Hey,

It seems like you're running into a parsing issue with the Pfam domtblout file in IsoformSwitchAnalyzeR (ISAR). The tool expects the standard HMMER domtblout format, typically with 22 columns (based on HMMER 3.x documentation), but variations in column counting or file formatting can cause errors, especially if headers or descriptions are mishandled.

First, ensure you're using the latest development version of ISAR, as updates often fix parsing bugs. Install it from GitHub:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("kvittingseerup/IsoformSwitchAnalyzeR")

Restart your R session after installation.

If you're using a local HMMER installation (current version is 3.4 as of 2025), double-check your command: hmmscan --domtblout output.txt Pfam-A.hmm your_sequences.fasta. Open the file in a text editor to confirm it's space-delimited without extra lines or rich text artifacts.

As an alternative, try the Pfam web server (https://www.ebi.ac.uk/interpro/search/sequence/). Submit your FASTA, wait for the email, then copy only the results table into a plain .txt file (not Word). Supply this to analyzePFAM().

If problems persist, share a sample of your Pfam file header and your ISAR code for more specific help.

Kevin