Commit 0ddd21bd authored by Joanna Fourquet's avatar Joanna Fourquet
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Update use_case.md

parent f31b9765
......@@ -578,7 +578,7 @@ The `raw` directory contains others files which are not main files. For more inf
### A. Explanations
With the next script, we want to run metagWGS on test dataset in order to have **`06_func_annot` step** results. This new script is the same script than `Script_filtering_binning.sh` where we have changed `08_binning` by `06_func_annot` into the `--step` parameter and where we have added the parameter `--eggnogmapper_db` to build eggNOG-mapper database for functional annotation. All previous choices have beed conserved: we don't know the real host genome for this dataset but we want to test host filtering: we decided to use **sus scrofa** as host genome. We also want to **filter contigs** after assembly with the default cpm value (10). It is this assembly that will be used in the following steps requiring the assembly files. Assembly tool used in this script is `metaspades`.
With the next script, we want to run metagWGS on test dataset in order to have **`06_func_annot` step** results. This new script is the same script than `Script_filtering_binning.sh` where we have changed `--step "03_filtering,08_binning"` by `--step "03_filtering,08_binning,06_func_annot"` into the `--step` parameter and where we have added the parameter `--eggnogmapper_db` to build eggNOG-mapper database for functional annotation. All previous choices have beed conserved: we don't know the real host genome for this dataset but we want to test host filtering: we decided to use **sus scrofa** as host genome. We also want to **filter contigs** after assembly with the default cpm value (10). It is this assembly that will be used in the following steps requiring the assembly files. Assembly tool used in this script is `metaspades`.
### B. Write the script `Script_filtering_functional.sh`
......@@ -596,7 +596,7 @@ module purge
module load bioinfo/Nextflow-v20.01.0
module load system/singularity-3.5.3
nextflow run -profile big_test_genotoul metagwgs/main.nf --reads "test_data/*_{1,2}.fastq.gz" --step "03_filtering,06_func_annot" --host_bwa_index "/work/bank/ebi/ensembl/sus_scrofa_genome/ensembl_sus_scrofa_genome_2020-07-20/bwa/ensembl_sus_scrofa_genome.{amb,ann,bwt,pac,sa}" --host_fasta "/work/bank/ebi/ensembl/sus_scrofa_genome/ensembl_sus_scrofa_genome_2020-07-20/bwa/ensembl_sus_scrofa_genome" --kaiju_db_dir "/bank/kaijudb/kaijudb_refseq_2020-05-25" --assembly metaspades --diamond_bank "/work/bank/diamonddb/nr.dmnd" --cat_db "CAT_prepare_20190108.tar.gz" --eggnogmapper_db -with-report -with-timeline -with-trace -with-dag -resume
nextflow run -profile big_test_genotoul metagwgs/main.nf --reads "test_data/*_{1,2}.fastq.gz" --step "03_filtering,08_binning,06_func_annot" --host_bwa_index "/work/bank/ebi/ensembl/sus_scrofa_genome/ensembl_sus_scrofa_genome_2020-07-20/bwa/ensembl_sus_scrofa_genome.{amb,ann,bwt,pac,sa}" --host_fasta "/work/bank/ebi/ensembl/sus_scrofa_genome/ensembl_sus_scrofa_genome_2020-07-20/bwa/ensembl_sus_scrofa_genome" --kaiju_db_dir "/bank/kaijudb/kaijudb_refseq_2020-05-25" --assembly metaspades --diamond_bank "/work/bank/diamonddb/nr.dmnd" --cat_db "CAT_prepare_20190108.tar.gz" --eggnogmapper_db -with-report -with-timeline -with-trace -with-dag -resume
```
If you want to understand each metagWGS parameter and Nextflow option used in this script, see [usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md) documentation page.
