LoReAn
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lfaino
Long Reads Annotation pipeline
I was successfully able to run LoReAn on both example datasets, and when I attempt to run the pipeline on my dataset, genome masking, STAR, Trinity, and long read mapping...
Hi! I installed LoReAn via Docker with: `sudo docker run -it --rm -v /home/hannah/Augustus/config/:/opt/LoReAn/third_party/software/augustus/config/ -v $HOME:/home/lorean -v $PWD:/data -u $(id -u ${USER}):$(id -g ${USER}) lfaino/lorean:latest lorean -h` (Docker Image ID:...
 I have a sample file of this size. At present, 1t of memory is not enough.
It has reached the `RUNNING iASSEMBLER ` step: ``` earlier logs... ###UPDATE WITH PASA DATABASE STARTED AT: 03:39:16 17-03 ### ###CREATING CONFIGURATION FILE### ###LOADING GFF3 FILE INTO DATABASE### ###UPDATING GFF3...
I met some problems (not the latest docker image). After checking my gff3 file and getRightStrand.py I found that error occurred when a gene contained an mRNA but lost CDS,...
I met some problems when running LoReAn which was installed using docker. It may be a small bug. In lines 181 and 194 an integer was added to a string....
I have run LoReAn on docker but it shows the following error when processing the long reads. I used the following code docker run -it --rm -v /home/sajjad/Augustus/config:/opt/LoReAn/third_party/software/augustus/config/ -v $HOME:/home/lorean...
Hi, I keep getting this error when running lorean with a genome of 580 Mb and ~240 G short read RNASeq data. I ran it in a singularity container. I...
I have run LOREAN with examples without any issue but when i used my own plant genome sequences it shows the following errores. pleas help. i am using docker version...
Dear @lfaino Do you think it would be difficult to implement an option to use several bam files for short reads (many libs), instead of merging in a very huge...
