Trouble with processing paired-end data with Pandaseq, any help appreciated

[Jimothy]

Hi all,

Not sure if this is best off posted in the Illumina forum or here really but here goes.

I've been trying to use the Pandaseq tool to process some paired end MiSeq data, but I get an error message when I try to run it with my files.

Output looks like this:

jimothyh@manager-desktop[Documents] pandaseq -f 0454_Houghton_NoIndex_L001_R1_001.fastq -r 0454_Houghton_NoIndex_L001_R2_001.fastq
INFO VER pandaseq 2.0 <[email protected]>
ERR BADID @MISEQ:9:000000000-A1BL8:1:1101:17377:1320 1:N:0:
STAT TIME Tue Sep 18 11:48:38 2012

STAT ELAPSED 0
STAT READS 0
STAT NOALGN 0
STAT LOWQ 0
STAT OK 0
INFO API 1

I checked the program using some sample data and it worked fine. Someone else reported an identical error on github also as a result of trying to process MiSeq data with pandaseq. I'm wondering if there is something about the MiSeq ID that the program does not like, and if so if there might be a way of altering it so that it does work?

My fastq files look like this:

@MISEQ:9:000000000-A1BL8:1:1101:17377:1320 1:N:0:
NGCCTGACACCTGCCCGGTGCTGGAAGGTTAAAAGGAGAAGTCATCGCAAGAGAAGCTTTGAATTGAAGCCCCAGTAAACGGCGGCCGTAACAATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGG
+
#5<???BBDDEDDDDDGGCGGGIIFIIHFHIIIIIHHFHIHHHHHIIHHHHIIIIIIIIIIIIIIIIIHIIIHHHHIIHIEHHHHHGGGGGGGGGGGGEECEGGGHGGGGGGGG;;ECGCEGGGGGDGE<ECC?EGEEDGEEECE??EGGG
@MISEQ:9:000000000-A1BL8:1:1101:16243:1320 1:N:0:
NTCTTTTTTTTTTTTTTTTTTCTTTGAACGCCCATTCCACACCCGCTGATCGCCTCGATCCACTCATCCGGCTCAGGAATATTAACCTGATTCCCTTTCGATCGGGTGGGAGACAGCCTTATGACTAGGACGAAGCCTACGAGTCACCTCG
+
#5<===>>@@@EE@@@CCCCC-CEE>EE;+<CCCDEDEDD=DEE=ADDEDDDEE+@EEDDD9D*8;@@@:@@)8@@E@;@@7;?6<EE<EEE<EEEEE6-669;E;<;;;6<6<<(666;6;<;;E?=E==;;;6;E6;E696(6?EEE##
@MISEQ:9:000000000-A1BL8:1:1101:17345:1320 1:N:0:
NATGATTGATAGGTGCTGACCCCAGTACGAGAGGACCGGGTCGGACTAACCTCTGGTGTACCAGTTGTAACGCCAGTTGCAGTGCTGGGTATCTAAGTTGGGCAGGGATAAGCGCTGAAAGCATCTAAGCGCGAAGCTCTCCTAGAGATGA

The sample data that run successfully looked like this:

@ILLUMINA-BE9C3F:29:FC:3:1:8146:1021 1:Y:0:GCTATA
NNNGCNNNNNNNNNNNNNNNNNGNNGAATATTGGACAATGGGCGCANNNNNGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTAAGCA
+
###+2#################)##)*0*)@@@@@@@@@@@@@@@###############################################################
@ILLUMINA-BE9C3F:29:FC:3:1:2932:1024 1:Y:0:GCTATA
NNNTCNNNNNNNNNNNNNNNNNGNGGAATATTGGACAATGGGCGCANNNNNGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTAAGCA
+
###+0#################+#.+(*,&@@@@@@@@@@@@@@@)#####'((055225@@@@@@@@@@<<<<:@@@@@@@@@@#######################
@ILLUMINA-BE9C3F:29:FC:3:1:8004:1030 1:Y:0:GCTATA
CNNCCNNNNNNNNNNNNNNNNTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGCGGGTTGTAAAGCACTTTAAGCA

Any help or suggestions appreciated!