error in line 109 Grid_options

[saras224]

Hi @bsiranosian
I am trying run your tool but it is giving some error:
snakemake -s /home/rsharma/lathe/Snakefile --configfile /home/rsharma/lathe/config.yaml --cores 5
KeyError in line 109 of /home/rsharma/lathe/Snakefile:
'grid_options'
File "/home/rsharma/lathe/Snakefile", line 109, in
How do I resolve the error?

Thanks in Advance
Saraswati

[bsiranosian]

Hi, this looks like it might be an error in the config file, where usegrid is set True when you need it to be false.

Look at rule assemble_canu: in the Snakefile for the different ways canu can be executed.

[saras224]

Thanks @bsiranosian for the quick response!
I corrected the error line in config.yaml, but now it shows a new error saying that :
Building DAG of jobs...
WildcardError in line 242 of /home/rsharma/lathe/Snakefile:
Wildcards in input files cannot be determined from output files:
'contig_cutoff'

Thanks
Saraswati

[bsiranosian]

Can you post your config file and file_names_txt?

[saras224]

config.yaml:
config.txt
file_names.txt:
file_names.txt

[saras224]

Hi @bsiranosian
I have posted the files.
I want to know what should be the genome_size. I have environmental metagenome sample. I have used 50m,100m, What does "m" mean here? Is it mbasepairs?

[saras224]

Hey Ben! I posted the files(config.yaml and file_names.txt), please have a look on GitHub and help me resolve the error so that I can proceed with the assembly. Thanks Saraswati

…

On Fri, 30 Jul 2021 at 18:21, Ben Siranosian ***@***.***> wrote: Can you post your config file and file_names_txt? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASPIOTJTJZOK3Y6VSDPX6M3T2KN63ANCNFSM5BGD3COA> .

[saras224]

just a reminder still waiting for your response :) @bsiranosian

Saraswati

[dgmaghini]

Hi Saraswati,

To answer your questions:

1. The "m" in genome size is in megabase pairs. The default parameters in the config file are for a standard human gut - you can adjust these values up or down depending on whether you expect your sample to be more or less diverse.
2. Please pull the repo; I just made some changes that should hopefully solve that particular error. In general, it's fine to use a contig cutoff size of 0 to avoid filtering out any contigs.
3. In your file_names.txt file, please delete your header line or add a comment character (#) at the start- otherwise, the Snakefile will think that the header line corresponds to a sample.

[saras224]

Hi @dgmaghini
Thanks for your response.
I tried running with 0 contig size and it started to process but is not doing assembly and showing strange lines on the terminal that I am not able to figure out. Please help me understand where it demands the changes in the config file. I have given sample name as W1, on the terminal it shows :
find: 'W1/0.basecall/raw_calls//.fastq': No such file or directory
Does it want me to put the nanopore reads in this directory?
But I observed that it makes a W1 directory in my home directory and puts the results in that.
I am pasting the whole terminal output here so that you can see where it is wrong.
terminalout.txt

Thanks in Advance
Saraswati