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LangilleLab / microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
GNU General Public License v3.0
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scons: building terminated because of errors. #39

Closed yjiakang closed 4 years ago

yjiakang commented 4 years ago

I did metagenomic analysis in the microbiomehelper virtualbox, after blastx my concatenated pair-end reads against kegg.reduced.dmnd database and linking the result file into /home/shared/humann-0.99/input, then I run "scons -j 4 " in the /home/shared/humann-0.99/. However I got an error: **'''Results are saved in file: /dev/null Details are saved in file: /tmp/tmpMpZe0 scons: building terminated because of errors.'''** Can anyone help?

gavinmdouglas commented 4 years ago

Hi @yjiakang,

It's difficult to troubleshoot this error without more info - was a logfile created or were any other details written to the screen?

I would suggest you shift to using HUMAnN2, which is a greatly improved approach for functional profiling and doesn't use scons.

yjiakang commented 4 years ago

There were no more info, and I have tried HUMAnN2. When I want to use the legacy database "kegg“ according to the user manual, however, a compatible sequence database (referred to as genes.pep below) is needed. I cannot get the genes.pep though I have tried many ways. Would it be convenient for you to send me a "gene.pep" copy to me? Thanks in advance.

yjiakang commented 4 years ago

@gavinmdouglas

gavinmdouglas commented 4 years ago

@yjiakang could you email me at: gmail_screenshot

Thanks

yjiakang commented 4 years ago

@gavinmdouglas it is difficult for me to send a gmail because of the inaccessibility to the foreign network. I use QQ email instead. It is: 1652750913@qq.com

gavinmdouglas commented 4 years ago

Hey @yjiakang,

You can download the last free version (v56) of the KEGG sequence database here: https://www.dropbox.com/s/awa46dar435nn0w/kegg.reduced.fasta.tar.bz2?dl=1

I believe you can swap in that decompressed file for genes.pep in their examples.

yjiakang commented 4 years ago

@gavinmdouglas Thanks a lot.