Question: Filtering for redundancy in transcriptome de novo assembly using CD-HIT EST_fatal error: file opening failed Program halted
0
gravatar for c.evang
3.3 years ago by
c.evang10
Italy
c.evang10 wrote:

Hi,

I'm performing transcriptome de novo assembly from plant RNA-seq data using two strategies (the multiple k-mer approach and the single k-mer approach uising different assemblers) and then merging the several pre-assemblies. Now I'm trying to filter for redundancy using CD-HIT EST (Program: CD-HIT, V4.6), but the program stopped with an error.

 Error looks like this:

228085  finished     175242  clusters

Apprixmated maximum memory consumption: 455M
writing new database

Fatal Error:
file opening failed
Program halted !!

Can someone help me to understand what happens?

Thanks

rna-seq assembly • 2.0k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by c.evang10

Is this the first write operation? Could be a permission issue..

ADD REPLYlink written 3.3 years ago by 5heikki8.4k

Could you write the command you have used, please?
And as @5heikki has pointed out.. maybe is a permission issue. Check out folder permissions, files permissions...

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by iraun3.5k
0
gravatar for c.evang
3.3 years ago by
c.evang10
Italy
c.evang10 wrote:

This is the coomand:

cd-hit-est -i /media/universita/Archivio/WATBIO/CHIARA/ARUNDO_RNA-Seq_092015/TransAbySS_03-04122015/transabyss_merge/MergeAssembly_K21_25/MergeAssembly_k21_25 -o /media/universita/Archivio/WATBIO/CHIARA/ARUNDO_RNA-Seq_092015/cd-hit-est_output -c 0.95 -n 8 -M 0 -T 8

 

ADD COMMENTlink written 3.3 years ago by c.evang10

Please edit your question instead of posting an 'answer', this will increase the readability of the post for future readers.

For other hand, I guess that this /media/universita/Archivio/WATBIO/CHIARA/ARUNDO_RNA-Seq_092015/TransAbySS_03-04122015/transabyss_merge/MergeAssembly_K21_25/MergeAssembly_k21_25 file is a fasta file, isn't it? Because you did not specify the extension and it is always a good practice.

ADD REPLYlink written 3.3 years ago by iraun3.5k

Sorry!
It is a fasta file; I tried adding the extension but I obtained always the same error.

 

ADD REPLYlink written 3.3 years ago by c.evang10

Now it works properly; I have to add also the file extension for the output file.

Thanks for all your suggestions!

ADD REPLYlink written 3.3 years ago by c.evang10
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