Datrie

[bhanusakhamuri]

I already installed the Datrie using pip install but this error pops and the assembly gets exiting.

python3.7 go_metacompass.py -r ~/Desktop/MGS\ ref/G.Vaginalis/g.vaginalis.fna -P /Volumes/G-DRIVE\ USB-C/Binned_reads/DN00207A_10/DN00297A_host_removed_r1.fastq,/Volumes/G-DRIVE\ USB-C/Binned_reads/DN00207A_10/DN00297A_host_removed_r2.fastq -o example1_output -m 1 -t 4 confirming file containing reference genomes exists.. usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory [OK] checking for dependencies (Bowtie2, Blast, kmermask, Snakemake, etc) Bowtie2--->[OK] /Users/bhanuprakashchowdarysakhamuri/miniconda2/bin//blastn Blast+--->[OK] /Users/bhanuprakashchowdarysakhamuri/MetaCompass/bin//kmer-mask kmer-mask--->[OK] /usr/local/bin/snakemake Snakemake--->[OK] Traceback (most recent call last): File "/usr/local/bin/snakemake", line 6, in from pkg_resources import load_entry_point File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 3095, in @_call_aside File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 3079, in _call_aside f(*args, **kwargs) File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 3108, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 570, in _build_master ws.require(requires) File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 888, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 774, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'datrie' distribution was not found and is required by snakemake ERROR: snakemake command failed; exiting.. touch: example1_output/DN00297A_host_removed_r1.0.assembly.out/run.fail: No such file or directory

[vcepeda]

Before this, were you able to run the examples on the Readme successfully?

[bhanusakhamuri]

No, I directly started running them on my sample data.

[vcepeda]

Can you run the examples to see if any error pops up? I have never encountered the error you mentioned before but it could be a dependency issue.

[bhanusakhamuri]

I did upgrade by miniconda and tried the example dataset. Works perfectly fine. When I tried with my dataset the snakemake gets exiting returining

"Config entries have to be defined as name=value pairs."