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AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
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Missin: Metabolic_Sankey_diagram , Functional_network and MW-score result. The all are empty #93

Open Philippemetagenomica opened 2 years ago

Philippemetagenomica commented 2 years ago

Hello everyone

So I have run the METABOLIC-C pipeline. However some results are missing. I don't know why. I configured the data and database correctly. What is my mistake?

Here was the log file METABOLIC_log.log

ChaoLab commented 2 years ago

Hi, I guess that DIAMOND and Bowtie 2 were not set up well under your system. MEROPS peptidase annotation is depending on DIAMOND BLASTP. Bam file generation is depending on Bowtie 2.

Philippemetagenomica commented 2 years ago

Hi, I guess that DIAMOND and Bowtie 2 were not set up well under your system. MEROPS peptidase annotation is depending on DIAMOND BLASTP. Bam file generation is depending on Bowtie 2.

Hi! So I have Bowtie2 but not Diamond. I have installed it. I will run again

Philippemetagenomica commented 2 years ago

Hii, I have configured DIAMOND and Bowtie2 was already configured. But I'm still getting this message

([2022-08-09 18:01:52] Searching MEROPS peptidase... ls: cannot access '/home/philippe/work/teste4_metabolic_kraft37/intermediate_files/MEROPS_Files/.MEROPSout.m8': No such file or directory) '[2022-08-09 18:02:02] MEROPS peptidase searching is done' '[2022-08-09 18:02:05] METABOLIC table has been generated' '[2022-08-09 18:02:05] Drawing element cycling diagrams...' 'rm: cannot remove '/home/philippe/work/teste4_metabolic_kraft37/.bam': No such file or directory' 'rm: cannot remove '/home/philippe/work/teste4_metabolic_kraft37/.sorted.stat': No such file or directory' 'rm: cannot remove '/home/philippe/work/teste4_metabolic_kraft37/.bai': No such file or directory'

How should I proceed?

ChaoLab commented 2 years ago

Hi,

  1. There is no genome id in this file ".MEROPSout.m8", so I guess it is because that some MAGs might be like this - ".fasta". Can you check all the genome files in the input folder?
  2. There is no id in this file ".bam", so I guess it is because you have an empty line in the read file. You will need to strictly follow this instruction to prepare the read file - https://github.com/AnantharamanLab/METABOLIC/wiki/METABOLIC-Usage#all-required-and-optional-flags