Question: Error For End Coordinate When Running Cuffdiff
0
gravatar for camelbbs
7.5 years ago by
camelbbs670
China
camelbbs670 wrote:

Hi, while i run cuffdiff I got an error like this:

cuffdiff  -p 8  -o /s1_s2  -b  /bowtie2index/hg19.fa  -u  /all_merged/merged.gtf  /s1.bam  /s2.bam

[20:01:09] Loading reference annotation and sequence.
Error (GFaSeqGet): end coordinate (108996652) cannot be larger than sequence length 107349540
Error (GFaSeqGet): end coordinate (108996652) cannot be larger than sequence length 107349540
Error (GFaSeqGet): end coordinate (108996652) cannot be larger than sequence length 107349540
Error (GFaSeqGet): end coordinate (108996652) cannot be larger than sequence length 107349540
Error (GFaSeqGet): end coordinate (108996652) cannot be larger than sequence length 107349540
Error (GFaSeqGet): end coordinate (108996652) cannot be larger than sequence length 107349540
Error (GFaSeqGet): end coordinate (108996652) cannot be larger than sequence length 107349540
Error (GFaSeqGet): end coordinate (108996652) cannot be larger than sequence length 107349540

Anyone knows this? Thanks!!

cuffdiff rna-seq • 4.9k views
ADD COMMENTlink modified 3.0 years ago by Picasa530 • written 7.5 years ago by camelbbs670

Are you running on a 32-bit system?

ADD REPLYlink written 7.5 years ago by Arun2.3k

running on unix cluster. Do you mean that is because of cpu or memory exhausted?

ADD REPLYlink written 7.5 years ago by camelbbs670

Then most likely not. I was just wondering if the allocation was not possible due to memory restrictions of a 32-bit architecture.

ADD REPLYlink written 7.5 years ago by Arun2.3k
1
gravatar for matted
7.5 years ago by
matted7.3k
Boston, United States
matted7.3k wrote:

It's complaining about a read or annotation having a position larger than the reference chromosome length. 107349540 is the length of chromosome 14 in hg19, so I'd guess maybe you're using mouse reads mistakenly with a human reference here (mouse chromosome 14 is bigger than human: 125194864 bp). Basically, make sure the reference you hand to cuffdiff is the same as was used to generate the BAMs.

ADD COMMENTlink written 7.5 years ago by matted7.3k

I am sure I am using all hg19 reference to tophat and cuffdiff, may be the problem is the parameter -u?

ADD REPLYlink written 7.5 years ago by camelbbs670
1
gravatar for Arun
7.5 years ago by
Arun2.3k
Germany
Arun2.3k wrote:

There seems to be a similar post and an explanation here (suggested solution seems to be to run cufflinks with out the -b option).

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Arun2.3k

Thanks so much. While I run cuffdiff without -b option, it seems work. So which one is better to run with -b option, cufflinks or cuffdiff?

ADD REPLYlink modified 7.5 years ago • written 7.5 years ago by camelbbs670
0
gravatar for pengchy
5.1 years ago by
pengchy420
China/Beijing
pengchy420 wrote:

I also encounter this problem. I check the output transcripts.gtf, there indeed the coordinate larger than the reference genome sequence length. However,  when I rerun cufflinks for the error scaffolds specifically, the output transcripts.gtf become normal. Both running with "-b and -u" parameters.

ADD COMMENTlink written 5.1 years ago by pengchy420
0
gravatar for fta.mirzadeh
4.0 years ago by
fta.mirzadeh0 wrote:

I was getting this error using cuffmerge, ran cuffmerge without -s genome.fa option and it worked! dont know if was accurate or not but the program gave a merged.gtf as output. I proceeded to cuffdiff using THAT merged.gtf and received the error again! I omitted the -b and its running so far :)

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by fta.mirzadeh0
0
gravatar for super
4.0 years ago by
super60
super60 wrote:

Hi I have same problem with you! It seems that lots of people have this error.

I use the Ensembl genome(*dna.toplevel.fa) and GTF file.

If I ran cufflinks (even without -b genome.fa) but then run Cuffmerge with -s genome.fa, I got the error!

If I omitted -b genome.fa in both Cufflinks and Cuffdiff and meanwhile omit -s genome.fa in Cuffmerge, I didn't get the error! However, I don't know if it was accurate.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by super60
0
gravatar for Picasa
3.0 years ago by
Picasa530
Picasa530 wrote:

I have the same error even without using the -s in cuffmerge ... any solution ?

ADD COMMENTlink written 3.0 years ago by Picasa530
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