Empty consensus.fasta

[A-J-F-Mackintosh]

Hi Mikhail,

I am trying out flye for the first time on some corrected Pacbio reads. The configure and assembly stages went fine, but then I get an error at the start of the repeat stage.

[2020-07-23 22:48:21] INFO: >>>STAGE: consensus
[2020-07-23 22:48:29] INFO: Running Minimap2
[2020-07-23 22:48:49] INFO: Computing consensus
[2020-07-23 22:48:59] INFO: Alignment error rate: 0.000000
[2020-07-23 22:48:59] INFO: >>>STAGE: repeat
[2020-07-23 22:48:59] INFO: Building and resolving repeat graph
[2020-07-23 22:49:00] INFO: Parsing disjointigs
[2020-07-23 22:49:00] ERROR: parse error in 
/scratch/amackintosh/gonepteryx_rhamni.flye.ratatosk/10-consensus/consensus.fasta on line 1: empty sequence
[2020-07-23 22:49:00] ERROR: Command '['flye-modules', 'repeat', '--disjointigs', 
'/scratch/amackintosh/gonepteryx_rhamni.flye.ratatosk/10-consensus/consensus.fasta', 
'--reads', '../0_correction/gonepteryx_rhamni.GR_164.sequel.ratatosk.fasta',
 '--out-dir', '/scratch/amackintosh/gonepteryx_rhamni.flye.ratatosk/20-repeat', '--config', 
'/ceph/users/amackintosh/.conda/envs/assembly/lib/python3.7/site-packages/flye/config/bin_cfg/asm_corrected_reads.cfg', 
'--log', '/scratch/amackintosh/gonepteryx_rhamni.flye.ratatosk/flye.log', '--threads', '64', '--min-ovlp', '5000', 
'--kmer', '17']' returned non-zero exit status 1.
[2020-07-23 22:49:00] ERROR: Pipeline aborted

It is true that the consensus.fasta is empty, and I think this is because minimap never runs properly as it seems to 'finish' after only 20 seconds and produces an alignment error rate of 0. I can't find any error message from minimap though. Here is the flye.log file which doesn't show any minimap error either:

-----------End assembly log------------
[2020-07-23 22:48:21] root: DEBUG: Disjointigs length: 622101514, N50: 1090485
[2020-07-23 22:48:21] root: INFO: >>>STAGE: consensus
[2020-07-23 22:48:29] root: INFO: Running Minimap2
[2020-07-23 22:48:49] root: INFO: Computing consensus
[2020-07-23 22:48:59] root: INFO: Alignment error rate: 0.000000
[2020-07-23 22:48:59] root: INFO: >>>STAGE: repeat
[2020-07-23 22:48:59] root: INFO: Building and resolving repeat graph
[2020-07-23 22:48:59] root: DEBUG: -----Begin repeat analyser log------               

Any thoughts on what is going on here? I am using version 2.7.1-b1590 that I installed through conda a couple of days ago. Maybe there is a bug which results in minimap being called incorrectly?

Many thanks for your help,

Alex

[A-J-F-Mackintosh]

Hi again,

The conda environment I was using contained minimap2 already - which may have 'confused' flye? - so I made a new env with only flye.

I resumed from the consensus stage and all seems to be running fine now.

Thanks,

Alex