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SouthGreenPlatform / arcad-hts

Scripts for the analysis of high-throughput sequencing data from the ARCAD project.
http://www.arcad-project.org/
GNU General Public License v3.0
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bug in arcad_hts_4_Mapping_Arcad.pl #14

Closed timflutre closed 9 years ago

timflutre commented 9 years ago

Here is my cmd-line:

arcad_hts_4_Mapping_Arcad.pl -i config.txt -o gbs.bam -r /data/chroms -q bioinfo.q -mapper bwa_mem

And here is what it returns:

Argument "exitval" isn't numeric in subtraction (-) at /usr/local/bioinfo/bin/arcad_hts_4_Mapping_Arcad.pl line 124.
Argument "Cannot find the reference file reference and/or config f..." isn't numeric in subtraction (-) at /usr/local/bioinfo/bin/arcad_hts_4_Mapping_Arcad.pl line 124.
Odd number of elements in anonymous hash at /usr/local/bioinfo/bin/arcad_hts_4_Mapping_Arcad.pl line 124.

In /data, there are all files, such as chroms.ann, chroms.bwt, etc.

My env:

$ perl -v
This is perl, v5.8.8 built for x86_64-linux-thread-multi
gsarah commented 9 years ago

Should be solved. There was a bug in the error message construction Anyway I think your refrence path is not correct as /data/chrom will look for an absolute path.