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According to discussion in #6 these scripts should work with recent Pfam releases using HMMER3 and a recent pfam_scan.pl.
However, the current version of ``bash_scripts/run_pfam_scan.sh`` when call…
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I am an absolute beginner in bioinformatics, how can I solve the problem?
`zctea@zctea:~/biowork/TAIR10$ funannotate predict -i TAIR10_genome.fasta --species "Arabidopsis thaliana" --busco_db emb…
zctea updated
6 years ago
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Hi
I am using Prokka to annotate a set of genomes using a custom nucleotide hmm database I built using hmmer (hmmbuild). I used the following pipeline to do this
1. Create hmms for each gene using…
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## Expected Behavior
When using a MSA DB from a fasta MSA with multi-lines **msa2profile** should create a profile.
## Current Behavior
Now it fails with the error `Member sequence 0 in entry 0 too…
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Per our discussion about pushing gene2product updates I wanted to update in the install dir
Is this expected error message when the -f is not provided? (it works fine if I give it -f)
```
./fu…
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#### Problem Description:
Currently many of the CLI dependancies are installed in the following manner:
```Shell
echo "Installing HMMER & Easel mini-applications.\n"
if [ ! `which hmmsearch` ]…
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Hi,
I can run InterProScan (v5.25-64.0) on the test file test_proteins.fasta but I get an error when I try to use my own data.
Any suggestions on what went wrong?
I used the command:
`inte…
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The effectR package seems to be working in OSX and Ubuntu. Need to test it on Windows
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@mcscimenc I moved your last bug report to this new thread.
Start forwarding:
OK, the program runs for a little while and now gives this error:
ERROR: No such file or directory at /home/joshd/s…
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Wiki accidentlly says "When running deltaBS, the option -hd specifies the directory that HMMER3 has been installed in and -hp specifies the directory that the Pfam HMMs have been dowloaded to."
Inste…