questions

[zhaoxvwahaha]

Hi,

Thank you for your wonderful Lathe, I am very new to snakemake, so apologies this might be a very basic stupid question.
I would like to start Lathe from assembly rather than basecalling.
So I create a folder and copy my long-reads.fq file to here : /MyWorkingPath/sample/0.basecall/sample.fq, then run the following command and encounter the error:
/PathToSnakemake/bin/snakemake --use-singularity --singularity-args '--bind /MyWorkingPath/sample/,/scg/,/home/ ' -s /MySoftwarePath/software/lathe/Snakefile --configfile /MySoftwarePath/software/lathe/config.yaml.altered --restart-times 0 --keep-going --latency-wait 30 --cores 16
Building DAG of jobs...
WildcardError in line 242 of /ldfssz1/ST_INFECTION/P18Z10200N0164_Resistance_PN/User/zhaohailong/software/lathe/Snakefile:
Wildcards in input files cannot be determined from output files:
'contig_cutoff'

How could I resolve this problem.
BTW, I used other people's snakemake path, because I failed to install it by myself through conda because of web connection, I'm not sure, if this has an impact.