[mira_talk] Re: MITObim/Mira aborting process with Genbank data

  • From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
  • To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
  • Date: Mon, 6 Apr 2015 17:13:07 +0100

On Mon, Apr 6, 2015 at 5:08 PM, Hernan Vazquez Miranda <miran050@xxxxxxx> wrote:

Hello everybody,

I've been fighting with the following problem trying to extract the
mitogenome of the recently deposited woodpecker genome in Genbank. I
downloaded one full lane, merge all pair-end reads, and concatenated them in
a single file. I had to subsample the full file to 10% because it wouldn't
run (Killed:9 error). Now it doesn't die but Mira won't work. ...

Loading data from FASTQ file:
/Users/Odontodactylus/Sanger_data/melanerpes/downyS10.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Read SRR949787.4.1: invalid quality 170
Read SRR949787.20.1: invalid quality 171
Read SRR949787.20.1: invalid quality 167
... 4GB od these error lines
Read SRR949787.119142778.1: invalid quality 171
Read SRR949787.119142778.1: invalid quality 167
Read SRR949787.119142778.1: invalid quality 165


That looks to be the problem - bad FASTQ quality lines,
given the number of message, probably the entire file.

What does that file look like? e.g. read SRR949787.4.1

Peter

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