Problem while running shhh.flows

Hi all,
I’ve just got some 454 data and willing to start my analysis. I’ve made it to shhh.flows, but I get an error that says the program couldn’t open the names and the fasta files: [ERROR]: Could not open D:\454 Data\D:\454 Data\HM2J0ZL01.shhh.fasta
[ERROR]: Could not open D:\454 Data\D:\454 Data\HM2J0ZL01.shhh.names
and repeated the error while processing every single sample…
But aren’t the fasta and the names file what shh.flows should generate? Why is it asking for these files as inputs?
Anyways the program continued running till the end and did everything in 5 minutes (is this possible?) and it said it generated the following files:

D:\454 Data\HM2J0ZL01.MID51.shhh.counts
D:\454 Data\HM2J0ZL01.MID51.shhh.groups
D:\454 Data\HM2J0ZL01.MID52.shhh.qual
D:\454 Data\HM2J0ZL01.MID52.shhh.fasta
D:\454 Data\HM2J0ZL01.MID52.shhh.names
D:\454 Data\HM2J0ZL01.MID52.shhh.counts
D:\454 Data\HM2J0ZL01.MID52.shhh.groups
D:\454 Data\HM2J0ZL01.MID53.shhh.qual
D:\454 Data\HM2J0ZL01.MID53.shhh.fasta
D:\454 Data\HM2J0ZL01.MID53.shhh.names
D:\454 Data\HM2J0ZL01.MID53.shhh.counts
D:\454 Data\HM2J0ZL01.MID53.shhh.groups
D:\454 Data\HM2J0ZL01.MID54.shhh.qual
D:\454 Data\HM2J0ZL01.MID54.shhh.fasta
D:\454 Data\HM2J0ZL01.MID54.shhh.names
D:\454 Data\HM2J0ZL01.MID54.shhh.counts
D:\454 Data\HM2J0ZL01.MID54.shhh.groups
D:\454 Data\HM2J0ZL01.MID55.shhh.qual
D:\454 Data\HM2J0ZL01.MID55.shhh.fasta
D:\454 Data\HM2J0ZL01.MID55.shhh.names
D:\454 Data\HM2J0ZL01.MID55.shhh.counts
D:\454 Data\HM2J0ZL01.MID55.shhh.groups
D:\454 Data\HM2J0ZL01.MID56.shhh.qual
D:\454 Data\HM2J0ZL01.MID56.shhh.fasta
D:\454 Data\HM2J0ZL01.MID56.shhh.names
D:\454 Data\HM2J0ZL01.MID56.shhh.counts
D:\454 Data\HM2J0ZL01.MID56.shhh.groups
D:\454 Data\HM2J0ZL01.MID57.shhh.qual
D:\454 Data\HM2J0ZL01.MID57.shhh.fasta
D:\454 Data\HM2J0ZL01.MID57.shhh.names
D:\454 Data\HM2J0ZL01.MID57.shhh.counts
D:\454 Data\HM2J0ZL01.MID57.shhh.groups
D:\454 Data\HM2J0ZL01.MID58.shhh.qual
D:\454 Data\HM2J0ZL01.MID58.shhh.fasta
D:\454 Data\HM2J0ZL01.MID58.shhh.names
D:\454 Data\HM2J0ZL01.MID58.shhh.counts
D:\454 Data\HM2J0ZL01.MID58.shhh.groups
D:\454 Data\HM2J0ZL01.MID59.shhh.qual
D:\454 Data\HM2J0ZL01.MID59.shhh.fasta
D:\454 Data\HM2J0ZL01.MID59.shhh.names
D:\454 Data\HM2J0ZL01.MID59.shhh.counts
D:\454 Data\HM2J0ZL01.MID59.shhh.groups
D:\454 Data\D:\454 Data\HM2J0ZL01.shhh.fasta
D:\454 Data\D:\454 Data\HM2J0ZL01.shhh.names

but in the directory I can’t find HM2J0ZL01.shhh.fasta andHM2J0ZL01.shhh.names, while I do have the single fasta file for each separate sample but they are really small (around 150kb each)… is this normal?

Thanks in advance for your help!

Hi all,

Since this is my first posting in this forum, I first would like to say “hello” to all readers.

Dear Joanito,

I am experiencing exactly the same problem with the shhh.flows command. As an emergency work-around until this bug is exterminated, I suggest running mothur in the same directory that holds your .flow files.


What version of mothur are you using?

v.1.25.0 win-64Bit

Thanks for bringing this to our attention. It will be fixed in the next release.