Error: wrong header

[Chandrima-04]

Hi,

I have installed metapi using micromamba. Now am trying to run the code, but getting this error:

`'/pbtech_mounts/homes051/chb4004/micromamba/envs/metapi/lib/python3.11/site-packages/metapi'
wrong header: Index(['short_forward_reads', 'short_reverse_reads'], dtype='object')
Running metapi mag_wf:
snakemake --snakefile /pbtech_mounts/homes051/chb4004/micromamba/envs/metapi/lib/python3.11/site-packages/metapi/snakefiles/mag_wf.smk --configfile ./config.yaml --cores 240 --until all --rerun-incomplete --keep-going --printshellcmds --reason --use-conda --conda-prefix ~/.conda/envs --profile ./profiles/slurm --local-cores 8 --jobs 30

Real running cmd:
snakemake --snakefile /pbtech_mounts/homes051/chb4004/micromamba/envs/metapi/lib/python3.11/site-packages/metapi/snakefiles/mag_wf.smk --configfile ./config.yaml --cores 240 --until all --rerun-incomplete --keep-going --printshellcmds --reason --use-conda --conda-prefix ~/.conda/envs --profile ./profiles/slurm --local-cores 8 --jobs 30
`

I had initialized my folder using
metapi init -d . -s metapi.tsv

This is my slurm script:
`#!/bin/sh

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --time=168:00:00
#SBATCH --mem=25GB
#SBATCH --job-name=metapi
#SBATCH --error metapi--%j.err

micromamba shell hook -s bash
eval "$(~/bin/micromamba shell hook -s bash)"
micromamba activate metapi

metapi mag_wf all --use-conda --run-remote`

This is my sample file. The header seems to be correct based on documentation. Can you let me know what is going wrong?
Is there an example code/more documentation available?

metapi - Sheet1.csv

[alienzj]

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.

[Chandrima-04]

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

[alienzj]

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

[Chandrima-04]

Thanks, can you also share the link of the other dbs? I saw in config.yaml, there are multiple files needed.

[alienzj]

Hi, I updated README.md.
Pleaser refer to README here for downloading databases and scripts used in metapi: