Issue with non-existing file

[RenzoTale88]

Hi, I'm trying to mask a genome using Red. I run it with the following command line:

mkdir -p GENOMES/mygenome/masks/rpt
Red -gnm GENOMES/mygenome/ -cor 4 -msk ./GENOMES/mygenome/masks/ -tbl ./GENOMES/mygenome/masks/ -rpt GENOMES/mygenome/masks/rpt

This produces a segmentation fault, with the error ERROR: ./GENOMES/mygenome/masks/rpt/ does not exist

This is Red (REpeat Detector) designed and developed by Hani Zakaria Girgis, PhD.

Version: 2.0

Using 4 threads.
Calculating the length, k, of the k-mer based on the input genome ...
        GENOMES/mygenome//mygenome.fa
The recommended k is 15.

Using the default output format chrName:start-end
Using the default background order: 6.
Using the default threshold: 2.
Using the default minimum of the observed count of k-mers: 3.
Calculating GC content ...
        GENOMES/mygenome//mygenome.fa
Using the default half width: 20 based on the GC content of 41.9222

List of final parameters:
-cor: 4
-frm: 1
-gau: 20
-gnm: GENOMES/mygenome/
-len: 15
-min: 3
-msk: ./GENOMES/mygenome/masks/
-ord: 6
-rpt: GENOMES/mygenome/masks/rpt/
-tbl: ./GENOMES/mygenome/masks/
-thr: 2

Deleting pre-existing files under ./GENOMES/mygenome/masks/
Deleting: ./GENOMES/mygenome/masks//rpt
Deleting pre-existing files under GENOMES/mygenome/masks/rpt/
Segmentation fault (core dumped)

File Does Not Exist Exception
ERROR: ./masks/rpt/ does not exist.

terminate called after throwing an instance of 'exception::FileDoesNotExistException'

I also tried to run it directly in the masks folder, but this causes the software to delete the directory and not save any output at all. Am I doing something wrong?

Andrea

[kfuku52]

I ran into the same problem, but all output files were produced with unique directory names passed to output options. My command looks like:

Red \
-gnm ${dir_sp_tmp}/red_infile \
-rpt ${dir_sp_tmp}/${sp_ub}.red.rpt \
-msk ${dir_sp_tmp}/${sp_ub}.red.msk \
-cor ${NSLOTS}

I tried other output options as well. -tbl produced the file in the current directory rather than in the specified dir in my case... but the file was produced anyway.