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Old 11-03-2014, 08:20 AM   #1
wendy liu
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Default cummeRbund errors when "readCufflinks"

Dear readers,
When using library cummeRbund, I got errors:
----------------------------------------------------------
> readCufflinks('diff_out')
Error in sqliteSendQuery(con, statement, bind.data) :
error in statement: no such table: genes
----------------------------------------------------------
The same computational environment made it when I analyzed the other cuffdiff output "diff_out_1":
> readCufflinks('diff_out_1')
CuffSet instance with:
8 samples
39170 genes
94818 isoforms
88478 TSS
46842 CDS
1095696 promoters
2477384 splicing
646716 relCDS

I have tried a lot, however, I can not figure out what is the problem. All packages on my computer and files in 'diff_out' are totally fine. Could you please give me some suggestions? I appreciate your time and reply.
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Old 11-03-2014, 08:49 AM   #2
ddias
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Default Same problem

I'm having the same issue. Did you find a solution?
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Old 11-03-2014, 01:22 PM   #3
wendy liu
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Not yet ......
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Old 11-04-2014, 05:01 AM   #4
Gonza
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I am having the same issue. I also analyzed other dataset and indeed worked. Now i have new cuffdiff dataset I am loading to R and get this:

Error in sqliteSendQuery(con, statement, bind.data) :
error in statement: no such table: genes

does anyone know how to fix this?
G
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Old 11-08-2014, 05:52 PM   #5
YazBraimah
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With the recent changes in RSQLite, there have been some incompatibility issues between cummerbund and RSQLite. The cummerbund developer(s) have addressed this, so you need to make sure you have the latest version of cummerbund (2.8.2) and RSQLite (1.0.0). If you download through bioconductor, make sure your bioconductor is up-to-date.

Once everything is current, make sure you use the "rebuild" option when reading the cuffdiff data. e.g.:

data<-readCufflinks("your cuffdiff folder", rebuild = T).

Hope that helps.

~YB
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Old 11-09-2014, 12:25 PM   #6
Gonza
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Thanks Yaz,

I still get error messages (through after updating to cummerbund (2.8.2) and RSQLite (1.0.0) they are different errors):

> library ("cummeRbund")
> cuff<-readCufflinks("05_cuffdiff_ncServ",rebuild=T)
Creating database 05_cuffdiff_ncServ/cuffData.db
Error in sqliteNewConnection(drv, ...) :
RS-DBI driver: (could not connect to dbname:
unable to open database file
)
> cuff
Error: object 'cuff' not found
>

Any idea what could this be?

thanks
G

Last edited by Gonza; 11-09-2014 at 12:27 PM.
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Old 11-09-2014, 12:38 PM   #7
YazBraimah
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You may be in the wrong directory. When you run:

>cuff<-readCufflinks("05_cuffdiff_ncServ",rebuild=T)

Make sure you're in the directory where the folder "05_cuffdiff_ncServ" sits. So you should be in "/Users/YOU/someDirectory/" and ""05_cuffdiff_ncServ" is in "/Users/YOU/someDirectory/05_cuffdiff_ncServ".

See if that works.

~YB
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Old 11-09-2014, 01:03 PM   #8
Gonza
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Thanks for your reply. I have the cufdiff folder (05_cuffdiff_ncServ) in desktop. This is what I do to read the output:

rm(list=ls())
setwd("/Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/")
getwd()
library ("cummeRbund")
cuff<-readCufflinks(rebuild=T)
cuff

When I try with rebuild=T i get this in red:

Creating database /Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/cuffData.db
Reading Run Info File /Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/run.info
Writing runInfo Table
Reading Read Group Info /Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/read_groups.info
Writing replicates Table
Reading /Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/genes.fpkm_tracking
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
line 1390 did not have 17 elements
> cuff
Error: object 'cuff' not found
>


When I try WITHOUT rebuild=T I get this :


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



Any ideas please.....?
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Old 11-14-2014, 04:24 AM   #9
blakeoft
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Gonza,

