Finder

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Error: EXITING: Did not find the genome in memory, did not remove any genomes from shared memory

4

Hi, I just came across this software as I have been struggling with MAKER. Running the example data and my data, I have encountered this same isssue. It says it...

lenshinaagbor

alignment files empty in example run

3

Hi. Thanks for providing the Finder tool, I'm keen to use it. I installed it fine (I think) and ran the Arabidopsis example. The following messages appeared (saved in 'Log.out'),...

g-d-w

Missing CDS annotation for some genes and transcripts

5

I was working with Finder and I am glad to report that the run completed without any errors for the dataset I was working with. I noticed that for some...

priyanka8590

Error in installation?

10

Hello. I'm getting this error when trying to run finder--the error occurs with example data as well. Any help would be greatly appreciated. `Traceback (most recent call last): File "/data/selaginella/finder/finder",...

vizzerra

using RNA-Seq gzipped fastq files

4

Usually we receive or download gzipped fastq files. It would be convenient not to have to gunzip them for Finder.

chklopp

exonerate result file input as novel finder command parameter

2

Exonerate is long to run. Would it be possible to add an option to give the exonerate result file as an input. We use a cluster with hundreds of nodes...

chklopp

STAR CPU limit

3

I tried to run finder with 24 CPUs but it failed during alignment step. The same command line worked with 12 CPUs. There seems to be an issue with STAR...

chklopp

using local RNA-Seq files

13

Even when setting a dummy BIOPROJECT and giving a local file prefix Finder tries to download the RNA-Seq files from the NCBI 2021-03-04 11:49:45,178 - finder - INFO - Started...

chklopp

Distant exon prediction

2

Hello @sagnikbanerjee15, During the CodAn step, the execution terminates due to the missing annotation.gtf file when findCDS function is launched. This is because CodAn process terminates due to duplicate entries...

Maxim-Karpov