Spades unequal amount of reads

[oyac]

Hello,

I am running my samples in sequential mode, and I did the trimming with trimmomatic first. When it gets to the assembly, with Spades, I get the error " Pair of read files contain unequal amount of reads". Is there a way to fix this, or a workaround?

Thanks!

[jtamames]

Hello Did you run trimmomatic in SqueezeMeta? If so, try running it externally and then provide the resulting fastq. If not, check that you are specifying the correct fastq files. Best, J

[oyac]

Hi , Yes, I used the --cleaning flag so it would run in SqueezeMeta. So, the best option is to run it externally? Thanks,

[fpusan]

Are the original fastq files properly paired?

[oyac]

Yes, the original ones are properly paired.

[fpusan]

Then try as Javier suggested and run trimommatic externally. I will leave this open so we remember to look at this potential bug. Can you share your syslog file with us so we can replicate as best as possible?

[oyac]

Hi, today i started the project in another folder, from the sample that had gone wrong and it went further without any problems.

Thanks,

[jtamames]

Glad to hear! Did you run trimmomatic externally, or in SqueezeMeta as before? Best, J

[oyac]

I started from zero, running trimmomatic within SqueezeMeta.

Cheers,

[jtamames]

Then it works properly. Thanks a lot! Closing issue

[fpusan]

Indeed, I just tested --cleaning on a sequential run with a mock dataset and got no errors