Have you looked at line 1390 of the genes.fpkm_tracking file?
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Old 11-21-2014, 04:18 PM   #10
Gonza
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Thanks.
I finally solved the problem. The gtf file i was using was corrupted with some '#' symbols. I removed them and now i can import cuffdiff to R without a problem.
cheers
-G
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Old 06-25-2017, 06:03 PM   #11
[email protected]
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> data<-readCufflinks("diff_out7", rebuild = T)
Creating database diff_out7/cuffData.db
Reading Run Info File diff_out7/run.info
Writing runInfo Table
Reading Read Group Info diff_out7/read_groups.info
Writing replicates Table
Reading Var Model Info diff_out7/var_model.info
Writing varModel Table
Reading diff_out7/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Warning messages:
1: In rsqlite_fetch([email protected], n = n) :
Don't need to call dbFetch() for statements, only for queries
2: In rsqlite_fetch([email protected], n = n) :
Don't need to call dbFetch() for statements, only for queries
3: In rsqlite_fetch([email protected], n = n) :
Don't need to call dbFetch() for statements, only for queries
4: In rsqlite_fetch([email protected], n = n) :
Don't need to call dbFetch() for statements, only for queries

How can I solve this problem? Thanks a lot.

Last edited by [email protected]; 06-25-2017 at 06:07 PM.
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Old 06-28-2017, 05:57 PM   #12
rxjing
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i've got the same problem, just can not readcufflinks() correctly, and i wonder whether u solve the issue or not?
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Old 07-02-2017, 11:24 PM   #13
[email protected]
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Sorry,I haven't already solved the problems in cummeRbund packages. If there is any other way can address, please reply for me.
Thanks a lot.
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Old 07-03-2017, 10:49 AM   #14
Oskar
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Default Same issue: can't create the database using readCufflinks

HTML Code:
> cuff_data <- readCufflinks("diff_out_R", rebuild = TRUE)
Creating database diff_out_R/cuffData.db
Reading Run Info File diff_out_R/run.info
Writing runInfo Table
Reading Read Group Info  diff_out_R/read_groups.info
Writing replicates Table
Reading Var Model Info  diff_out_R/var_model.info
Writing varModel Table
Reading diff_out_R/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)
I think this is something to do with the updated version, since it worked when I used the same files with a previous version, but with this version they don't work anymore.
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Old 07-10-2017, 11:53 AM   #15
jkofsky
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Does anyone have a good solution for these errors? Mine looks like this:

Creating database /cuffData.db
Error in rsqlite_connect(dbname, loadable.extensions, flags, vfs) :
Could not connect to database:
unable to open database file

or

50+ of these:

1: In rsqlite_fetch([email protected], n = n) :
Don't need to call dbFetch() for statements, only for queries

depending on how I submit it

From what I've read people have solved these issues by altering with the input (no symbols in the table) or by correcting the working directory. I have tried these and everything else I can think of. I have tried a cuffdiff output from a previous version and experiment and it runs in cummerbund fine...

I'm stuck. does anyone have a suggestion?
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Old 07-10-2017, 12:23 PM   #16
Oskar
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Hi jkofsky -

We are just having the same discussion in biocinductor - and we came across with some alternatives since seems to be a bug in the new version of bioconductor/cummeRbund. Here you are the link.

https://support.bioconductor.org/p/97561/#97888

Hope it helps.
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Old 07-10-2017, 12:32 PM   #17
jkofsky
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Quote:
Originally Posted by Oskar View Post
Hi jkofsky -

We are just having the same discussion in biocinductor - and we came across with some alternatives since seems to be a bug in the new version of bioconductor/cummeRbund. Here you are the link.

https://support.bioconductor.org/p/97561/#97888

Hope it helps.
Thanks, I will follow the thread.

I'm a little hesitant to assume its a bug considering data from cuffdiff (that was produced a year ago) is working fine ....
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