TEdenovo blasting with Recon perpetuates..!

Question

[mthm]

I have already ran one whole cycle of TEdevono (S1-S8) on one of my samples successfully, when starting to run the second sample, the -S 3 -s Blaster -c Recon gets stuck at this step, without returning an error or any output file, last time I let it be for almost 3 days but it was still at the

beginning of step 3
self-alignment with Blaster
clustering with Recon

stage without any single output in the directory! when I checked the CPU usage, it was 0.7% of 80 cpus! so it is not running anything! just stuck there.. Does anyone have an idea of why that happens and how to fix this?

Answer 1

[mthm]

the reason for that is that if you already have a failed launch once, there are going to be the batch files remained in the mysql database which prevents the Recon or any other blasting tools (piler, grouper..) from running again, so we have to first remove the failed batch scripts from the database:

mysql> select * from jobs; 
mysql> delete from jobs;