Filtering for redundancy in transcriptome de novo assembly using CD-HIT EST_fatal error: file opening failed Program halted
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6.1 years ago
c.evang ▴ 10

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 • 3.1k views
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Is this the first write operation? Could be a permission issue..

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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...

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This is the command:

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
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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.

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Sorry!

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

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

Thanks for all your suggestions!

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