error in line 109 Grid_options

Question

error in line 109 Grid_options

saras224 opened this issue 3 years ago · comments

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

Ben Siranosian · Answer 1 · Fri Jul 30 2021 01:11:34 GMT+0800 (China Standard Time)

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 · Answer 2 · Fri Jul 30 2021 14:19:42 GMT+0800 (China Standard Time)

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

Ben Siranosian · Answer 3 · Fri Jul 30 2021 20:51:45 GMT+0800 (China Standard Time)

Can you post your config file and file_names_txt?

saras224 · Answer 4 · Fri Jul 30 2021 20:56:56 GMT+0800 (China Standard Time)

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

saras224 · Answer 5 · Fri Jul 30 2021 21:03:39 GMT+0800 (China Standard Time)

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 · Answer 6 · Wed Aug 04 2021 14:30:05 GMT+0800 (China Standard Time)

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 · Answer 7 · Fri Aug 06 2021 14:08:13 GMT+0800 (China Standard Time)

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

Saraswati

Dylan Maghini · Answer 8 · Wed Aug 11 2021 07:01:39 GMT+0800 (China Standard Time)

Hi Saraswati,

To answer your questions:

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.
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.
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 · Answer 9 · Wed Aug 11 2021 14:49:48 GMT+0800 (China Standard Time)

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