index out of bounds error

[jesgomez]

Hi,
I'm trying to run Sailfish + Rapclust in my data. I had some RNAseq samples from several conditions and I assembled with Trinity each condition separately, obtaining 4 different transcriptomes. Now, I'm trying to cluster them together in order to get a unique transcriptome for the specie (instead of 1 per each condition), so I concatenated all the transcriptomes in a single multifasta file and tried to run sailfish and Rapclust as I usually do. I indexed the combined transcriptome with sailfish and quantified each sample without getting any error. But when I run Rapclust, I get the following error:
Traceback (most recent call last):
File "/apps/RAPCLUST/0.1/bin/RapClust", line 89, in
processQuant()
File "/apps/RAPCLUST/0.1/lib/python2.7/site-packages/click/core.py", line 716, in call
return self.main(_args, *_kwargs)
File "/apps/RAPCLUST/0.1/lib/python2.7/site-packages/click/core.py", line 696, in main
rv = self.invoke(ctx)
File "/apps/RAPCLUST/0.1/lib/python2.7/site-packages/click/core.py", line 889, in invoke
return ctx.invoke(self.callback, *_ctx.params)
File "/apps/RAPCLUST/0.1/lib/python2.7/site-packages/click/core.py", line 534, in invoke
return callback(_args, **kwargs)
File "/apps/RAPCLUST/0.1/bin/RapClust", line 54, in processQuant
eqnet.buildNetFile(sampleDirs, netFile, cutoff)
File "/apps/RAPCLUST/0.1/lib/python2.7/site-packages/rapclust/eqnet.py", line 100, in buildNetFile
if (diagCounts[i] > cutoff):
IndexError: index 1423084 is out of bounds for axis 0 with size 1423084
Do you know why is this happening? How can I fix this error?
Thanks a lot,
Jèssica

[k3yavi]

This error looks strange, in my opinion what it means is that the length of TPM and NumReads columns in the sailfish quantification output file is different, which doesn't make sense.
Can you forward your data somewhere so that I can check?

[jesgomez]

Sorry for the delay in my response. I've been making some more tests and it
seems to me that the problem could be because I'm trying to combine
transcriptomes obtained from different runs of Trinity. Could that be? When
I run it on the different transcriptomes separately it works fine, as well
as with other data. But when I run it in the whole set of transcripts
(after doing a cat */Trinity.fasta > all_transcripts.fa) it gives the
error.
I make the sailfish index on this all_transcripts.fa file and then quantify
each sample separately.
Thanks for your help.

2016-07-27 19:35 GMT+02:00 Avi Srivastava notifications@github.com:

This error looks strange, in my opinion what it means is the length of
TPM and NumReads columns in sailfish quantification output file are
different, which doesn't make sense.
Can you forward your data somewhere so that I can check?

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[k3yavi]

You are right, RapClust is designed with the assumptions or rather motivation that quantification information is already present from different conditions separately. However, you should not get error like this while running Sailfish (i.e. different number of TPM and Num Reads in .sf file).
One problem which we can think of (thanks to @laraib85) could be that combining transcriptome (i.e. cat */Trinity.fasta > all_transcripts.fa) can result in multiple entries with the same transcript ids (depending on the assembler you use).
Please check your file all_transcripts.fa for redundant transcript id if present try renaming them.
Let us know how does this work out.

[jesgomez]

Hi again,
You were right, the problem were the redundant ids... I gave uniq ids to
each transcript and repeated the process, and it worked! So, thank you for
the advice.

2016-08-08 5:45 GMT+02:00 Avi Srivastava notifications@github.com:

You are right, RapClust is designed with the assumptions or rather
motivation that quantification information is already present from
different conditions individually. However, you should not get error like
this while running Sailfish (i.e. different number of TPM and Num
Reads in .sf file).
One problem which we can think of (thanks to @laraib85
https://github.com/laraib85) could be that combining transcriptome
(i.e. `cat */Trinity.fasta > all_transcripts.fa) can result in multiple
entries with the same transcript ids (depending on the assembler you use).
Please check your file all_transcripts.fa for redundant transcript id if
present try renaming them.
Let us know how does this work out.

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[k3yavi]

Glad to hear.