Redundans: no pairs aligned

Question

[el97004]

Hello,

Does anyone know what would cause "No paris were aligned!" message during the scaffolding step in Redundans?

I am running it using this command:

redundans.py --identity 0.70 -v -i R1.fastq R2.fastq -f contigs.fa -o Results

I've checked all of the documentation and the examples to see if I am missing something and I cannot pinpoint what could be wrong. The only difference I see is the authors use compressed fastq files and I am not.

Any input would be greatly appreciated

[GenoMax]

Were these read files trimmed independently? Perhaps reads in the files are no longer in sync as a result.

[el97004]

Thanks for the suggestion! They were trimmed together but i do have a step where I remove reads that map to certain scaffolds (scaffolds that are not part of my target organism (contamination)) and so I think this might be what is causing it

[el97004]

But I just double checked and both read files (R1 and R2) have the same number of reads in them. Is there any other way to test that they are in "sync"

[GenoMax]

Use repair.sh from BBMap suite and make sure reads are in correct order in both files.

[el97004]

Just ran repair.sh from BBMap successfully on my reads. Unfortunately the message persists even after doing this.

##################################################
[Wed Oct 30 16:48:25 2019] Scaffolding...
 iteration 1.1: run1/contigs.reduced.fa 603 4122740 34.603  204 3945123 44917   5866    1   155966
   No pairs were aligned!
    No pairs were aligned!
 iteration 1.2: run1/_sspace.1.1.fa 603 4122740 34.603  204 3945123 44917   5866    1   155966
   No pairs were aligned!
    No pairs were aligned!

[GenoMax]

So the problem is not read order then. I am not familiar with redundans so can't directly comment. If you are familiar with python then you could look in the code to see where that error message is coming from to get a further clue.

You could also post to the support forum.

[el97004]

I will try those two things. Thank you for the help!

[hnt001]

Hello! I am having the same error. Did you happen to solve the "no pairs were aligned" error? thank you!