Problems with rfam_scan.pl

Palgrave · 09-08-2011, 03:58 AM

I ran the program, but got the following error (in bold):

robin@robin-Aspire-3810T:~/Downloads$ perl rfam_scan.pl -o test4h --nobig /home/robin/Downloads/Rfam.cm /home/robin/Downloads/4hLong.fastaWARN: 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 $rfamid in hash element at rfam_scan.pl line 276, <GEN1> line 988228.
Died at rfam_scan.pl line 281, <GEN1> line 988228.
Any idea?

asperjelly · 04-23-2014, 12:55 PM

I just had the same error. Did you ever get this figured out and running properly?

okapick · 07-28-2014, 04:44 AM

Same error. What is it about the sequence format some lost N or what?

asperjelly · 08-04-2014, 09:31 AM

Ok. So I finally got back to this. It seems it is failing due to the wrong Infernal version. You must have Infernal-1.0.2 for the script to run. I removed Infernal1.1.1 and then installed version 1.0.2 and the rfam_scan.pl script seems to run fine after that.

okapick · 09-14-2014, 02:24 AM

The original script from last version of RFAM_v11 (rfam_scan.pl) is wrong. Due to it does not change some options than works in the last infernal software v1.0 but it is not update for infernal v1.1. For example, my rfam is blocked when the cmsearch are working. And /tmp you can see why cmsearch file is stop. The first time was because the option "--tabfile" instead of "--tblout" or "--ga" instead of "--cut_ga". Although the last option changed (--cut_ga) work neither. A new error appear "Error: Format tag is 'HMMER3/f': unrecognized or not supported."

In sum up, You have to explore the rfam_scan with infernal 1.0. I guess.

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09-08-2011, 03:58 AM	#1
Palgrave Member Location: norway Join Date: Aug 2011 Posts: 73	Problems with rfam_scan.pl I ran the program, but got the following error (in bold): robin@robin-Aspire-3810T:~/Downloads$ perl rfam_scan.pl -o test4h --nobig /home/robin/Downloads/Rfam.cm /home/robin/Downloads/4hLong.fastaWARN: 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 $rfamid in hash element at rfam_scan.pl line 276, <GEN1> line 988228. Died at rfam_scan.pl line 281, <GEN1> line 988228. Any idea?

09-14-2014, 02:24 AM	#5
okapick Junior Member Location: Alicante Join Date: Sep 2013 Posts: 6	The original script from last version of RFAM_v11 (rfam_scan.pl) is wrong. Due to it does not change some options than works in the last infernal software v1.0 but it is not update for infernal v1.1. For example, my rfam is blocked when the cmsearch are working. And /tmp you can see why cmsearch file is stop. The first time was because the option "--tabfile" instead of "--tblout" or "--ga" instead of "--cut_ga". Although the last option changed (--cut_ga) work neither. A new error appear "Error: Format tag is 'HMMER3/f': unrecognized or not supported." In sum up, You have to explore the rfam_scan with infernal 1.0. I guess. Last edited by okapick; 09-14-2014 at 02:29 AM.

04-23-2014, 12:55 PM	#2
asperjelly Member Location: Wisconsin Join Date: Jan 2013 Posts: 11	I just had the same error. Did you ever get this figured out and running properly?

07-28-2014, 04:44 AM	#3
okapick Junior Member Location: Alicante Join Date: Sep 2013 Posts: 6	Same error. What is it about the sequence format some lost N or what?

08-04-2014, 09:31 AM	#4
asperjelly Member Location: Wisconsin Join Date: Jan 2013 Posts: 11	Ok. So I finally got back to this. It seems it is failing due to the wrong Infernal version. You must have Infernal-1.0.2 for the script to run. I removed Infernal1.1.1 and then installed version 1.0.2 and the rfam_scan.pl script seems to run fine after that.