Metaspades has stuck when it is processing reversed reads

[Menglinhsy]

Hi, Remi,

I found some of my jobs have stuck in processing R2 reads when I do assembly using MitoFinder 1.4.

To investigate whether it was because of Spades assembler or Mitofinder itself, I tried Spades 1.13 using the same sample and the assembly worked well.

here I attached the metaspades.log file generated by both Mitofinder and Spades.

Spades_spades.log

MitoFinder_metaspades.log

In addition, I have some samples sequenced using different sequencing platforms, so I also want to know if it is
ok if I use four input files? I know it is possible for Spades, but how about Mitofinder?

[RemiAllio]

Hi,

Well, honestly, I have no idea about what is happening with metaspades in your case. It's even stranger that no errors seem to occur...
MitoFinder uses Spades 3.13, but I guess this is the version you tried (instead of 1.13 indicated in your comment).

Unfortunately, I can't give you a solution. I had never encountered this situation before. I am sorry for the inconvenience.
Fortunately, you can use the resulting assembly of spades to run MitoFinder using the -a option.

Regarding the data generated by different sequencing platforms, if they are of the same kind, you can simply concatenate the fastq files of the forward reads on the one hand and the fastq files of the reverse reads on the other hand. Then you can use the resulting files. However, if you can't concatenate the files for any reason, there is no option to tell MitoFinder to deal with multiple input files... I have to think about it for the next version. Once again, you should use Spades separately and then use MitoFinder with the -a option.

I hope this helps,
Again, I am sorry for the inconvenience,
Cheers,
Rémi

[Menglinhsy]

Hi Rémi,

Thanks for your reply and suggestion~ I will try that!

Best,
Menglin