trim.seqs in version 1.24 producing empty fasta

mothur bugs
1

Hello,

When running Linux 64 version 1.24, I am unable to use trim.seqs. The same commands in version 1.23 generates the expected output.

Thank you,
Mariam.

2

Could you send your logfile and input files to mothur.bugs@gmail.com?

3

Hi Sarah,

I have a similar problem with the latest version (v.1.25.0)

After running the trim.flow command:

_mothur > trim.flows(flow=sample.flow, oligos=sample.oligos, pdiffs=2, bdiffs=1, processors=2)

Output File Names:
sample.trim.flow
sample.scrap.flow
sample.flow.files_

I run the shhh.flows command and obtain the following error message:
_mothur > shhh.flows(file=sample.flow.files, processors=2)

[ERROR]: sample.flow.files is blank. Please correct.
[ERROR]: no valid files._

Any idea what the problem might be?

Thanks,

Matthias

4

Normally the output of trim.flows should include file names with the group names in them. I suspect everything is getting sent to the scrap.flows file. Can you take a look at the codes in the scrap.flow file and see what’s there and confirm that trim.flows is empty?

5

After running trim.flows it looks like all my data went into the scrap.flow file and the flow.files is empty. What should I do?

6

Can you try updating to our current version?

7

Maybe it’s a pyrosequencing technology problem

Look in your flow file, if the number on the first line is 800, this is not the problem,
If the number is 1779, you must use the order=B parameter in trim.flows and shhh.flows,

without it, all your sequences will be scraped

I had the same problem as you, and this was the solution

(sorry for my bad english, i’m french)