Barcode splitter error on Galaxy

[nilmot13]

Hi,

I've been trying to de-multiplex my sequencing data using the interface on Galaxy. However I keep getting the following error message.


Use of uninitialized value $barcode in uc at /home/g2main/linux3.2-x86_64/bin/fastx_barcode_splitter.pl line 156, <BCFILE> line 10.
Error: bad barcode value () at barcode file (/galaxy/main_pool/pool4/files/005/946/dataset_5946981.dat) line 10

gzip: stdout: Broken pipe

The barcode file I've used include.

#Barcode
BC1 GATCAG
BC2 TTAGGC
BC3 TAGCTT
BC4 TGACCA
BC5 GGCTAC
BC6 ACAGTG
BC7 CTTGTA
BC8 GCCAAT

-mismatch i've tried 0,1,and 2 but none of them works.

The fastq raw files (illumina platform) I've uploaded does not qualify for splitting, so i've groomed it to fastqsanger.

Any suggestion?

[Rhizosis]

It looks like there is a new line character at the end of the file. The $barcode value is populated with an empty line (or a null value) resulting in a uninitialized value.
Chomp / remove the last (empty) line of the data input and try again.

If this is the case, this error should not occur though. Bad programming on part of Galaxy' side.

[JackieBadger]

PS just to save you time...if your data is already in fastqsanger (e.g. MiSeq) you don't need to groom your data if you specify that it is already fastqsanger during upload....the auto detection only detects that its fastq and not the quality scoring...
pps if the barcode splitter still causes issues just use the command line version

[nilmot13]

Thanks for the reply, I'll be sure to try those suggestion out.