mothur

Bug in rarefaction.shared command in version 1.41.3 in linux


#1

When I tried to run the rarefaction.shared command, I got a “Segmentation fault (core dumped)”, using 1.41.3 in linux RedHat.
However, it works fine in v.1.39.5.

Best regards,
Caio Rachid


#2

Could you send your logfile and input files to mothur.bugs@gmail.com so I can take a closer look?


#3

Hello,

Here is the logfile from the first time the error happened (mothur.1549547102-1.logfile / the error is in the end), and the logfile when it worked, with a older version (mothur.1549557032.logfile).

(Attachment design is missing)

(Attachment mothur.1549547102.logfile is missing)

(Attachment ok.opti_mcc.0.03.abund.shared is missing)

(Attachment mothur.1549557032.logfile is missing)


#4

Thanks for reporting this bug and sending your files. The rarefaction.shared command is having an issue running with the design file. I have fixed this and the change will be part of our next release. In the meantime you can work around the issue by running each set individually.

mothur > get.groups(shared= ok.opti_mcc.0.03.abund.shared, groups=C8-C9-C10-C11-C12) - select set Y
mothur > rarefaction.shared(shared=current) - run rarefaction.shared for set Y
mothur > get.groups(shared= ok.opti_mcc.0.03.abund.shared, groups=C13-C14-C15-C16-C17) - select set O
mothur > rarefaction.shared(shared=current) - run rarefaction.shared for set O
mothur > get.groups(shared= ok.opti_mcc.0.03.abund.shared, groups=C18-C19-C20-C21-C22) - select set N
mothur > rarefaction.shared(shared=current) - run rarefaction.shared for set N


closed #5

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