analyzePFAM error with isoquant data

[rsalz]

I wanted to bring this issue to your attention I use pfam_scan.pl (conda) on the command line and input the results with analyzePFAM(). I am using IsoQuant data. I get this error:

Error in h(simpleError(msg, call)) :                                                                                                                            
  error in evaluating the argument 'x' in selecting a method for function 'unique': error in evaluating the argument 'x' in selecting a method for function 'unique': error in evaluating the argument 'x' in selecting a method for function 'which': undefined columns selected

I tried to manipulate the results file but nothing worked. I am able to submit all the subfiles to the webserver to run and the output of that reads fine with analyzePFAM() but I would rather continue using the command line pfam_scan so it would be great if you could fix this. TY

[kvittingseerup]

I think this has been fixed? Which version of IsoformSwitchAnalyzeR are you running?

[rsalz]

I am running the latest version, i downloaded from github yesterday

[kvittingseerup]

Sounds strange. What do you get when running: packageVersion('IsoformSwitchAnalyzeR')?

Also could you post the first couple of lines of the output from pfam_scan.pl?

[rsalz]

package version is: '2.1.12'

i am using pfamscan from conda: https://anaconda.org/bioconda/pfam_scan so I don't actually have the perl script somewhere...

[kvittingseerup]

Could you post the head of the result file?

tor. 30. mar. 2023 kl. 14.16 skrev Renee Salz @.***>:

package version is: '2.1.12'

i am using pfamscan from conda: https://anaconda.org/bioconda/pfam_scan so I don't actually have the perl script somewhere...

— Reply to this email directly, view it on GitHub https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues/182#issuecomment-1490202597, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFU7JYYGOIXDJKKRDR4RDVLW6V2R5ANCNFSM6AAAAAAWGIW45Q . You are receiving this because you commented.Message ID: @.***>

-- Cheers Kristoffer

[rsalz]

here are the first 31 lines:

# pfam_scan.pl,  run at Thu Mar 30 11:43:35 2023
#
# Copyright (c) 2009 Genome Research Ltd
# Freely distributed under the GNU 
# General Public License
#
# Authors: Jaina Mistry (jaina@ebi.ac.uk), 
#          Rob Finn (rdf@ebi.ac.uk)
#
# This is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>. 
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
#      query sequence file: isoformSwitchAnalyzeR_isoform_AA_complete.fasta
#     cpu number specified: 30
#        searching against: /mnt/xomics/renees/data/host_pathogen_PID/pbmc_isoseq/analysis//Pfam-A.hmm, with cut off --cut_ga
#    resolve clan overlaps: on
#     predict active sites: off
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
#
# <seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan>

transcript8917.chr1.nnic       83    130     83    130 PF00018.31  SH3_1             Domain     1    48    48     66.8   9.4e-19   1 CL0010   
transcript8917.chr1.nnic      144    226    144    226 PF00017.27  SH2               Domain     1    77    77     96.9   5.6e-28   1 CL0541

[vasikara17]

Hello, I have exactly the same error and my out put looks like this: I used the PfamScan webserver and the output files are txt format. I made a new txt file and just copied all the results there and I get exactly the same error.

I also found a comment in Bioconductor that if the input is 20 transcripts it works and after testing it, it works indeed. Is there any way to input the whole file without having to split it?

Best, Vasiliki

[sparthib]

Hi, are there any updates on this? thanks!