr SPLIT_PAIRS=True QUALS=True' at /share/apps/allpathslg-52488/bin/PerlRunTime.pm line 127. PerlRunTime::run_or_die('/share/apps/allpathslg-52488/bin/SplitReadsByLibrary READS_IN...') called at /share/apps/allpathslg-52488/bin/ErrorCorrectReads.pl line 315 srun: error: c8-96: task 0: Exited with exit code 2 .