Question: error in cuffmerge
0
gravatar for mra8187
21 months ago by
mra818720
mra818720 wrote:

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 (http://cufflinks.cbcb.umd.edu).
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
    [FAILED]
Error: could not execute cuffcompare
rna-seq • 951 views
ADD COMMENTlink modified 21 months ago by Philipp Bayer6.0k • written 21 months ago by mra818720
0
gravatar for Philipp Bayer
21 months ago by
Philipp Bayer6.0k
Australia/Perth/UWA
Philipp Bayer6.0k wrote:

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?

ADD COMMENTlink written 21 months ago by Philipp Bayer6.0k

thank you .. it's working ..

ADD REPLYlink written 21 months ago by mra818720
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