trim.seqs error for V1.18

mothur bugs
1

Hello,

I have just compiled and installed the V1.18 of mothur on Mac OSX 10.5.8. I tried using the following mothur command:

trim.seqs(fasta=test_1.fna,qfile=test_1.qual,qaverage=25,flip=T,pdiffs=2, qwindowaverage=35, qwindowsize=50, maxambig=0, maxhomop=8, processors=5)

and I get a following error, and the program just stalls:

ERROR]: Could not open test_1.trim.fasta41982.temp
[ERROR]: Could not open test_1.scrap.fasta41982.temp
[ERROR]: Could not open test_1.trim.fasta41983.temp
[ERROR]: Could not open test_1.trim.qual41982.temp
[ERROR]: Could not open test_1.scrap.fasta41983.temp
[ERROR]: Could not open test_1.scrap.qual41982.temp
[ERROR]: Could not open test_1.trim.qual41983.temp
[ERROR]: Could not open test_1.scrap.qual41983.temp
[ERROR]: Could not open test_1.trim.fasta
[ERROR]: Could not open test_1.scrap.fasta
[ERROR]: Could not open test_1.trim.qual
[ERROR]: Could not open test_1.scrap.qual
[ERROR]: Could not open test_1.trim.fasta
[ERROR]: Could not open test_1.scrap.fasta
[ERROR]: Could not open test_1.trim.qual
[ERROR]: Could not open test_1.scrap.qual
[ERROR]: Could not open test_1.trim.fasta41984.temp
[ERROR]: Could not open test_1.trim.fasta41985.temp
[ERROR]: Could not open test_1.scrap.fasta41984.temp
[ERROR]: Could not open test_1.scrap.fasta41985.temp
[ERROR]: Could not open test_1.trim.qual41984.temp
[ERROR]: Could not open test_1.trim.qual41985.temp
[ERROR]: Could not open test_1.scrap.qual41984.temp
[ERROR]: Could not open test_1.scrap.qual41985.temp
362
177
[ERROR]: Could not open test_1.fna41982.num.temp
158
[ERROR]: Could not open test_1.fna41983.num.temp
155
[ERROR]: Could not open test_1.fna41984.num.temp
148
[ERROR]: Could not open test_1.fna41985.num.temp
Appending files from process 41982
[ERROR]: Could not open test_1.trim.fasta
[ERROR]: Could not open test_1.scrap.fasta
[ERROR]: Could not open test_1.trim.qual
[ERROR]: Could not open test_1.scrap.qual
[ERROR]: Could not open
[ERROR]: Could not open test_1.fna41982.num.temp

I had a similar problem once, and I remember that the quality file needs to have a return character at the end of it. This time, even when there is a return character at the end, I am getting this error. Your help would be much appreciated.
I have attached and sent the quality file and the fasta file into mothur.bugs@gmail.com. Thank you in advance.

2

Thanks for bringing this bug to our attention. I ran your files with version 1.19.3, and found the bug only occurs when using multiple processors with no oligos file. I have fixed the issue and the change will be part of 1.20 releasing next month. I would recommend upgrading to version 1.19.3, and running your dataset with one processor on the trim.seqs command.