......@@ -642,17 +642,17 @@ executor > slurm (2)
[- ] process > download_taxonomy_db -
[- ] process > genome_length -
[- ] process > diamond_parser -
[- ] process > quantif_and_taxonomic_table... -
[- ] process > metabat -
[- ] process > busco_download_db -
[- ] process > busco -
[- ] process > busco_plot -
[- ] process > quast_bins -
[- ] process > merge_quast_and_busco -
[- ] process > cat_db -
[- ] process > cat -
[- ] process > quantif_and_taxonomic_table... - -
[d6/26aeb6] process > metabat [100%] 3 of 3, cached: 3 ✔
[fa/d48e80] process > busco_download_db [100%] 1 of 1, cached: 1 ✔
[30/617208] process > busco [100%] 60 of 60, cached: 60 ✔
[db/f91457] process > busco_plot [100%] 1 of 1, cached: 1 ✔
[9e/0fc4c3] process > quast_bins [100%] 3 of 3, cached: 3 ✔
[71/5e95c1] process > merge_quast_and_busco [100%] 1 of 1, cached: 1 ✔
[d6/4314ca] process > cat_db [100%] 1 of 1, cached: 1 ✔
[9c/3cf218] process > cat [100%] 3 of 3, cached: 3 ✔
[a8/7c8a44] process > get_software_versions [100%] 1 of 1, cached: 1 ✔
[3f/4ebe6e] process > multiqc [100%] 1 of 1, cached: 1 ✔
[3f/4ebe6e] process > multiqc [100%] 1 of 1 ✔
Completed at: 16-févr.-2021 21:04:06
Duration : (see below)
CPU hours : (see below)
......@@ -931,7 +931,7 @@ PFAMs ERR3201914.featureCounts.tsv ERR3201918.featureCounts.tsv ERR3201928.featu
### A. Explanations
With this last script, we want to run metagWGS on test dataset in order to have **`07_taxo_affi` step** results. This new script is the same script than `Script_filtering_functional.sh` (and so close to `Script_filtering_binning.sh)` where we have changed `06_func_annot` by `07_taxo_affi` into the `--step` parameter. All previous choices have beed conserved: we don't know the real host genome for this dataset but we want to test host filtering: we decided to use **sus scrofa** as host genome. We also want to **filter contigs** after assembly with the default cpm value (10). It is this assembly that will be used in the following steps requiring the assembly files. Assembly tool used in this script is `metaspades`. We have left the parameter `--eggnogmapper_db` but it is not really necessary here since it is not linked to the stage we wish to launch.
With this last script, we want to run metagWGS on test dataset in order to have **`07_taxo_affi` step** results. This new script is the same script than `Script_filtering_functional.sh` (and so close to `Script_filtering_binning.sh)` where we have added `07_taxo_affi` into the `--step` parameter: `--step "03_filtering,08_binning,06_func_annot,07_taxo_affi"`. All previous choices have beed conserved: we don't know the real host genome for this dataset but we want to test host filtering: we decided to use **sus scrofa** as host genome. We also want to **filter contigs** after assembly with the default cpm value (10). It is this assembly that will be used in the following steps requiring the assembly files. Assembly tool used in this script is `metaspades`.
### B. Write the script `Script_filtering_taxo.sh`
......@@ -949,7 +949,7 @@ module purge
module load bioinfo/Nextflow-v20.01.0
module load system/singularity-3.5.3
nextflow run -profile big_test_genotoul metagwgs/main.nf --reads "test_data/*_{1,2}.fastq.gz" --step "03_filtering,07_taxo_affi" --host_bwa_index "/work/bank/ebi/ensembl/sus_scrofa_genome/ensembl_sus_scrofa_genome_2020-07-20/bwa/ensembl_sus_scrofa_genome.{amb,ann,bwt,pac,sa}" --host_fasta "/work/bank/ebi/ensembl/sus_scrofa_genome/ensembl_sus_scrofa_genome_2020-07-20/bwa/ensembl_sus_scrofa_genome" --kaiju_db_dir "/bank/kaijudb/kaijudb_refseq_2020-05-25" --assembly metaspades --diamond_bank "/work/bank/diamonddb/nr.dmnd" --cat_db "CAT_prepare_20190108.tar.gz" --eggnogmapper_db -with-report -with-timeline -with-trace -with-dag -resume
nextflow run -profile big_test_genotoul metagwgs/main.nf --reads "test_data/*_{1,2}.fastq.gz" --step "03_filtering,08_binning,06_func_annot,07_taxo_affi" --host_bwa_index "/work/bank/ebi/ensembl/sus_scrofa_genome/ensembl_sus_scrofa_genome_2020-07-20/bwa/ensembl_sus_scrofa_genome.{amb,ann,bwt,pac,sa}" --host_fasta "/work/bank/ebi/ensembl/sus_scrofa_genome/ensembl_sus_scrofa_genome_2020-07-20/bwa/ensembl_sus_scrofa_genome" --kaiju_db_dir "/bank/kaijudb/kaijudb_refseq_2020-05-25" --assembly metaspades --diamond_bank "/work/bank/diamonddb/nr.dmnd" --cat_db "CAT_prepare_20190108.tar.gz" --eggnogmapper_db -with-report -with-timeline -with-trace -with-dag -resume
```
If you want to understand each metagWGS parameter and Nextflow option used in this script, see [usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md) documentation page.
