Question: Problem With Rfam Search
0
gravatar for Ajw
8.2 years ago by
Ajw30
Columbus, OH
Ajw30 wrote:

I am trying to do a Rfam search for a unique sequence tags for small RNA. I am getting the following error message:

Command line: rfam_scan-1.0.2.pl -o rfamunmapped.txt-blastdb Rfam.fasta PolyAreomevedS1.fastq_unmapped_reads_collapsed.txt
WARN: No BLAST database specified.  Your search may be extremely slow.
Also, the model-specific global/local mode is not used, therefore
curated Rfam thresholds may not be meaningful.
Use of uninitialized value $fh in <HANDLE> at rfam_scan-1.0.2.pl line 527.
readline() on unopened filehandle at rfam_scan-1.0.2.pl line 527.
Use of uninitialized value $rfamid in hash element at rfam_scan-1.0.2.pl line 276.

Error: Failed to open covariance model save file Rfam.fasta

Can anyone help me with Rfam search? Thanks,

database small • 2.6k views
ADD COMMENTlink modified 8.1 years ago by Paul Gardner190 • written 8.2 years ago by Ajw30
3
gravatar for Neilfws
8.2 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

If what you ran on the command line is exactly as you typed it here, the problem could be a missing space between the -o switch and the -blastdb switch:

You typed:

rfam_scan-1.0.2.pl -o rfamunmapped.txt-blastdb Rfam.fasta...

Should be:

rfam_scan-1.0.2.pl -o rfamunmapped.txt -blastdb Rfam.fasta...

That might explain why the program cannot find a BLAST database, which I assume is Rfam.fasta.

ADD COMMENTlink written 8.2 years ago by Neilfws48k
3
gravatar for Paul Gardner
8.2 years ago by
Paul Gardner190
Christchurch, New Zealand.
Paul Gardner190 wrote:

Have you tried indexing Rfam.fasta for blast searching? eg. formatdb. Also, you are missing the latest Rfam.cm file: ftp://ftp.sanger.ac.uk/pub/databases/Rfam/10.0/Rfam.cm.gz Then try: rfam_scan-1.0.2.pl -o rfamunmapped.txt -blastdb Rfam.fasta Rfam.cm PolyAreomevedS1.fastq_unmapped_reads_collapsed.txt

ADD COMMENTlink written 8.2 years ago by Paul Gardner190

Thanks Paul - yes, it looks like it is running now. AJW

ADD REPLYlink written 8.2 years ago by Ajw30
0
gravatar for Ajw
8.2 years ago by
Ajw30
Ajw30 wrote:

Thanks neilws. I corrected the error and still gives the same results. The other thing that I am not sure is that whether or not Rfam.fasta is the correct file.

ADD COMMENTlink written 8.2 years ago by Ajw30

Please comment under answers, rather than writing a new answer.

ADD REPLYlink written 8.2 years ago by Neilfws48k

Sure, I will do this next. Thanks again

ADD REPLYlink written 8.2 years ago by Ajw30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1292 users visited in the last hour