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. I
even tried the dos2unix trick and the reduced fastq file still doesn't
work. I've tried it with my experimental reads and it works fine.
Am I doing something wrong? Most likely, but I cannot find what it is. Any
help will be greatly appreciated. This is my run.log:
MITObim - mitochondrial baiting and iterative mapping
version 1.7
author: Christoph Hahn, (c) 2012-2014
quick option selected! -maf option will be ignored (if given)
Full command run:
/Users/Odontodactylus/Programs/MITObim/MITObim_1.7_beta.pl
<http://mitobim_1.7_beta.pl/> -sample downy -ref DQ780882_Pteroglossus
-readpool downyS10.fastq --quick DQ780882_Pteroglossus.fasta -end 100
--denovo --clean
All paramters seem to make sense:
startiteration: 0
enditeration: 100
sample: downy
refname: DQ780882_Pteroglossus
readpool: /Users/Odontodactylus/Sanger_data/melanerpes/downyS10.fastq
maf: 0
quick:
/Users/Odontodactylus/Sanger_data/melanerpes/DQ780882_Pteroglossus.fasta
paired: 0 (off=0, on=1)
assembly mode: 1 (mapping=0, denovo=1)
verbose: 0 (off=0, on=1)
clean: 1 (off=0, on=1)
trim reads: 0 (off=0, on=1)
trim overhang: 0 (no=0, yes=1)
platform: SOLEXA
kmer baiting: 31
Starting MITObim
==============
ITERATION 0
==============
Apr 3 21:53:47
quick option baits reads from provided reference in iteration 0
fishing readpool using mirabait (k = 31)
/Users/Odontodactylus/Sanger_data/melanerpes/downyS10.fastq 1
/Users/Odontodactylus/Sanger_data/melanerpes 2 downyS10 3 fastq
Loading baits ...Localtime: Fri Apr 3 21:53:47 2015
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Fri Apr 3 21:53:47 2015
rnm size: 0
No FASTA quality file given, using default qualities for all reads just
loaded.
Localtime: Fri Apr 3 21:53:47 2015
Done.
Loaded 1 reads with 0 reads having quality accounted for.
baitrp.size(): 1
Localtime: Fri Apr 3 21:53:47 2015
Writing temporary hstat files:
freemem: 27016318976
TNH: 18706
XME 1: 0.00074331
XME 2: 0.1
NEPB 1: 104857
NEPB 2: 104857
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] done
Localtime: Fri Apr 3 21:53:47 2015
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Fri Apr 3 21:53:47 2015
clean up temporary stat files...Localtime: Fri Apr 3 21:53:47 2015
Raw MHI: 17003
Raw avg. freq. : 1
HSS 33824 HSST: 30442
Localtime: Fri Apr 3 21:53:47 2015
Will save to: fastq
Loading data from fastq ...Localtime: Fri Apr 3 21:53:47 2015
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
In func: size_t ReadPool::loadDataFromFASTQ_rgid(const string & filename,
int8 fastqoffset, const ReadGroupLib::ReadGroupID rgid, bool countonly,
void (*callback)(ReadPool &))
Throw message: Unrecoverable error while loading data from FASTQ (see
output above) Fix your input please.
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* Unrecoverable error while loading data from FASTQ (see output above) Fix
*
* your input please.
*
********************************************************************************
->Thrown: size_t ReadPool::loadDataFromFASTQ_rgid(const string & filename,
int8 fastqoffset, const ReadGroupLib::ReadGroupID rgid, bool countonly,
void (*callback)(ReadPool &))
->Caught: main
Aborting process, probably due to error in the input data or
parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /Users/Odontodactylus/Sanger_data/melanerpes/iteration0
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
mirabait seems to have failed - see detailed output above
Thank you for your help!
