mothur

Empty .flow.files

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

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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