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

  • From: Hernan Vazquez Miranda <miran050@xxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 6 Apr 2015 12:26:39 -0400

They look like this (head downyS10.fastq). I don't recall "I"s being so
pervasive in fastq file but I figured they'd be a little different coming
from a SRA file deposited in Genbank. Is there a solution or a way to
transform them?

Thanks! Hernán


@SRR949787.4.1 FCB065HABXX:6:1101:1197:1966 length=100

AGTCATTCACTTCGGGATCTTGTAAGGTGTCAAACTCATGGAGACCTGAAAGAATTCAAGCAAGGGAAAGGATGCACACCTGTAAAAGGGAAACGATGCACACCTGTAAAAATACTGCCCATCTACTTACCGTCCCACCCAAACCTTGATTATCTTTATGGTTACACAAGTGCTTTTCTTCAGGCAT

+

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII?IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

@SRR949787.14.1 FCB065HABXX:6:1101:1472:1976 length=100

GGGAGACTGCTGTGCTGGGAGACAGCTCAGCAGCTTGCAAAACTGAGAAATCAAGAAATAGGATGGGATAGGATGGGATAGGAGGGATAGGATGGGATAGGATGGGATAGGATAGGGTAGGATAGGATAGGATAGGATAGGATAGAATAGGATAGAATAGAATAGAATAGAATAGAATAGAAT

+

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

@SRR949787.18.1 FCB065HABXX:6:1101:1462:1999 length=100

AAACTGATCTACTACCAATACCAAATGAGGTAGAAATGCATAAGGGAACTAGGTCTTGGAATGTTACAGGTTTGAAATCAGTAATACCATTGACCATTGCCTGCAATTTGCCCAAATATAATTTGTTTCTCATGGTTGTCCAAATACAGAAGGCTTCAGGGTTCTTTCCAGTTCATACTCTGACTTG

+

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

On Mon, Apr 6, 2015 at 12:13 PM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
wrote:

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

--
You have received this mail because you are subscribed to the mira_talk
mailing list. For information on how to subscribe or unsubscribe, please
visit http://www.chevreux.org/mira_mailinglists.html




--


*----*

__ __
/ <` '> \
( / @ @ \ )
\(_ _\_/_ _)/
(\ `-/ \-' /)
"===\ /==="
.==')___(`==. hjw
' .=' `=.

*Hernán Vázquez Miranda, PhD*



*Postdoctoral Research AssociateFlorida International
UniversityBracken-Grissom Lab*

http://www.brackengrissomlab.com


previous

,___,
(9v9)
(_^((\
jgs "^" \\



*University of MinnesotaDept. of Ecology, Evolution, and Behaviorhernan[at]*
umn.edu

and


*Bell Museum of Natural HistoryUniversity of Minnesota*
http://www.bellmuseum.umn.edu/

Other related posts: