Open Mechah opened 3 years ago
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
"bc" and "ed" were installed on our Cluster. Now it seems as GRiD performs as expected. Thanks!
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’:
The following objects are masked from ‘package:base’:
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!