Entering edit mode
8.4 years ago
hana ▴ 190
I want to use cuffmerge to merge assemblies made with cufflinks (with Ensemble GRCH38 refrences ). I am running the command:
cuffmerge -o /home/ra/cuffmerge -g /home/ra/Ensemble_GRCH38/Homo_sapiens.GRCh38.77.gtf /home/ra/cuffmerge/assemblies.txt
and I get the following output:
Error: duplicate GFF ID 'ENST00000361547' encountered! [FAILED] Error: could not execute gtf_to_sam
I tried :
sudo chmod +xr /uer/bin/gtf_to_sam
and still have the same error.
I have downloaded the references fasta and gtf file from ensemble database.
How can I fix this error?
You need to check SAM header and whether SAM is sorted.
If there are no SQ records in the header, or if the header is missing, then also it would show same error.
The alignments must be sorted lexicographically by chromosome name and by position.
my alignment result is in bam format ,should I convert it to sam and sort it ?
yes, check it by viewing it by samtools
This is the header of my bam file
still I have the same error.
Would you please let me know what can I do to solve it.
do you still have two errors?
check your reference gtf and assembled gtf.txt are they in listed, separated by new line,
did you use same gtf for cufflinks
see if its in your path
try to run
transcripts.gtfjust to check that if there is an issue with
gtf_to_samis in my path. I run it separately on
transcripts.gtfand get the same error as below:
I understand this is very annoying that
gtf_to_samis running but there is problem with
I think that this is some bug in latest versions of cufflinks, (I guess older version does not have this issue but the newer has)
From my point of view there can two remedies
Thank you so much for your reply. I have sent the email to Cole Trapnel about this issue.
Would you please tell me how I can remove duplicates from transcripts.gtf file?
thanks in advance
A simple R script might work in this case, (but also recheck it with someone that this approach is okay, may be someone in this forum might also intervene if any alternative is possible)
thank you .I will try it
I have the same problem here! The version of cufflinks is 2.2.1...
When I ran
gtf_to_sam -r /share2/hlibyar/tophat/Am_genome.fa 101_S1_L001_R1_001/101_S1_L001_R1_001.gtf out.sam, it worked
The bam file is sorted.
Did you combine several assembled gtf files into one before running cuffmerge? I had same problem before because I used
catto combined two gtf into one.
I am running cuffmerge using cufflinks v2.1.1 and I ran into the exact same problem you mentioned above. I was wondering if you ever figured it out? Also, which version of cufflinks were you using (I understand it has been a while since you made the post)?
How did you solve your problem? I got exact same one. Really need your suggestion.
Hello Hana and Ellie,
I also got the exact same problem while running Cuffmerge. I previously didn't encounter this problem, but this time I turned on the RABT option in Cufflinks. Could it be RABT causing the problem for us? Did you turn that option on? Thanks.
I have the same exact problem running cuffmerge v2.1.1 and also with v 2.2.1. I tried
gtf_to_samseparately and it didn't work. I keep on getting the same error:
Did anyone find a solution for this?
I have the same errors and need help. This is my input and output:
If anyone knows how to fix can you please reply?
I have the same problems, have someone solved it?