Problem With Rfam Search

Question

[Ajw]

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,

Answer 1

[Neilfws]

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.

Answer 2

[Paul Gardner]

Have you tried indexing Rfam.fasta for blast searching? eg. formatdb.

Also, you are missing the latest Rfam.cm file.

Then try:

rfam_scan-1.0.2.pl -o rfamunmapped.txt -blastdb Rfam.fasta Rfam.cm PolyAreomevedS1.fastq_unmapped_reads_collapsed.txt

[Ajw]

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

Answer 3

[Ajw]

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.

[Neilfws]

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

[Ajw]

Sure, I will do this next. Thanks again