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Old 10-24-2012, 05:17 PM   #1
steindorff
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Location: Brazil

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Default CummeRbund error

Hi,
I'm stuck in this cummeRbund error:

library(cummeRbund)
cuff_data <- readCufflinks('diff_out')
Creating database diff_out/cuffData.db
Reading diff_out/genes.fpkm_tracking
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
line 1 did not have 33 elements

If someone can help...
Thanks
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Old 11-14-2012, 11:58 AM   #2
mikeyt
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Hi,

I am having the same error:

cuff_data <- readCufflinks ('diff_out')
Creating database diff_out/cuffData.db
Reading diff_out/genes.fpkm_tracking
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
line 1 did not have 25 elements


Were you able to resolve this problem?

Thanks.
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Old 11-14-2012, 12:10 PM   #3
steindorff
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I look all the files searching the problem...the problem was in the GFF3 (or GTF) file. The '#' character appeared in some gene names.
Probably your annotation file have some character that the R don't recognize.
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Old 11-14-2012, 03:53 PM   #4
mikeyt
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Thanks. I deleted all the '#' characters and received some progress but another error.

> cuff_data <- readCufflinks ('diff_out')
Creating database diff_out/cuffData.db
Reading diff_out/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading diff_out/gene_exp.diff
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
line 1 did not have 14 elements

It may just be the same problem but with the gene_exp.diff file this time.
Thanks again and I appreciate your help!
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Old 11-14-2012, 04:14 PM   #5
steindorff
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I'm glad that I can help.
I ran all the TopHat and cufflinks pipeline with the GFF3 corrected to avoid errors and it worked well for me.
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Old 12-05-2012, 12:22 PM   #6
s869023
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Hi
I have similar problem while loading database in commeRbund

> library("cummeRbund")
> cuff_data<-readCufflinks('cuffdiff_output_sample-ATvsBC')
Creating database /cuffdiff_output_sample-ATvsBC/cuffData.db
Reading Run Info File cuffdiff_output_sample-ATvsBC/run.info
Writing runInfo Table
Reading Read Group Info cuffdiff_output_sample-ATvsBC/read_groups.info
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
line 1 did not have 7 elements

Then I try

> cuff_data
CuffSet instance with:
0 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS

The cuffData.db file is only 70kb, so I assume there are some error in loading db.
Any help will be highly appreciated.
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Old 07-30-2013, 05:37 AM   #7
jp.
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Location: NikoNarita.jp

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Posts: 142
Question

Hi there
I got the same problem... any solution ?


Quote:
Originally Posted by s869023 View Post
Hi
I have similar problem while loading database in commeRbund

> library("cummeRbund")
> cuff_data<-readCufflinks('cuffdiff_output_sample-ATvsBC')
Creating database /cuffdiff_output_sample-ATvsBC/cuffData.db
Reading Run Info File cuffdiff_output_sample-ATvsBC/run.info
Writing runInfo Table
Reading Read Group Info cuffdiff_output_sample-ATvsBC/read_groups.info
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
line 1 did not have 7 elements

Then I try

> cuff_data
CuffSet instance with:
0 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS

The cuffData.db file is only 70kb, so I assume there are some error in loading db.
Any help will be highly appreciated.
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