Rfam database is not working

Pfam data and new releases are available through InterPro.
Needs to be updated for getPfam and the alignment downloads

I am getting the following error

Command error:
  --2023-12-11 02:44:16--  http://gydb.org/gydbModules/collection/collection/db/GyDB_collection.zip
  Resolving gydb.org (gydb.org)... 147.156.56.230
  Connecting to gydb.org (gydb.org)|147.156.56.230|:80... connected.
  HTTP request sent, awaiting response... 302 Found
  Location: https://gydb.org/gydbModules/collection/collection/db/GyDB_collection.zip [following]
  --2023-12-11 02:44:17--  https://gydb.org/gydbModules/collection/collection/db/GyDB_collection.zip
  Connecting to gydb.org (gydb.org)|147.156.56.230|:443... connected.
  ERROR: The certificate of ‘gydb.org’ is not trusted.
  ERROR: The certificate of ‘gydb.org’ has expired.

Looks like GyDB is quite different now.

Solution

Convert to the new link

https://gydb.org/extensions/Collection/collection/db/GyDB_collection.zip

and also use wget with no certification

wget --no-check-certificate -O https://gydb.org/extensions/Collection/collection/db/GyDB_collection.zip

Check sub-profiles and singularity docker

The command for specific species doesn't work

--rm_species fungi

Species "fungi" is not known to RepeatMasker.  There may
not be any TE families defined in the libraries for this
species/clade or there may be an error in the spelling.
Please check your entry against the NCBI Taxonomy database
and/or try using a broader clade or related species instead.
The full list of species/clades defined in the library may be
obtained using the famdb.py script.

The file format has changed and needs an update for the new RepeatMakser version

Current versions and available ones

Major

• RepeatModeller 1.0.11-> 2.0.3

Minor

• RepeatMasker open-4.0.9 -> 4.1.5
• MMseqs 9-d36de -> v14.7e284
• vsearch v2.14.1 -> v2.26.1
• HMMer 3.2.1 -> 3.4
• Blast+ 2.9.0 -> 2.14.1 #dependency
• bedtools 2.28.0 -> v2.31.1
• viennarna 2.4.13 -> 2.6.4
• Decipher 2.14.1 -> v2.30.0
• genometools 1.5.10 -> 1.6.5

Patch version

• t-RNAscan2 2.0.3 -> 2.0.12
• Infernal 1.1.2 -> v1.1.4 (dependency of tRNAscan-SE)
• Arargon 1.2.38 -> v1.2.41
• RepeatScout 1.0.5 -> v1.0.6

No changes

• trf 409 #dependecy
• RECON 1.08 #dependency

GiHub installations

• MITEFINDER https://github.com/screamer/miteFinder.git
• EAhelitron https://github.com/dontkme/EAHelitron.git
• StructureFinder https://github.com/viniciusmaracaja/structRNAfinder.git

Python setup - pip instalations

• SeqRenamer https://github.com/darcyabjones/seqrenamer.git (this has to be updated for the linked dependencies. I am using this forked repo)
• Gffpal https://github.com/darcyabjones/gffpal.git # dependency

Other manual installations

• occultercut 1.1.0 - no changes

Proprietary

Rnammer 1.2 - different container

Decipher is not working, the link that points to the version DECIPHER_2.10.0 is not available anymore, it has been replaced by 2.26. Unfortunately, the biostrings package is requires an update and this is not available as a library in linux. There are several other options for manual compilation but it looks quite tedious and painful

Make sure it works with that option

Check this library for more details
https://github.com/Dfam-consortium/FamDB

This will remove the hmm and the unpacking of the large file. Pante requires quite a lot of disk space for each step

The software is now on Bioconda

Working with this command on downloading the database

https://github.com/KristinaGagalova/pante2/blob/b2813a24fc0a3c4601c34ff4c83a2d28957d4828/main.nf#L370-L374

in several cases, it restarts the download and creates a new command path, while carrying on with the old ones. however, it keeps on dying if the connection is unstable.

Reset the number of downloads in wget to 1 to avoid this behavior (any alternatives to that?)

wget --tries=1

Error message

Reading the RepeatMasker EMBL file: RepeatMaskerLib.embl
Warning...unknown stuff <
>

refers to the following process in prepRepeatMaskerDB

https://github.com/KristinaGagalova/pante2/blob/2d629274ef9360152391d7e9f007b1313a21d176/main.nf#L1244-L1249

Gives the following

N E X T F L O W  ~  version 22.10.0
Pulling KristinaGagalova/pante2 ...
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/KristinaGagalova/pante2/contents/nextflow.config?ref=main
Remote resource not found: https://api.github.com/repos/KristinaGagalova/pante2/contents/main.nf?ref=main

config file needs to be changed

I am getting this error

Command exit status:
  127

Command output:
  (empty)

Command error:
  /bin/bash: line 0: cd: /data/projects/pante2/work/ea/fe51f157bc953f9d43f53bf7230651: No such file or directory
  /bin/bash: .command.run: No such file or directory

This is related to the following

Easily solved with the config file for singularity

Using -with-docker does not work for the Rnammer.