......@@ -983,27 +983,27 @@ executor > slurm (9)
[fd/3bbb88] process > reads_alignment_on_contigs [100%] 3 of 3, cached: 3 ✔
[87/8562a3] process > diamond [100%] 3 of 3, cached: 3 ✔
[91/3a9bea] process > diamond_header [100%] 1 of 1, cached: 1 ✔
[- ] process > individual_cd_hit -
[- ] process > global_cd_hit -
[- ] process > quantification -
[- ] process > quantification_table -
[- ] process > eggnog_mapper_db -
[- ] process > eggnog_mapper -
[- ] process > best_hits_diamond -
[- ] process > merge_quantif_and_functiona... -
[- ] process > make_functional_annotation_... -
[96/bdcb3a] process > individual_cd_hit [100%] 3 of 3, cached: 3 ✔
[a5/6b6fea] process > global_cd_hit [100%] 1 of 1, cached: 1 ✔
[57/8f1078] process > quantification [100%] 3 of 3, cached: 3 ✔
[fe/d01e78] process > quantification_table [100%] 1 of 1, cached: 1 ✔
[7c/0f9637] process > eggnog_mapper_db [100%] 1 of 1, cached: 1 ✔
[aa/fbb17b] process > eggnog_mapper [100%] 3 of 3, cached: 3 ✔
[e7/8f3dd1] process > best_hits_diamond [100%] 3 of 3, cached: 3 ✔
[a2/80f1d4] process > merge_quantif_and_functiona... [100%] 1 of 1, cached: 1 ✔
[ea/4b93b2] process > make_functional_annotation_... [100%] 1 of 1, cached: 1 ✔
[61/e8c0f3] process > download_taxonomy_db [100%] 1 of 1 ✔
[56/3ff48d] process > genome_length [100%] 3 of 3 ✔
[ea/e69c9e] process > diamond_parser [100%] 3 of 3 ✔
[ee/9eefb2] process > quantif_and_taxonomic_table... [100%] 1 of 1 ✔
[- ] process > metabat -
[- ] process > busco_download_db -
[- ] process > busco -
[- ] process > busco_plot -
[- ] process > quast_bins -
[- ] process > merge_quast_and_busco -
[- ] process > cat_db -
[- ] process > cat -
[d6/26aeb6] process > metabat [100%] 3 of 3, cached: 3 ✔
[fa/d48e80] process > busco_download_db [100%] 1 of 1, cached: 1 ✔
[30/617208] process > busco [100%] 60 of 60, cached: 60 ✔
[db/f91457] process > busco_plot [100%] 1 of 1, cached: 1 ✔
[9e/0fc4c3] process > quast_bins [100%] 3 of 3, cached: 3 ✔
[71/5e95c1] process > merge_quast_and_busco [100%] 1 of 1, cached: 1 ✔
[d6/4314ca] process > cat_db [100%] 1 of 1, cached: 1 ✔
[9c/3cf218] process > cat [100%] 3 of 3, cached: 3 ✔
[a8/7c8a44] process > get_software_versions [100%] 1 of 1, cached: 1 ✔
[38/01c0a5] process > multiqc [100%] 1 of 1 ✔
Completed at: 21-févr.-2021 19:32:59
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