# Empty .flow.files

**URL:** <https://forum.mothur.org/t/empty-flow-files/20570>\
**Category:** mothur bugs\
**Created:** [June 11, 2020, 7:48pm UTC](https://forum.mothur.org/t/empty-flow-files/20570 "2020-06-11T19:48:50Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![gtrini](https://avatars.discourse-cdn.com/v4/letter/g/3bc359/32.png) [@gtrini](https://forum.mothur.org/u/gtrini)\
**Post date:** [June 11, 2020, 7:48pm UTC](https://forum.mothur.org/t/empty-flow-files/20570/1 "2020-06-11T19:48:50Z")

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Hello there,

I’m new to mothur and have been having issues with the trim.flows command, although it could be an error for the mac version of mothur because someone I know tried the same files and commands on Linux and it worked fine.

I want to start by saying that the sffinfo(sff=2012.sff) worked just fine, and it did create a successful 2012.flow file.

Here is the command I am having an issue with, for bdiffs I did try bdiffs=0 and the error was the same.

mothur \> trim.flows(flow=2012.flow, oligos=2012.oligos, pdiffs=2, order=A, minflows=360)

after this command it ran through but the 2012.flow.files was empty

below I have the 2012.oligos file

forward AGRGTTTGATCMTGGCTCAG   
barcode ACGAGATC 2012Apalm1   
barcode ACGTACAA 2012Apalm10   
barcode ACGTCCAG 2012Apalm11   
barcode ACGTCGCA 2012Apalm12   
barcode ACGTCTGA 2012Apalm13   
barcode ACGTGTAG 2012Apalm14   
barcode ACTAACCC 2012Apalm15   
barcode TACACGCG 2012Apalm16   
barcode TACACGGC 2012Apalm17   
barcode TACACTCA 2012Apalm18   
barcode TACCAACT 2012Apalm19   
barcode ACGATCTG 2012Apalm2   
barcode TACCAAGC 2012Apalm20   
barcode TACCAAGG 2012Apalm21   
barcode TACCACGG 2012Apalm22   
barcode TACCGTAG 2012Apalm23   
barcode TACCTATA 2012Apalm24   
barcode TACGAAGA 2012Apalm25   
barcode TACGAATC 2012Apalm26   
barcode TAGACTGC 2012Apalm27   
barcode TACTATTG 2012Apalm28   
barcode TACTCTCC 2012Apalm29   
barcode ACGCAACC 2012Apalm3   
barcode TACTGAAG 2012Apalm30   
barcode TACTGTTC 2012Apalm31   
barcode TACTTAAC 2012Apalm32   
barcode ACGCAACG 2012Apalm4   
barcode ACGCATCG 2012Apalm5   
barcode ACGCGAAC 2012Apalm6   
barcode ACGGGTAA 2012Apalm7   
barcode ACGGTAAG 2012Apalm8   
barcode ACGGTGTT 2012Apalm9

any help would be appreciated!

Thanks,

Glenda

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**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [June 15, 2020, 7:48pm UTC](https://forum.mothur.org/t/empty-flow-files/20570/2 "2020-06-15T19:48:41Z")

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Hi Glenda,  
Thanks for sending your files and reporting this bug. I was able to find the source of the problem. Mothur was not properly passing the parsed flow file names from the split.groups command back to the trim.flows command. The flow files for each sample are created properly, but the \*flow.files file was blank. The change will be part of our 1.45.0 release. In the meantime, you can also generate this file manually by copying and pasting the parsed flow file names from the logfile into a plain text file.  
Kindly, Sarah

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**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [June 25, 2020, 7:48pm UTC](https://forum.mothur.org/t/empty-flow-files/20570/3 "2020-06-25T19:48:45Z")

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