[mira_talk] problem with loading reads

  • From: Peter Menzel <ptr@xxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 5 Oct 2011 11:01:21 +0200

Hi all,

I am starting to use mira for illumina de-novo assembly, and for one
data set I have problems to load the reads.
Mira produces this output:

Loading data (Solexa) from FASTQ files,
Localtime: Wed Oct  5 10:47:31 2011
Counting sequences in FASTQ file: found 23408624 sequences.
Localtime: Wed Oct  5 10:48:09 2011
Solexa will load 23408624 reads.
Longest Sanger: 0
Longest 454: 0
Longest IonTor: 0
Longest PacBio: 0
Longest Solexa: 44
Longest Solid: 0
Longest overall: 44
Total reads to load: 23408624
Reserving space for reads (this may take a while)
tcmalloc: large alloc 5430804480 bytes == 0x132d000 @
Reserved space for 23408634 reads.
Loading data (Solexa) from FASTQ files,
Localtime: Wed Oct  5 10:48:09 2011
Counting sequences in FASTQ file: found 23408624 sequences.
Localtime: Wed Oct  5 10:48:43 2011
Using calculated FASTQ quality offset: 59
Guessing FASTQ quality values to be in Illumina/Solexa 1.0 format.
Localtime: Wed Oct  5 10:48:43 2011
Loading data from FASTQ file:
 [0%]
Fatal error (may be due to problems of the input data or parameters):

"Read I330_1_FC30JM6AAXX:4:1:0:199/1: tried to set 1 qualities
although the read has 44 bases.
"

The mentioned read is the first one in the file and looks like this:

@I330_1_FC30JM6AAXX:4:1:0:199/1
TTCANATATGGAAAAACAGGGAGCGGAAATCACGTTACTTGCGT
+I330_1_FC30JM6AAXX:4:1:0:199/1
hhhh;XhZhhh[HI[LSTbhPRZL\XRJOSUNO[PYLOU]SMQJ

So it seems, that the quality line cannot be read somehow.. any ideas?

The data are from the human gut metagenomics project, first two files
(concatenated) from here:
ftp://public.genomics.org.cn/BGI/gutmeta/Raw_Reads/


best, Peter

-- 
Peter Menzel, Ph.D.

The Bioinformatics Centre
Department of Biology
Copenhagen University
Ole Maaleoes Vej 5, DK-2200, Denmark

email: ptr@xxxxxxxxxx

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