Closed levinas closed 9 years ago
This bug affects single end libraries too.
This is probably due to bayers hammer not working for fasta files which have no quality scores. As a result, nothing gets to run. We should modify the bhammer plugin to handle fasta files gracefully.
Two options:
processed_reads
if error correction fails. @cbun do we already have a FASTA detector in the plugin?
Are you sure Spades runs this correctly?
BayesHammer will run, which also uses spades.py
but theoretically all the assemblers should fail.
Yes, all assemblers failed. This fixes it.
This bug can be reproduced against the dev server.
On the server, SPAdes launched the assembly correctly: Command: spades.py --pe2-1 forward.fa --pe2-2 reverse.fa -t 4 ...
But velvet missed all the read files and tried to run:
However, if I launch with the
-a velvet
option explicitly, the job runs. Is there an issue with the wasp interpretation?