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crimBubble / ECCsplorer

The ECCsplorer is a bioinformatics pipeline for the automated detection of extrachromosomal circular DNA (eccDNA) from paired-end read data of amplified circular DNA.
GNU General Public License v3.0
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ERROR: RepeatExplorer2 not found! #10

Closed inud3mon closed 1 year ago

inud3mon commented 2 years ago

Hi @crimBubble

I have been trying to run ECCsplorer but every I have tried i get the same error telling me RepeatExplorer2 is not installed

2022-09-09 12:42:57,003 - [setup_logging] INFO: Starting ECCsplorer pipeline with... Output directory: eccpipe Prefix data set A: TR File 1 data set A (f1a): Trimm_R1_paired.fastqsanger File 2 data set A (f2a): Trimm_R2_paired.fastqsanger Prefix data set B: CO File 1 data set B (f1b): --- File 2 data set B (f2b): --- Reference genome sequence: reference.fasta Custom BLAST+ database: None Taxon: met Read trimming option: None Mapping window size: 100 Genome size: --- User read count: not set, using max. available reads Run mode: all Image format: png Max threads used: 8 Logging to file: Yes 2022-09-09 12:42:57,003 - [basic_checkups] INFO: Performing basic checkups. 2022-09-09 12:42:57,003 - [basic_checkups] ERROR: RepeatExplorer2 not found!

Please make sure RepeatExplorer2 is installed. If you installed RepeatExplorer2 using conda, please activate the environment before starting the ECCsplorer pipeline. If not in PATH modify location: config > REPEATEXPLORER_PATH.

I have changed the file path in config.py and I have independently confirmed RepeatExplorer2 will run using a test data set

And for ls all total 188 -rwxrwxr-x 1 jenn jenn 31687 Sep 8 22:10 seqclust

Thanks,

Jenn

crimBubble commented 2 years ago

Hi @inud3mon sorry for the late reply, but I was unavailable due to vacation/illness.

Please check if inside the config.py file (in the lib folder) the path/file-location to your RepeatExplorer executable is set correctly. Open the file with any text-editor and set the variable REPEATEXPLORER_PATH to match the location of the seqclust file. It should look something like:

REPEATEXPLORER_PATH = /home/user/.../RepeatExplorer/seqclust

inud3mon commented 2 years ago

Hi @crimBubble

Thank for you for your reply.

Yea I have modified the config.py file to include the correct location but it still is not finding repeat explorer. A colleague of mine tried as well and also could not independently get repeat explorer to run. The mapping module runs fine, Trimmomatic etc.

I'm not sure what else to do.

Thank for your time