metaGEM

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After installing the pipeline through the manual installation guide (which worked better for me than the automatic installation), I was receiving the following error when trying the check with `bash...

Poccia

Run the workflow locally

1

**I just want to know if it is possible to run the workflow locally on my computer.** I've setup the workflow e just then noticed that it is designed for...

Poccia

documentation on running metaGEM using user-generated contig assemblies

3

I am trying to run metaGEM using a dataset that has already been quality filtered and assembled into contigs. I'm trying to format the data the way metaGEM wants it,...

zoey-rw

Question about using crossMapParallel

10

Dear Mr. Zorrilla, Thank you for inventing wonderful tool. I could go through all tasks described in https://github.com/franciscozorrilla/unseenbio_metaGEM/README.md, using **crossMapSerial**. But, after using **crossMapParallel**, concoct task fails with following error...

yhbae6022

Question about applying method for different biomes

1

Hi Francisco! Fantastic tool! Super excited to try it out. I am interested in applying your tool for the skin. A lot of the samples in your paper were from...

sskashaf

other inputs

9

Is there a way to input MAGs that we have generated using other pipelines into the tool? If so, at what point?

smb20200615

Error in rule binRefine (one of the commands exited with non-zero exit code)

11

Hi Francisco, When running `bash metaGEM.sh -t binRefine --local` with the metagem env activated, I seem to get a "`(one of the commands exited with non-zero exit code; note that...

slambrechts

Errors in env_setup.sh

1

Hi, I tried to install metagem on my server and found two problems. 1. `env_setup.sh` tries to install GTBK's database at line 67, but it cannot find "download-db.sh` (https://github.com/franciscozorrilla/metaGEM/blob/master/env_setup.sh#L67). 2....

yumyai

No metabat/samplename/cov/*.all.depth file and an empty concoct coverage_table.tsv

1

Hi Francisco, For 4 out of 43 samples, the `/metabat/samplename/cov/*.all.depth` files are missing, the concoct `coverage_table.tsv` file is empty, but the `/maxbin/samplename/cov` folder does contain depth files. Does that mean...

slambrechts

troubleshooting: poor assembly/binning in complex samples

3

Hi Francisco! I think a poor assembly is preventing soil samples from producing decent bins. I do plan to try re-assembling with a lower minimum contig length, but I was...

zoey-rw