Closed fcamara7 closed 11 months ago
Hi @fcamara7 I just came back. I will look into this ;)
Hi @fcamara7 please check the updated script, let me know if it's working
Thanks @diegomics !! It seems to work just fine now! I will show it to Tyler tomorrow and I will get back to you if there are any further issues but I think it is fine now. Thanks for acting on this so quickly! :)
Hi Diego,
Over here at the CNAG, as you know, we currently assemble genomes using ONT technology and I have had a bit of trouble getting your report to work for us. One issue we have is that since we have a "collapsed" assembly merqury only produces three st.png files and your python script is expecting four.
Thanks for helping us with this when you have time!
Our yaml is below.
This is the yaml file for generating the ERGA Assembly Report (EAR) using the make_EAR.py script
Please complete the required information pointed as <Insert ...>
The file [example]rCarCar2_EAR.yaml contains an example of a completed yaml file
GENERAL INFORMATION
ToLID: fValHis Species: Valencia hispanica Sex: unknown # for example: XX, XY, ZZ, ZW, unknown, NA... Submitter: Francisco Camara Ferreira Affiliation: CNAG Barcelona Tags: ERGA-BGE # valid tags are ERGA-Pilot, ERGA-BGE, ERGA-Satellite
SEQUENCING DATA
DATA:
GENOME PROFILING DATA
PROFILING: GenomeScope: version: 2.0 results_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/s02.2_p01.1_preprocess_illumina_reads/genomescope2_k21
ASSEMBLY PIPELINE
CONTIGGING: nextdenovo: version: 2.5.0 collapsed: gfastats--nstar-report_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/s03.2_p02.1_nextdenovo/nextdenovo.assembly.gfastats.txt busco_short_summary_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s03.2_p02.1_nextdenovo/busco/nextdenovo.assembly.short_summary.txt merqury_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s03.2_p02.1_nextdenovo/merqury/nextdenovo.assembly
hypo: version: 1.0.3 collapsed: gfastats--nstar-report_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/s04.2_p03.2_polishing/hypo/nextdenovo.assembly.hypo1.gfastats.txt busco_short_summary_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s04.2_p03.2_polishing/busco/nextdenovo.assembly.hypo1.short_summary.txt merqury_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s04.2_p03.2_polishing/merqury/nextdenovo.assembly.hypo1
purge_dups: version: 1.2.6 collapsed: gfastats--nstar-report_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/s05.1_p04.1_run_purgedups/flye.assembly.hypo1.purged.gfastats.txt busco_short_summary_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s05.3_p04.2_run_purgedups/busco/nextdenovo.assembly.hypo1.purged.short_summary.txt merqury_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s05.3_p04.2_run_purgedups/merqury/nextdenovo.assembly.hypo1.purged_complete
SCAFFOLDING: YaHS: version: 1.2a collapsed: gfastats--nstar-report_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/curation/yahs_scaffolding/fValHis_yahs_scaffolds_final.gfastats.txt busco_short_summary_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/yahs_scaffolding/busco/fValHis_yahs_scaffolds_final.short_summary.txt merqury_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/yahs_scaffolding/merqury/fValHis_yahs_scaffolds_final pretext_FullMap_png: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/curation/hic_remap/out_fValHis_yahs_scaffolds_final/snapshots/three_wave_blue_green_yellow/assembly_mq40.fValHis_yahs_scaffolds_final_FullMap.png