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AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
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The result files "All_gene_collections_mapped.depth.txt" ,"Functional_network_figures" are empty. #177

Open mojingmj123 opened 10 months ago

mojingmj123 commented 10 months ago

Hello,

I am encountering some issues while running METABOLIC-C.pl. I used the following command: nohup perl METABOLIC-C.pl -in-gn /home/.../dereplicated_genomes/ -r /home/.../all-merged-1.fastq,/home/.../all-merged-2.fastq -o /home/.../metabolic-c2 &.

I have 95 dereplicated MAGs obtained through coassembly, so I used the merged clean reads as input files.

However, after the program finished running, I noticed that the result files "All_gene_collections_mapped.depth.txt" and "Functional_network_figures" are empty. Additionally, the files "energy_flow_figures" and "Metabolic Alluvial Diagram" are missing.

The log file is attached for your reference.

Could you please assist me in resolving this issue? I would greatly appreciate your help. Thank you very much. METABOLIC_log.log

patriciatran commented 10 months ago

Hi, I think it's because the -r argument should be a text file containing the paths to your fastq files, not listing them directly in the command line. See Note #2 here: https://github.com/AnantharamanLab/METABOLIC/wiki/METABOLIC-Usage#Metabolic_usage Please try that and let us know if that solves the issue. Thank you, Patricia

HAIS-st commented 8 months ago

I have a similar issue, but my -r argument is a text file containing the fastq path