Perl Error when building Ref

[liscruk]

Hi there,

I use this command as per the doc to built the reference:

bin/IRFinder -m BuildRef -r REF/Human-GRCh38-release100 -e REF/extra-input-files/RNA.SpikeIn.ERCC.fasta.gz -b REF/extra-input-files/Human_hg38_nonPolyA_ROI.bed ftp://ftp.ensembl.org/pub/release-100/gt    f/homo_sapiens/Homo_sapiens.GRCh38.100.gtf.gz

And it runs but then produces error messages and yet finishes:

<Phase 1: STAR Reference Preparation>
Feb 21 09:39:07 ..... started STAR run
Feb 21 09:39:07 ... starting to generate Genome files
Feb 21 09:40:30 ... starting to sort Suffix Array. This may take a long time...
Feb 21 09:40:53 ... sorting Suffix Array chunks and saving them to disk...
Feb 21 09:55:47 ... loading chunks from disk, packing SA...
Feb 21 09:57:38 ... finished generating suffix array
Feb 21 09:57:38 ... generating Suffix Array index
Feb 21 10:04:43 ... completed Suffix Array index
Feb 21 10:04:43 ..... processing annotations GTF
Feb 21 10:05:01 ..... inserting junctions into the genome indices
Feb 21 10:09:17 ... writing Genome to disk ...
Feb 21 10:09:20 ... writing Suffix Array to disk ...
Feb 21 10:09:49 ... writing SAindex to disk
Feb 21 10:09:52 ..... finished successfully
<Phase 2: Mapability Calculation>
Feb 21 10:09:53 ... mapping genome fragments back to genome...
Feb 21 10:23:42 ... sorting aligned genome fragments...
[bam_sort_core] merging from 75 files...
Feb 21 10:33:28 ... indexing aligned genome fragments...
Feb 21 10:34:15 ... filtering aligned genome fragments by chromosome/scaffold...
xargs: warning: options --max-args and --replace/-I/-i are mutually exclusive, ignoring previous --max-args value
Feb 21 10:35:57 ... merging filtered genome fragments...
Feb 21 10:36:43 ... calculating regions for exclusion...
Feb 21 10:40:21 ... cleaning temporary files...
<Phase 3: IRFinder Reference Preparation>
Feb 21 10:40:30 ... building Ref 1...
Use of uninitialized value $_ in concatenation (.) or string at /usr/share/perl5/core_perl/sort.pm line 19.
sort: unknown subpragma '' at /IRFinder-1.3.0/bin/util/gtf2bed-custom.pl line 33.
BEGIN failed--compilation aborted at /IRFinder-1.3.0/bin/util/gtf2bed-custom.pl line 33.
Feb 21 10:40:30 ... building Ref 2...
Feb 21 10:40:31 ... building Ref 3...
Feb 21 10:40:31 ... building Ref 4...
Feb 21 10:40:34 ... building Ref 5...
Feb 21 10:40:37 ... building Ref 6...
Feb 21 10:40:37 ... building Ref 7...
Feb 21 10:40:37 ... building Ref 8...
Feb 21 10:40:37 ... building Ref 9...
Feb 21 10:40:37 ... building Ref 10c...
Feb 21 10:40:37 ... building Ref 11c...
Error: exclude.directional.bed is empty.
Error: introns.unique.bed is empty.
Error: ref-cover.bed is empty.
Error: ref-read-continues.ref is empty.
Error: ref-sj.ref is empty.

Could it be the perl error ?
Any suggestions on how to fix this?

Thanks!

[dg520]

@liscruk Yes. Can you set your default Perl to a version >=5 and <= 6?

[liscruk]

@dg520 I checked and we are running a version of perl that fullfill this:

perl -v
This is perl 5, version 38, subversion 2 (v5.38.2) built for x86_64-linux-thread-multi

Any specific version you would suggest?

Thanks!