Comments (5)
Hi, @Chandrima-04,
I found that the latest documentation doesn't align with metapi v2.5.0.
Now I released metapi v3.0.0, you can install latest metapi by runing:
mamba install -c bioconda -c conda-forge metapi=3.0.0
.
Then the error about headers will dispear.
By the way, if you want to run metapi on remote server,
there is no need to add metapi mag_wf all --use-conda --run-remote
to SLURM script.
You just run metapi mag_wf all --use-conda --run-remote
in login node,
then snakemake will help you to submit the jobs.
If you want to adjust any information about SLURM job, such as partition, qos,
take a look at <working_folder>/profiles/slurm/cluster.yaml
.
Please let me know if you have any questions.
from metapi.
do you have the zenodo file with all the databases and scripts you used (the ones that will be input to config.yaml)? I have been running in login node but this is the error
Building DAG of jobs... MissingInputException in rule rmhost_bowtie2_index in file /pbtech_mounts/homes051/chb4004/micromamba/envs/metapi/lib/python3.11/site-packages/metapi/snakefiles/../rules/rmhost.smk, line 205: Missing input files for rule rmhost_bowtie2_index: output: /home/jiezhu/databases/genomics/human/CHM13/chm13v2.0_plusY/chm13v2.0.fa.1.bt2, /home/jiezhu/databases/genomics/human/CHM13/chm13v2.0_plusY/chm13v2.0.fa.2.bt2, /home/jiezhu/databases/genomics/human/CHM13/chm13v2.0_plusY/chm13v2.0.fa.3.bt2, /home/jiezhu/databases/genomics/human/CHM13/chm13v2.0_plusY/chm13v2.0.fa.4.bt2, /home/jiezhu/databases/genomics/human/CHM13/chm13v2.0_plusY/chm13v2.0.fa.rev.1.bt2, /home/jiezhu/databases/genomics/human/CHM13/chm13v2.0_plusY/chm13v2.0.fa.rev.2.bt2 affected files: /home/jiezhu/databases/genomics/human/CHM13/chm13v2.0_plusY/chm13v2.0.fa
from metapi.
Hi, @Chandrima-04
Not yet, I have no plan to redistribute these databases.
To improve reproducibility, I will update code to let metapi download and build database automicatlly from the original source.
For hot fix, may I know can you download the database by yourselft?
CHM13 can be downloaded from here: https://genome-idx.s3.amazonaws.com/bt/chm13.draft_v1.0_plusY.zip
from metapi.
Thanks, can you also share the link of the other dbs? I saw in config.yaml, there are multiple files needed.
from metapi.
Hi, I updated README.md.
Pleaser refer to README here for downloading databases and scripts used in metapi:
from metapi.
Related Issues (20)
- without -1 HOT 1
- error : r1 should be r HOT 1
- support plasmidSPAdes
- support biosyntheticSPAdes
- support Bandage
- support OPERA-MS
- Long reads is comming
- metaeuk
- conterminator
- Project: Documentation
- Project: Manuscript
- bug report HOT 1
- Reduce files number
- Name 'directory' is not defined HOT 5
- [A little feedback] HOT 2
- Need to install those software before running? HOT 2
- add deduplication option HOT 3
- add save_host_reads option HOT 2
- Support PE + SE parallelly HOT 3
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from metapi.