Different results between Windows and Linux

I was running my first small set of data this week on the Windows version of Mothur 1.44.2 and found that my results seemed strange after the make.contigs(file=…, oligos=…, checkorient=t, pdiffs=0), so I installed a Virtual box with Ubuntu 16 to try the linux version. With the same command and the same file and oligos, I got a totally different results. Here is the result of the windows version:
*Group count: *
11R1T0 4280
11R1T24 4634
11R1T48 4267
11R1T51 4056
11R1T54 4368
11R1T6 4841
11R1T60 4222
11R1T72 3726
CRTLNeg 668
Spikein 4985
TN 3713
Zymo 4588

Total of all groups is 49074

And here is the results of the Linux version:
MI.M06648 5253
MI.M06648_0066.001.FLD0194.CTRLNEG 10545
MI.M06648_0066.001.FLD0200.11R1T0 98572
MI.M06648_0066.001.FLD0202.CRTLNEG 14503
MI.M06648_0066.001.FLD0208.11R1T6 121786
MI.M06648_0066.001.FLD0210.Spikein 118455
MI.M06648_0066.001.FLD0216.11R1T24 111142
MI.M06648_0066.001.FLD0218.CTRL 120289
MI.M06648_0066.001.FLD0224.11R1T48 113344
MI.M06648_0066.001.FLD0232.11R1T51 113992
MI.M06648_0066.001.FLD0240.11R1T54 109904
MI.M06648_0066.001.FLD0248.11R1T60 117502
MI.M06648_0066.001.FLD0256.11R1T72 110561
MI.M06648_0066.001.FLD0264.FFMF 233
MI.M06648_0066.001.FLD0272.TN 89741

Total of all groups is 1255822

Sample are the same, only I didn’t change their name on my virtual machine.

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Can you post the commands you are running and how you generated the linux results?


To get to these results, I simply did, in both case:
make.file(inputdir=…, type=gz)
make.contigs(file=current, oligos=…, checkorient=t, pdiff=0)

I can provide both logfile and other files if needed.


Thanks for reporting this issue. Could you send one of the file pairs, the oligos and log files to mothur.bugs@gmail.com so I can take a closer look?

I just sent you a onedrive link with the resquested files.


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I released version 1.44.3 which includes the fix to make.contigs. https://github.com/mothur/mothur/releases/tag/v1.44.3 Thanks again for your help resolving this issue.

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