error in cuffmerge
Entering edit mode
6.8 years ago
mra8187 ▴ 20

Dear all i am using cuffmerge and get this error ; what can i do ?

my script is : cuffmerge -p 4 -o '/home/mra/Desktop/ensan/merge-out' -g '/home/mra/Desktop/ensan/Homo_sapiens.GRCh37.75.gtf' -s '/home/mra/Desktop/ensan/Homo-sapiens(hg19).fa' '/home/mra/Desktop/ensan/all'

and it is the log :

[Sat Jun 17 22:04:28 2017] Beginning transcriptome assembly merge

[Sat Jun 17 22:04:28 2017] Preparing output location /home/mra/Desktop/ensan/merge-out/
[Sat Jun 17 22:04:55 2017] Converting GTF files to SAM
[22:04:55] Loading reference annotation.
[22:05:09] Loading reference annotation.
[22:05:24] Loading reference annotation.
[22:05:38] Loading reference annotation.
[Sat Jun 17 22:05:54 2017] Quantitating transcripts
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (
Command line:
cufflinks -o /home/mra/Desktop/ensan/merge-out/ -F 0.05 -g /home/mra/Desktop/ensan/Homo_sapiens.GRCh37.75.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 4 /home/mra/Desktop/ensan/merge-out/tmp/mergeSam_filetUtpZp 
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File /home/mra/Desktop/ensan/merge-out/tmp/mergeSam_filetUtpZp doesn't appear to be a valid BAM file, trying SAM...
[22:06:14] Loading reference annotation.
[22:06:35] Inspecting reads and determining fragment length distribution.
Processed 55874 loci.                       
> Map Properties:
>   Normalized Map Mass: 1048774.00
>   Raw Map Mass: 1048774.00
>   Fragment Length Distribution: Truncated Gaussian (default)
>                 Default Mean: 200
>              Default Std Dev: 80
[22:06:47] Assembling transcripts and estimating abundances.
Processed 55874 loci.                       
[Sat Jun 17 22:24:14 2017] Comparing against reference file /home/mra/Desktop/ensan/Homo_sapiens.GRCh37.75.gtf
/bin/sh: 1: Syntax error: "(" unexpected
Error: could not execute cuffcompare
RNA-Seq • 2.2k views
Entering edit mode
6.8 years ago

I haven't encountered this before, but it looks like it doesn't like the () in the file name for '/home/mra/Desktop/ensan/Homo-sapiens(hg19).fa'? Have you tried just renaming that file, removing those brackets?

Entering edit mode

thank you .. it's working ..


Login before adding your answer.

Traffic: 2498 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6