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ohlab / GRiD

Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
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Issue report: Fatal error: cannot open file 'check_R_libraries.R': No such file or directory #12

Closed zhssakura closed 5 years ago

zhssakura commented 5 years ago

Dear @ohlab,

I have installed GRiD on MacOS system with conda environment. When I was trying to test with example data, I encountered an error as following: (GRiD)User$ grid single -r . -g S_epidermidis.LRKNS118.fna -o output_single

readlink: illegal option -- f usage: readlink [-n] [file ...] readlink: illegal option -- f usage: readlink [-n] [file ...] readlink: illegal option -- f usage: readlink [-n] [file ...] readlink: illegal option -- f usage: readlink [-n] [file ...] single option activated /Users/User/Bioinfo/software/GRiD-master/test is present directory is the reads directory is the output directory is the path to reference genome ################ Checking for dependencies ######## parallel found R found bowtie2 found seqtk found samtools found bedtools found bamtools found blastn found pathoscope found All required packages found ################ Checking for required R libraries ######## Fatal error: cannot open file 'check_R_libraries.R': No such file or directory R libraries ok rm: .checkedR: No such file or directory usage: mkdir [-pv] [-m mode] directory ... Output directory not Empty

I do not know why this issue happens. Could you please help me with it? Thank you very much!

Best,

Shan

aemiol commented 5 years ago

Hi Shan,

This has to do with a dependency in the latest version of GRiD (mosdepth) that is currently unavailable via conda for macOS. Please refer to this thread on ways to circumvent this issue. https://github.com/ohlab/GRiD/issues/3

Regards,

zhssakura commented 5 years ago

Hi Tunde,

Thanks for your quick reply. I can install GRiD 1.2 on the Unix system and it works well on example test. But I could not install GRiD 1.3. I wish this will be solved in the future. Thank you again!

Best,

Shan