Finder

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Finder generates no files and fails

1

Hello, I'm running Finder from local installation, not Docker. I'm running with PE RNAseq.fq but no protein file. It makes the necessary output directories and protein dummy file in temp...

ereyred

Issues during checkpoints 2/3

2

Hello, I've encountered 2 different issues when running Finder on 2 separate genomes. 1) INFO: Creating SIF file... /softwares/FINDER/Finder/scripts/fixOverlappingAndMergedTranscripts.py:350: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a...

Maxim-Karpov

Assembly issues, no combined gff file

1

Hello, I am trying to run the Finder With a bunch of RNA seq data. I am getting all the alignments files, however, in assembly psiclass is running into some...

mardal42

Singularity still calling docker

1

Hi, thank you for your time and work on this pipeline! Our HPC cluster does not use docker and so I am using the --framework singularity option. However, it is...

fiddlinwill

SRA Toolkit update for prefork and fastq-dump

1

Please update the SRA Toolkit packages (prefork and fastq-dump) in the dep folder to the latest 3.0.2 version. They no longer download data from NCBI due to an invalid SSL...

wesleyemason

I'm not able to do the initial example.

17

Good afternoon. My name is Fernando, I'm from Brazil and a student of computational biology at Fiocruz. First of all, I would like to thank you for the initiative to...

generalissimodeslock

Finder test issue

2

I'm having the same issue several other people have found, but I couldn't see a solution so I was wondering if you've found one. I run the example command as...

tomh1lll

I got gm_key_64.gz from the site

3

When I am on the license.download website to download the software and key. The key download as gm_key_64.gz and I can’t seem to unzip this file. Finder suggested the file...

angus821

docker: Error response from daemon: Duplicate mount point:

2

I just tried to run, but stopped with following error: ``` docker: Error response from daemon: Duplicate mount point: /home/user/Analyses/finder_v1.1.0. See 'docker run --help'. ``` /home/user/Analyses/finder_v1.1.0 is the folder which...

takeiga

avoiding docker and singularity

4

Hi, as part of an [Easybuild project ](https://easybuilders.github.io/) focused on installing software on HPC clusters, I need to patch Finder in a way that avoids using Docker and/or Singularity altogether....

deniskristak