Comments (8)
Hi,
there is no keyword for running medaka multiple times, so you can only do +medaka
.
From what I gathered, people usually run medaka only once.
You could actually try +medaka+medaka
, for running it twice, that might work.
from ont-assembly-snake.
Hi Peter,
thanks for the quick reply.
Still getting the error:
(ont-assembly-snake) [ngs@vngs20x /nexus/Analysis/microbiology/denovoAssemblies_ONT/ont-assembly-snake]$ snakemake -np -s /home/ngs/installed/snakemake/ont-assembly-snake/Snakefile --use-conda --cores 20
filtlong min. read length = 1000
Building DAG of jobs...
MissingInputException in line 64 of /home/ngs/installed/snakemake/ont-assembly-snake/Snakefile:
Missing input files for rule all:
assemblies/.snakemake.fa
assemblies/.snakemake/output.fa
with the following folder structure (removed the '2' after medaka
- which yes, according to my own pipeline, it does not change much the quality of the assembly):
.
├── assemblies
│ ├── BORD1705_flyehq+racon2+medaka
│ └── LEG829_flyehq+racon2+medaka
└── fastq-ont
├── BORD1705.fastq
└── LEG829.fastq
from ont-assembly-snake.
Missing input files for rule all:
assemblies/.snakemake.fa
assemblies/.snakemake/output.fa
You probably accidently run snakemake inside the assemblies/
folder, which created the folder .snakemake
in there.
Just remove that.
with the following folder structure (removed the '2' after medaka - which yes, according to my own pipeline, it does not change much the quality of the assembly):
I am curious how do you check the quality of your assemblies? Using any of the tools in https://github.com/pmenzel/score-assemblies or some others?
from ont-assembly-snake.
I happened to initially have called the snakemake from another directory, in which case, it does not crash, but is shows only the rules for no input at all.
In my command above you can see that I called snakemake from /nexus/Analysis/microbiology/denovoAssemblies_ONT/ont-assembly-snake
and if I do a tree
on that directory I get:
[ngs@vngs20x ~/installed/snakemake/ont-assembly-snake]$ tree /nexus/Analysis/microbiology/denovoAssemblies_ONT/ont-assembly-snake
/nexus/Analysis/microbiology/denovoAssemblies_ONT/ont-assembly-snake
├── assemblies
│ ├── BORD1705_flyehq+racon2+medaka
│ └── LEG829_flyehq+racon2+medaka
└── fastq-ont
├── BORD1705.fastq
└── LEG829.fastq
4 directories, 2 files
As for the quality of the assemblies I use QUAST, great tool
from ont-assembly-snake.
try tree -a
from ont-assembly-snake.
[ngs@vngs20x ~]$ tree -a /nexus/Analysis/microbiology/denovoAssemblies_ONT/ont-assembly-snake/
/nexus/Analysis/microbiology/denovoAssemblies_ONT/ont-assembly-snake/
├── assemblies
│ ├── BORD1705_flyehq+racon2+medaka
│ ├── LEG829_flyehq+racon2+medaka
│ └── .snakemake
│ ├── auxiliary
│ ├── conda
│ ├── conda-archive
│ ├── incomplete
│ ├── locks
│ ├── log
│ ├── metadata
│ ├── shadow
│ └── singularity
├── fastq-ont
│ ├── BORD1705.fastq
│ └── LEG829.fastq
└── .snakemake
├── auxiliary
├── conda
├── conda-archive
├── incomplete
├── locks
├── log
│ ├── 2022-06-14T142849.649163.snakemake.log
│ ├── 2022-06-14T143237.621696.snakemake.log
│ ├── 2022-06-14T143518.824018.snakemake.log
│ ├── 2022-06-14T143732.727613.snakemake.log
│ ├── 2022-06-15T102716.725747.snakemake.log
│ ├── 2022-06-15T102838.335849.snakemake.log
│ └── 2022-06-15T104224.438601.snakemake.log
├── metadata
├── shadow
└── singularity
from ont-assembly-snake.
See, the folder assemblies/.snakemake
is the one causing the trouble.
from ont-assembly-snake.
Yes, I think that folder was created by snakemake when I called it from the assemblies
directory.
Anyway, the hidden folder was empty and the pipeline starts after I removed it
Thanks for the support
from ont-assembly-snake.
Related Issues (16)
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