errors with grid single and grid multiplex

[Mechah]

Hi, after successful installation of GRiD and successful completion of the example test data (single and multi) I receive the following errors when I’m trying to use GRiD for my own data (I get similar errors irrespectively when I’m using the provided stool database, one of my reference genomes in single mode or my own database created with the update_database command):

grid multiplex -r GRiD/input_reads/ -e fastq.gz -d GRiD/Stool/ -p -m -o GRiD/output_Stool_database_local_execution/ -n 48

…
[samopen] SAM header is present: 1 sequences.
Clostridiales_bacterium_41_21_two_genomes.parallel.sh: line 38: bc: command not found

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Loading required package: proto
Warning message:
In fun(libname, pkgname) : couldn't connect to display "localhost:11.0"
Error in getopt(spec) : flag "c" requires an argument
Execution halted
paste: 'ERR1136916_R1_paired..GRiD.txt': No such file or directory
/miniconda3/envs/GRiD/bin/grid: line 695: ed: command not found
/miniconda3/envs/GRiD/bin/grid: line 696: ed: command not found
rm: cannot remove 'ERR1136916_R1_paired..GRiD.txt': No such file or directory
/miniconda3/envs/GRiD/bin/grid: line 724: ed: command not found
cut: '.temp.merge.txt': No such file or directory
rm: cannot remove '.temp.merge.txt': No such file or directory
/miniconda3/envs/GRiD/bin/grid: line 733: ed: command not found
run complete

After completion with those errors I only get the mosdepth.summary.txt output and an empty GRiD.txt as well as an empty merged_table.txt file.

Thanks for any support from your side!

[aemiol]

Hi, it seems "bc" and "ed" are not default on your system. Install using "sudo apt install bc" and "sudo apt install ed".

Thanks,
Tunde

[Mechah]

"bc" and "ed" were installed on our Cluster. Now it seems as GRiD performs as expected. Thanks!