ALLPATHS-LG error correction step problem
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Entering edit mode
3.7 years ago
Anand Rao ▴ 360

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 .  ALLPATHS-LG error correction ErrorCorrectReads.pl • 1.4k views ADD COMMENT 0 Entering edit mode merely replicating the bioinformatics steps of my colleague On a different machine or the same one as your colleague? ADD REPLY 0 Entering edit mode totally different machine ADD REPLY 0 Entering edit mode I initially thought the main problem is absence of a Perl module - called PerlRunTime.pm. But I am not so sure that is the reason because this module is found at /share/apps/allpathslg-52488/bin On the other hand, SplitReadsbyLibrary appears to be missing. Which is part of the error message posted above. After some digging, I found this ALLPATHS-LG forum link from June 2015, with a response from another user (?) in Dec, 2015 that reads - "Turns out that SplitReadsByLibrary (and a number of other execs) was part of a .../src/utils directory that was last included in version 52415 and is missing in subsequent releases." I wonder if any biostars forum member had run into this problem as well, but figured out any simple solution - like a preferred version of ALLPATHS-LG, perhaps? Thanks folks! ADD REPLY 0 Entering edit mode So it seems you and your friend used different versions of ALLPATHS-LG. You can either use the latest version, but update your commands, or install the same version he used, to replicate exactly what he did. ADD REPLY 0 Entering edit mode I am getting the same error with two versions of allpathslg ver 44837 (supposedly used by an former colleague per syntax record) and allpathslg ver 52488. The STDERR file reads Use of uninitialized value$args{"_extra"} in concatenation (.) or string at /share/apps/allpathslg-44837/bin/ErrorCorrectReads.pl line 291.


Yet, the run is proceeding. Some folks at the allpaths forum (http://bit.ly/2vzlFrw) suggested it is because

Turns out that SplitReadsByLibrary (and a number of other execs) was part of a .../src/utils directory that was last included in version 52415 and is missing in subsequent releases.

Not sure what this EXACTLY means, but under /share/apps/allpathslg-44837/, I've got amongst other files, 2 folders:

/share/apps/allpathslg-44837/bin and /share/apps/allpathslg-44837/share

Importantly SplitReadsByLibrary is indeed found under /share/apps/allpathslg-44837/bin

So if you any of you know something about the source of this run error, and how to fix it, please post your reply below. I am really stuck here! Thanks!