Chloe
Mars 11, 2021, 11:07
1
Bonjour
Pourriez vous installer l'assembleur pour long reads non corrigés Raven ?
Merci beaucoup par avance !
Bonjour,
Installation en cours du package conda:
Chloe
Mars 11, 2021, 2:31
3
merci beaucoup @Francois !!
Chloé
1 « J'aime »
Chloe
Mars 11, 2021, 3:26
4
@Francois ,
je viens de tester une ligne de commande de base, la suivante
[raven::Graph::Load] error: unable to load archive
merci pour votre retour
Chloé
Il semblerait que --resume soit fait pour reprendre un run déjà commencé
--resume
resume previous run from last checkpoint
Du coup vous aviez lancer une première fois la commande ? avec la même version de raven ?
Je trouve une seul référence à ce message d'erreur dans les issues du projet:
opened 01:23PM - 14 Dec 20 UTC
closed 12:44PM - 15 Feb 21 UTC
Hi Robert,
I've been running into some issues with assemblies not completing. I… t may be an issue with not giving the job enough time, but based on expectations and the logging, I'm not sure if it is an issue with the data or some loop.
I'm assembly a 2.8gb mammal genome with about 60x coverage. I've included the logging output below. Everything proceeds pretty quickly, until it gets "stuck" between minimising and mapping invalid reads. There is no further output after the first iteration of this loop until the job time expires.
```
[raven::Graph::Construct] mapped sequences 978.772839s
[raven::Graph::Construct] minimized 3141332 - 3275448 / 5662746 16.137639s
[raven::Graph::Construct] mapped sequences 1060.586259s
[raven::Graph::Construct] minimized 3275448 - 3407851 / 5662746 16.112244s
...
[raven::Graph::Construct] mapped sequences 1794.347470s
[raven::Graph::Construct] minimized 5549681 - 5662746 / 5662746 12.567266s
[raven::Graph::Construct] mapped sequences 1453.411794s
[raven::Graph::Construct] annotated piles 56.984509s
[raven::Graph::Construct] removed contained sequences 40.598622s
[raven::Graph::Construct] removed chimeric sequences 136.707741s
[raven::Graph::Construct] reached checkpoint 89.431498s
[raven::Graph::Construct] cleared piles 1.909425s
[raven::Graph::Construct] minimized 0 - 48009 / 193871 19.858725s
```
After calling with `--resume`, the cereal file is reloaded, and then it appears to get stuck again on the first iteration of mapping invalid reads.
```
[raven::] loaded previous run 73.293433s
[raven::] loaded 5662746 sequences 2374.362824s
[raven::Graph::Construct] cleared piles 21.914438s
[raven::Graph::Construct] minimized 0 - 48009 / 193871 27.706757s
```
Both of these jobs expired after about 650 cpu hours each, compared to the 500 hours suggested for human scale at 44x.
I also tried with a separate dataset with about 30x coverage, but it was the same story of never getting beyond the first iteration of mapping invalid reads.
This was based on building from tip, but a conda-based install seems to be having the same issue (stuck on the same spot after 400+ cpu hours).
Do you have any suggestions?
Thanks,
Alex
Et visiblement (si je comprend bien) c’était parce qu’il avait lancé une première fois avec une première version de raven et une deuxième fois avec une autre version.
Chloe
Mars 11, 2021, 4:53
6
merci merci beaucoup @Francois
Encore merci pour votre réponse
Chloé
