# trim.flows in version 1.32 producing empty flow.files
**URL:** https://forum.mothur.org/t/trim-flows-in-version-1-32-producing-empty-flow-files/1525
**Category:** mothur bugs
**Created:** [October 3, 2013, 10:07pm UTC](https://forum.mothur.org/t/trim-flows-in-version-1-32-producing-empty-flow-files/1525 "2013-10-03T22:07:41Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@Claudia](https://forum.mothur.org/u/Claudia)
#### Post date: [October 3, 2013, 10:07pm UTC](https://forum.mothur.org/t/trim-flows-in-version-1-32-producing-empty-flow-files/1525/1 "2013-10-03T22:07:41Z")
Hi, I have separate sff files for each of my samples and I am trying to work on them separately until I get to the unique.seqs step.
When I run
mothur \> trim.flows(flow=sample.flow, oligos=sample.oligos, pdiffs=2, bdiffs=1)
Output File Names:
sample.trim.flow
sample.scrap.flow
sample.flow.files
I run the shhh.flows command and obtain the following error message:
[ERROR]: sample.flow.files is blank, aborting.
values for either flow or file must be provided for the shhh.flows command.
Unable to open ~/LookUp\_Titanium.pat. Trying mothur’s executable location ~/LookUp\_Titanium.pat
Unable to open ~/LookUp\_Titanium.pat.
When I checked the sample.scrap.flow file I saw in the first row 450 and beneath that sequenceID|lbf or sequenceID|bf
Any idea what the problem might be?
Thanks,
Claudia
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [October 7, 2013, 3:18pm UTC](https://forum.mothur.org/t/trim-flows-in-version-1-32-producing-empty-flow-files/1525/2 "2013-10-07T15:18:50Z")
Are there any sequenceIDS in sample.trim.flow?
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### Author:  [@Claudia](https://forum.mothur.org/u/Claudia)
#### Post date: [October 7, 2013, 3:59pm UTC](https://forum.mothur.org/t/trim-flows-in-version-1-32-producing-empty-flow-files/1525/3 "2013-10-07T15:59:24Z")
Nope, only the number of flows that I selected. In my case, as I have tried with 450 and 360, these numbers are the only thing I see in two different trim.flow files.
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [October 7, 2013, 6:31pm UTC](https://forum.mothur.org/t/trim-flows-in-version-1-32-producing-empty-flow-files/1525/4 "2013-10-07T18:31:47Z")
If the \*.trim.flow file is empty then all your sequences are being scrapped. From the scrap codes you posted, it looks like they are failing due to barcodes and primers. Perhaps its a formatting issue on the oligos file? Can you post your oligos file?
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### Author:  [@Claudia](https://forum.mothur.org/u/Claudia)
#### Post date: [October 8, 2013, 4:07pm UTC](https://forum.mothur.org/t/trim-flows-in-version-1-32-producing-empty-flow-files/1525/5 "2013-10-08T16:07:19Z")
Yep! It was an issue with the barcodes. “Fortunately” the main problem was that the barcodes provided by the core facility where I sent my samples were nor the correct ones. That is why in the scrap.flow file all the sequences showed|b.
However, I still have a considerable amount of sequence in the scrap.flow file that were filtered by length (I see lots of |l). If I am using the primers 28F/519R for bacteria and 349F/806R for archaea in a GS FLX Titanium platform. In that case, is it save to use 450 as the number of flowgrams in trim.flow?
Thanks!