can not restart from last
catslu opened this issue · 4 comments
Description of bug
Hi dear, I am using spades.py --meta to process 10 metagenome data. I used -m 490 that our computer may no memory so the system got stuck. I ctrl + c to stop it. And I used a lower memory limit with -m 455, it showed that:
$user spades.py -o ./metaspades_out/ -m 455 --continue --restart-from last
== Error == you cannot specify reads with --restart-from option!
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
how I can do next step?
spades.log
params.txt
SPAdes version
SPAdes genome assembler v3.15.4
Operating System
Linux Red Hat 4.8.5-44
Python Version
3.10.14
Method of SPAdes installation
conda
No errors reported in spades.log
- Yes
Hello
You'd need to use either --restart-from or --continue, not both
Hello
You'd need to use either
--restart-fromor--continue, not both
(mpa) [liuxl@gnode5 con_lt_co-assemble]$ spades.py -o ./metaspades_out/ -m 455 --restart-from last
== Error == you cannot specify reads with --restart-from option!
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
(mpa) [liuxl@gnode5 con_lt_co-assemble]$ spades.py -o ./metaspades_out/ --continue
== Error == you cannot specify any option except -o with --continue option! Please use '--restart-from last' if you need to change some of the options from the initial run and continue from the last available checkpoint.
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
I cannot reproduce this issue, it seems there is something extra on command line, but we do not see it here. The next version of SPAdes will print these extra arguments, so it will be easier to debug. Please reopen if the issue sill be there.