Finder

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How to install via Conda

5

Dear Developer I am interested to try your pipeline. Could you please add information how to install your pipeline via Conda? Regards

ardy20

Singularity error: "destination must be an absolute path"

1

Hello, Just writing to report that I'm still having trouble getting the most recent version of Finder to work as documented on an HPC cluster via singularity. The run_finder job,...

claumer

Finder Stops Running during psi class assembly

2

Hello, I am trying to run Finder on a new genome. It is stalling out on the PSI class assembly (I think). The script stopped working in the middle of...

hopehealey

[error]docker: invalid reference format: repository name must be lowercase

2

`python3 run_finder-mf metadata.csv \ -g bin.masked.fasta \ -out_dir /finder_out/ \ -gm /home/soft/GeneMark-ESETEP.4.69/ \ -gml /home/soft/GeneMark-ESETEP.4.69/gm_key_64 \ -om PLANTS \ -n 30` It downloads the docker image successfully and then throws...

ShailNair

gz process

1

Dear Sagnik Banerjee, Finder use gunzip in RNA-Seq input, I think STAR and Olego could accept gz file, Finder might need to remove the step to facilitate the process, otherwise,...

wyim-pgl

really long introns create a problem with gffread

4

Hi, My Finder crashed during FindCDS at the codan steps. Codan throw an error about duplicate key : ``` ValueError: Duplicate key 'chr6:1-94332053.99_10_covsplit.0' ``` After checking this error, i found...

jkreplak

Unable to run example

1

Thank you very much for developing the finder! I have trouble with running example when executing the following command: ``` CUR_DIR=/home/kataoka/kataoka/finder/Finder-finder_v1.1.0/example GM_PATH=/home/kataoka/kataoka/finder/gmes_linux_64 GML_PATH=/home/kataoka/kataoka/finder/gm_key_64 cd $CUR_DIR && \ ../run_finder -no_cleanup \...

kataksk

error when downloading docker image

1

Hi, I am trying to download a docker image of finder but encountered a error, here is the error information: ``` => ERROR [44/53] RUN mkdir -p /softwares/NCBIBLAST && cd...

yz42

Not stranded annotation on the final GTF file

1

Dear Sagnik, I am trying to use the annotation file within CellRanger (10X genomics) but it doesn't accept non-stranded exons. In which step are they being considered, and how can...

vccarneiro

Are all those .sam mandatory ?

1

Hi, I was doing some tests using finder for a large plant genome. At the end of alignments steps, a *.sortedByCoord.out.sam* and a *_for_psiclass.sam* are created and removed only at...

jkreplak