UGENE Forum - SPAdes - Mac, no tool

Reply #15 - Mar 4^th, 2015 at 9:25pm

Olga Golosova Offline
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Posts: 338

Quote:

I think I am not able to test it on windows, there is no tool for that. Am I correct?

Yes, there is currently no SPAdes for Windows.

Quote:

So, I will change fastq files which gives me nice contig in clc software, and will test them with UGENE/SPADES

Let me sum up it:

It is an error that you can't run SPAdes on your data (R15011_S11_L003_R1_001.fastq and the other files).
If it is possible, please share the data with us. It will help a lot to investigate the problem. Currently we're not able to reproduce the error on our test data.
We will contact the SPAdes developers about the error and, I hope, it will be fixed in future.
SPAdes can be successfully run on other FASTQ files, so sure, you may try to use it with other input data.

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Reply #16 - Mar 5^th, 2015 at 6:31pm

Leiga Offline
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Posts: 14

So,
I have change source fastq files (different phage) and after successful assembly using clc I tried to do the same with spades,
log below:
Quote:

[ERROR][11:11] Spades: == Error == system call for: "['/Volumes/Unipro UGENE 1.16.0/Unipro UGENE.app/Contents/MacOS/tools/SPAdes-3.1.1/bin/hammer', '/Biofizyka/UGENE/Bakteriofagi/JD/ZK1_01/corrected/configs/config.info']" finished abnormally, err code: -6
[ERROR][11:11] == Error == system call for: "['/Volumes/Unipro UGENE 1.16.0/Unipro UGENE.app/Contents/MacOS/tools/SPAdes-3.1.1/bin/hammer', '/Biofizyka/UGENE/Bakteriofagi/JD/ZK1_01/corrected/configs/config.info']" finished abnormally, err code: -6
[ERROR][11:12] Task {GenomeAssemblyMultiTask} finished with error: Subtask {GenomeAssemblyTask} is failed: Subtask {SPAdes tool} is failed: SPAdes tool exited with code 1

Can you register to basespace (illumina) i think I will be able to share whole project with you, and you will get access to raw data from one of sequenced phages.

Regards,
L.

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Reply #17 - Mar 10^th, 2015 at 2:21pm

Olga Golosova Offline
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Posts: 338

Hi, we've just registered to basespace. The account is ugene@unipro.ru.

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Reply #18 - Mar 10^th, 2015 at 9:25pm

Leiga Offline
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Posts: 14

Hey,
can you check it? I try to share project with you, can you try to download data from basespace?
There is another option (transfer ownership - but it is not what I want to do

)
Regards
L.

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Reply #19 - Mar 20^th, 2015 at 7:17pm

Leiga Offline
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Posts: 14

Hi Olga,
Were you able to download data and try to solve a problem?
Regards
L.

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Reply #20 - Mar 24^th, 2015 at 5:35pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Hi Leiga,

Yes, we downloaded the data, thank you!

We're currently trying to reproduce the issue. We launched SPAdes with the test data about 1.5 days ago and it still does the calculations. I will write you as soon as it is finished.

Could you please confirm that all the FASTQ files are paired-end reads from the same experiment?

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Reply #21 - Mar 27^th, 2015 at 6:05pm

Leiga Offline
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Posts: 14

Yes,
I hope you were able to download proper data. What are the names of files which you have used?
Regards,
L.

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Reply #22 - Mar 31^st, 2015 at 12:54pm

Ivan Protsyuk Offline
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Posts: 2

Hi Leiga,
I'm a member of the UGENE team, and I worked on your issue along with Olga. Indeed, we managed to download your data from the BaseSpace platform. The example of a file name is "ZK1-01_S10_L001_R1_001.fastq.gz". Other file names differ in a couple of numbers.

As for SPAdes, we ran it via UGENE on several desktop computers with your data: two iMacs and one Linux machine. And it finished with errors, similar to what you posted previously, in two cases, and didn't finish at all on one of the iMacs during 4 days. Finally, we launched SPAdes on a server equipped with 2 CPUs with 6 cores each and 64 GB RAM, and it finished successfully in 18 hours. So, we inferred that a desktop computer is not powerful enough for running SPAdes with data like yours.

If you want, we can share the SPAdes output results using BaseSpace and account name strapag@biol.uni.lodz.pl.

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Reply #23 - Apr 1^st, 2015 at 1:59am

Leiga Offline
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Posts: 14

So,
do you think, it is because of:
1. somethink what is specific for nextseq's data (I mean "new" instrument);
2. Oversequencing... (as you probably see, this is really over sequenced phage genome:))
3. PC specification only.

I will try again to use that tool, now I have more optimsed codition for sequencing small genomes on taht instrument (0,8 - 0,5 Gb of data)
Will tell you about results later...

And, Yes, please send me your results using illumina account.
Regards,
L.

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Reply #24 - Apr 1^st, 2015 at 7:04pm

Ivan Protsyuk Offline
YaBB Newbies

Posts: 2

I suppose that the issues with SPAdes are caused by the hardware configuration, since in the end, it succeded to align your data on a powerful computer. Probably, there would be no problem if the genome wasn't oversequenced at this extent.

Unfortunately, BaseSpace doesn't allow uploading arbitrary files, therefore I added the data produced by SPAdes to Google Drive. You can access it here: http://bit.ly/1C78Eft. Please, let me know if you have any questions regarding it.

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