Setting dentist parameters #22
Comments
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Hi, yes, {
"__default__": {
"max-insertion-error": 0.15,
"min-anchor-length": 1500,
"min-reads-per-pile-up": 1,
"min-spanning-reads": 1,
"allow-single-reads": true,
"join-policy": "contigs"
}
}It seems like you want to create a more greedy configuration. Please be aware that you should not further reduce {
"// WARNING": [
"Use with care!",
"Always validate the closed gaps (e.g. manual inspection)."
],
"// NOTE": [
"The workflow creates an intermediate assembly",
"`workdir/{output_assembly}-preliminary.fasta` that contains all",
"closed gaps, i.e. before validation. It is accompanied by an AGP",
"and BED file. You may inspect these file for maximum sensitivity."
],
"__default__": {
"verbose": 2,
"agp": "true",
"allow-single-reads": true,
"best-pile-up-margin": 1.5,
"existing-gap-bonus": 3.0,
"join-policy": "contigs",
"min-reads-per-pile-up": 1,
"min-spanning-reads": 1,
"proper-alignment-allowance": 500
},
"// Uncomment the following block if": [
"the default value for min-coverage-reads",
"(0.5 * --read-coverage/--ploidy) is suboptimal. It is important to",
"revert --read-coverage and --ploidy because they are mutually exclusive",
"with --min-coverage-reads."
]
} |
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@Adamtaranto Did this help? BTW you should consider updating DENTIST to v2.0.0. 😉 |
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hello @a-ludi, I am trying to run DENTIST with the greedy mode using the example files. I used the This is the snakemake config: I then run it under the local mode but encounter the following errors: Can you give me some help? Thank you very much! Best, |
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Hi Shujun, just add a line with the proper read coverage below See https://github.com/a-ludi/dentist#how-to-choose-dentist-parameters for more details. Cheers, Arne |
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Dear Arne @a-ludi, Thank you for your suggestion. I added
I then added
Do you have any ideas to move forward? Thank you, |
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Hi Shujun, I forgot you need to add Cheers, Arne |
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HI Arne, Thanks for your instant response. I removed Best, |
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Please try starting over from the beginning by removing all outputs with |
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I removed the |
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Oh, yes. You have got dots in your filenames which confuse some tools in the workflow. Please replace all dots (except the suffix |
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Thank you for this trick! Yes, it's running now. |
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Hi Arne, Thank you for your guidance. I have finished DENTIST on the contig mode (patching scaffolds with assembled contigs), but no gaps were filled. Are there any log files I can check if DENTIST is running correctly? Or are there any parameters I can change to make it work better? Thanks! Best, |
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Hi @a-ludi, Thank you for the instructions. Here are the log files you mentioned. The following are the configurations used:
Command used to run DENTIST: Please kindly let me know if you spot anything incorrectly specified or parameters I can used to improve. Thank you! Best, |
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Hi Shujun, I generated a report using the new Python script (see below). The main issue is "consensus alignment is invalid". That is not conclusive on its own but hints that there might be a bug in DENTIST. Could you please add the following lines (replace the path with something reasonable) to your process:
tmpdir: /path/to/persistent/temp/directory
keep-temp: TrueThen I am interested in the contents of that In this run of DENTIST 108 potentially closable gaps were not closed. More details: Hint: use
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Hi Arne, Thank you very much for checking my results and providing suggestions to debug. I am not very familar with snakemake, and I want to make sure I am doing it correctly. I rerun DENTIST and encounter the following error:
Then I removed the DENTIST can be run with this yml file, the run is on going (84/457 steps), but the Thanks, |
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Hi Shujun, that first error was my mistake, sorry. The command names in the config file cannot be abbreviated so it requires It is expected that the temp directory remains empty for quite a while because the first steps in the workflow do not involve the You can just send me the directories |
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HI Arne, Thanks for the extra information. I added the I finished rerunning DENTIST without errors, however, the /temp/ directory is empty. Could it be due to rerunning DENTIST in the same folder as previous runs? I then remove the hidden
Did I set something wrong? Thanks! Shujun |
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Hi Shujun, did Snakemake execute the process rules? Check with Theoretically, you should be able to just issue the same command as before and it should recompute mostly everything because many rules depend on the DENTIST config file. Cheers! |
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Hi Arne, I think snakemake execute the process rules: But the specified /temp/ directory is still empty. I have specified new directories for results and log files, and remove previous Best, |
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Probably, the actual DENTIST config file was not updated properly. If feasible, please delete |
When setting the parameters below, do these need to be included in the dentist.json config file? and if so in which section?
--max-insertion-error
--min-anchor-length
--min-reads-per-pile-up
--min-spanning-reads
--allow-single-reads
--join-policy
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