Galaxy: What does this error mean? How do I fix it?

Hi,
I was trying to run count.seqs on my data but got this error:

What does this error mean? How do I fix this?

Thank you.

Hi @cp1,
this information is not enough for inferring the problem; could you share your history with me? My email is Screenshot from 2022-04-03 16-52-09

Regards

Hi Gallardo,

Yes, here is the history:
https://usegalaxy.org/u/cp1/h/v6-amplicons

Thank you for looking into it!

Hi @cp1,
since you are using make.groups for generating the groups file, it is necessary to collapse the FASTA collection into a single file. Here you can see what I mean: test history.

Regards

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Hi Gallardo,

Thank you SO much for this! This is brilliant.

I’m really new to all of this. May I ask why you set the maxlength to 275 instead of 450 for the input of screen.seqs command?

Is it better to analyze a shorter span of read lengths vs longer?

Hi @cp1,
in that case, I just followed the recommendations of the GTN training.

Our region of interest, the V4 region of the 16S gene, is only around 250 bases long. Any reads significantly longer than this expected value likely did not assemble well in the Make.contigs step. Furthermore, we see that 2,5% of our reads had between 6 and 249 ambiguous base calls ( Ambigs column). In the next steps, we will clean up our data by removing these problematic reads.

Since you are not using make.contains, probably in your case it won’t affect at all.

Regards

Hi @gallardoalba ,

Ah, got it! Thank you very much for the help.

Take care.

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