Question: run pfam scan
0
gravatar for dineshtripathy9658
4.5 years ago by
United States
dineshtripathy965810 wrote:

i am trying to run pfam scan....but everytime i get the same message:

 

"Can't locate IPC/Run.pm in @INC (@INC contains: /userdata/dinesh/PfamScan/ /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /userdata/dinesh/PfamScan//Bio/Pfam/Scan/PfamScan.pm line 39.
BEGIN failed--compilation aborted at /userdata/dinesh/PfamScan//Bio/Pfam/Scan/PfamScan.pm line 39.
Compilation failed in require at /userdata/dinesh/PfamScan/pfam_scan.pl line 8.
BEGIN failed--compilation aborted at /userdata/dinesh/PfamScan/pfam_scan.pl line 8."

 

 

can anybody help me


 

tool pfam pfamscan • 6.3k views
ADD COMMENTlink modified 3.4 years ago by Nilesh0 • written 4.5 years ago by dineshtripathy965810

This might help you. https://xfam.wordpress.com/2013/10/15/a-version-of-pfam_scan-pl-for-hmmer-3-1b/.

Which version of HMMER is installed in your machine?

Take a look at hmmscan, works better than .pl script.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by venu6.2k

some pfam modules are there ...i dont know if i installed it correctly

ADD REPLYlink written 4.5 years ago by dineshtripathy965810

If you just want to search a sequence against a HMM db, use hmmscan.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by venu6.2k

is hhhscan really better than pfamscan.pl?

ADD REPLYlink written 4.5 years ago by dineshtripathy965810

Do you want to search a sequence against HMM db? hmmscan is the best option. Fast and Efficient.

hmmscan -o output_scan --notextw --acc HMM_db seqFile.faa

--acc - is optional. If you want pfam acc.id use that, otherwise family name will be there in the same position.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by venu6.2k
1

From the README, so there is a slight difference in the output. 

Q:  Why are the results from running hmmscan different from those I get when I run pfam_scan.pl?
A:  We group together families which we believe to have a common evolutionary ancestor in clans.  Where there
    are overlapping matches within a clan, pfam_scan.pl will only show the most significant (the lowest E-value)
    match within the clan.  We perform the same clan filtering step on the Pfam website.  If you do want the
    script to report all the overlapping clan matches, you can use the -clan_overlap option.

If you want to get identical output to the pfam web-site, then using the perl script is the best option, otherwise you can use hmmscan directly.

 

 

ADD REPLYlink written 4.5 years ago by Michael Dondrup46k

yes against hmmA but again for hmmscan i will have to install. coz my protein file is too large

ADD REPLYlink written 4.5 years ago by dineshtripathy965810

HMMER is required anyway, so you will have to install it first, the script is a wrapper for hmmer.

ADD REPLYlink written 4.5 years ago by Michael Dondrup46k

Hi all!!!

Im using hmmscan, but i would like to know whats the right evalue in order to give significance to the results? the ouput looks like:

 --- full sequence --- -------------- this domain -------------   hmm coord   ali
      E-value  score  bias    c-Evalue  i-Evalue  score  bias 

So which e-value is that i need to use to infer significance?? the full sequence or this domain?? as you see there are 2 different E-value.

Thanks

ADD REPLYlink written 3.6 years ago by yesid.cuesta0

3 different E-values

ADD REPLYlink written 3.6 years ago by yesid.cuesta0
1
gravatar for Michael Dondrup
4.5 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

you need to install all the dependencies, did you check the documentation?

install the perl module IPC::Run via cpan, then try again, until no further Can't locate ... appears.

The README tells you to:

$ cpan
install Moose

did you do that?

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Michael Dondrup46k

let me check

ADD REPLYlink written 4.5 years ago by dineshtripathy965810

how to install Moose on server side?

ADD REPLYlink written 4.5 years ago by dineshtripathy965810

have a superuser run the cpan commands above.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Michael Dondrup46k

ok now i have installed the pfamscan and started working. this was yesterday night . the program still running. an idea on how much it will take. or did i do something wrong. my input was 6 frame translation of 3817 transcripts

ADD REPLYlink written 4.5 years ago by dineshtripathy965810
0
gravatar for Nilesh
3.4 years ago by
Nilesh0
India/New Delhi/ICGEB/Indian Institute of Information Technology
Nilesh0 wrote:

Unfortunately, I was also facing the same problem.

You need to just make sure that you have set the path of pfam folder correctly.

$ export PERL5LIB=/home/cyano/Pfam/PfamScan:$PERL5LIB

This worked for me :-)

Good luck !

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Nilesh0
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