[mira_talk] Re: No such file or directory after running for approx 360 hours
- From: Joel barratt <joelbarratt43@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Oct 2012 15:30:10 +1100
Hi Bastien,
Sorry about the slow reply. I have been trying to find the best way to
compress the log file - but it is too large to email (it is 1.4GB
uncompressed and I can compress it down to about 74MB - but still too large
for my email). Is there any other way I could get this file to you?
>You mean the files in "*_results_d" ?
Yep thats the one I meant. All the files in there look OK. Excellent - so
360 hours of waiting wasn't a waste.
The stuff in the *info_d directory I mostly don't need.
> Would it be a possibility you temporarily ran out of disk space?
Possibly? The hard disk was small (340GB) and the assembly consisted of
30million reads (approx) - about 1 million were 454, the rest illumina
HiSeq reads.
>Also, 360 hrs is a tad long......
Yep I thought so as well - I was getting a little worried it was looping
about or doing something strange. However, I think you will find it is "one
of those" projects. The sample came from cultures of a parasite which also
contained an undefined mixture of bacteria. I extracted the RNA and used
oligo dt cellulose chromatography to enrich for parasite mRNA but there was
still around 10-20% bacterial RNA's in there I'm guessing. ALso, Some of
the parasite mRNA's are quite repetitive as are some of the bacterial
mRNA's.
Anyway, thanks for the insights. I look forward to trying MIRA 3.9.5. Also,
let me know if you have an alternative way for me to send you the log file?
Perhaps dropbox??
Cheers!
Joel
On 15 October 2012 05:34, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Oct 14, 2012, at 10:07 , Joel barratt wrote:
> > I recently attempted an assembly using MIRA 3.9.4. The assembly ended
> with an error though all the output files seem to be present and intact.
>
> You mean the files in "*_results_d" ? That would mean that the assembly
> itself would have finished successfully and you would just be missing a
> couple of files in the *_info_d directory. Would there be anything in those
> files you need? Else the files in the results directory should be entirely
> valid.
>
> > [...]
> > Any insights into what could have caused this and how I could fix it?
> Let me know if you require further information.
>
> Would it be a possibility you temporarily ran out of disk space?
>
> Also, 360 hrs is a tad long. Could you send me the complete log (packed)?
> So that I can take a quick peek whether it's "one of those" projects where
> I think the upcoming 3.9.5 would make a big difference.
>
> B.
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