Issue running graftm create using docker

[erins1]

Hi,

I am a new user of graftM. Running using docker.
When I try to run graftM create to build a package I receive the following errors.

> docker run -v pwd:/data wwood/graftm:v0.13.1 create --sequences /Users/e/Documents/graftm_test/bsh_sequences.fasta --taxonomy /Users/e/Documents/graftm_test/bsh_taxonomy_file2.txt --output bsh_graftm_package.gpkg --log bsh_log.txt
Traceback (most recent call last):
File "/gnu/store/jcxdrw6c6z7n9q9wwqjyirk0lxgm715x-graftm-0.13.1/bin/.graftM-real", line 415, in
Run(args).main()
File "/gnu/store/jcxdrw6c6z7n9q9wwqjyirk0lxgm715x-graftm-0.13.1/lib/python3.7/site-packages/graftm/run.py", line 681, in main
threads = self.args.threads
File "/gnu/store/jcxdrw6c6z7n9q9wwqjyirk0lxgm715x-graftm-0.13.1/lib/python3.7/site-packages/graftm/create.py", line 593, in main
taxonomy_definition = GreenGenesTaxonomy.read_file(taxonomy).taxonomy
File "/gnu/store/jcxdrw6c6z7n9q9wwqjyirk0lxgm715x-graftm-0.13.1/lib/python3.7/site-packages/graftm/greengenes_taxonomy.py", line 51, in read_file
with open(input_filename) as f:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/e/Documents/graftm_test/bsh_taxonomy_file2.txt'

Even though the file clearly is in my current working directory:
Directory: C:\Users\e\Documents\graftm_test> ls
Mode LastWriteTime Length Name

---

-a---- 28/10/2020 10:48 AM 214479 bsh_sequences.fasta
-a---- 28/10/2020 12:05 PM 27362 bsh_taxonomy_file1.txt
-a---- 28/10/2020 1:55 PM 27362 bsh_taxonomy_file2.txt

Happens whether I run this on PC or MAC.

Including --user $(id -u):$(id -g) doesn't change anything other than generating the additional error "The term 'id' is not recognized as the name of a cmdlet, function, script file, or operable program."

Thanks for any help in understanding how to overcome this error.
Erin

[wwood]

See geronimp/graftM#268

[wwood]

I cannot close this issue, but it probably should be in favour of the above issue.