mothur

Metastats (Segmentation fault)

Hi, I’m new working with the Mothur program. I’ve been trying to run the metastats command but on the output, I get a segmentation fault error. I am using mothur version v.1.45.1. Here is the output. I hope someone can help me.

mothur > metastats(shared=MiSeq_SOP/stability.opti_mcc.0.03.subsample.shared, design=design.layout.R)

Using 4 processors.
0.03

Comparing Undetermined and Apalachicola…

Comparing Netherlands and Apalachicola…

Comparing Undetermined and Netherlands…

Segmentation fault: 11

Hi -

Can you post the contents of design.layout.R?

Thanks,
Pat

Design.layout.R contents:

SAB1 Apalachicola Bay sediment microbiome

SAB2 Apalachicola Bay sediment microbiome

SAB3 Apalachicola Bay sediment microbiome

SAB4 Apalachicola Bay sediment microbiome

SAB5 Apalachicola Bay sediment microbiome

SAB6 Apalachicola Bay sediment microbiome

SAB7 Apalachicola Bay sediment microbiome

SAB8 Apalachicola Bay sediment microbiome

SAB9 Apalachicola Bay sediment microbiome

SNLA Netherlands Bay sediment microbiome

SNLB Netherlands Bay sediment microbiome

SNLC Netherlands Bay sediment microbiome

SNLD Netherlands Bay sediment microbiome

WAB1 Apalachicola Bay water microbiome

WAB2 Apalachicola Bay water microbiome

WAB3 Apalachicola Bay water microbiome

WAB4 Apalachicola Bay water microbiome

WAB5 Apalachicola Bay water microbiome

WAB6 Apalachicola Bay water microbiome

WAB7 Apalachicola Bay water microbiome

WAB8 Apalachicola Bay water microbiome

WAB9 Apalachicola Bay water microbiome

FAB5 Apalachicola Bay Ammonia microbiome

FAB7 Apalachicola Bay Ammonia microbiome

FAB4 Apalachicola Bay Agglutinans microbiome

FAB6 Apalachicola Bay Agglutinans microbiome

FNLA Netherlands Bay Ammonia microbiome

FNLB Netherlands Bay Ammonia microbiome

FNLC Netherlands Bay Ammonia microbiome

FNLD Netherlands Bay Ammonia microbiome

Undetermined Undetermined

Undertemined undertermined

Thank,

Thanks - can you try removing the spaces in the second column? The only space that is expected is between he same name and the grouping variable name

Pat

I remove the space in the second column:

SAB1 ApalachicolaBaysedimentmicrobiome

SAB2 ApalachicolaBaysedimentmicrobiome

SAB3 ApalachicolaBaysedimentmicrobiome

SAB4 ApalachicolaBaysedimentmicrobiome

SAB5 ApalachicolaBaysedimentmicrobiome

SAB6 ApalachicolaBaysedimentmicrobiome

SAB7 ApalachicolaBaysedimenmicrobiome

SAB8 ApalachicolaBaysedimentmicrobiome

SAB9 ApalachicolaBaysedimentmicrobiome

SNLA NetherlandsBaysedimentmicrobiome

SNLB NetherlandsBaysedimentmicrobiome

SNLC NetherlandsBaysedimentmicrobiome

SNLD NetherlandsBaysedimentmicrobiome

WAB1 ApalachicolaBaywatermicrobiome

WAB2 ApalachicolaBaywatermicrobiome

WAB3 ApalachicolaBaywatermicrobiome

WAB4 ApalachicolaBaywatermicrobiome

WAB5 ApalachicolaBaywatermicrobiome

WAB6 ApalachicolaBaywatermicrobiome

WAB7 ApalachicolaBaywatermicrobiome

WAB8 ApalachicolaBaywatermicrobiome

WAB9 ApalachicolaBaywatermicrobiome

FAB5 ApalachicolaBayAmmoniamicrobiome

FAB7 ApalachicolaBayAmmoniamicrobiome

FAB4 ApalachicolaBayAgglutinansmicrobiome

FAB6 ApalachicolaBayAgglutinansmicrobiome

FNLA NetherlandsBayAmmoniamicrobiome

FNLB NetherlandsBayAmmoniamicrobiome

FNLC NetherlandsBayAmmoniamicrobiome

FNLD NetherlandsBayAmmoniamicrobiome

Undetermined Undetermined

and try again to execute the command but the same fault appeared and with missing share info:

mothur > metastats(shared=MiSeq_SOP/stability.opti_mcc.0.03.subsample.shared, design=design.layout.R)

Using 4 processors.

0.03

Missing shared info for NetherlandsBayAmmoniamicrobiome or ApalachicolaBaywatermicrobiome. Skipping comparison.

Missing shared info for ApalachicolaBaywatermicrobiome or ApalachicolaBayAmmoniamicrobiome. Skipping comparison.

Missing shared info for ApalachicolaBaywatermicrobiome or ApalachicolaBaysedimenmicrobiome. Skipping comparison.

Missing shared info for ApalachicolaBaywatermicrobiome or ApalachicolaBaysedimentmicrobiome. Skipping comparison.

Comparing Undetermined and ApalachicolaBayAgglutinansmicrobiome…

Comparing ApalachicolaBayAmmoniamicrobiome and ApalachicolaBayAgglutinansmicrobiome…

Comparing NetherlandsBayAmmoniamicrobiome and ApalachicolaBayAgglutinansmicrobiome…

Comparing NetherlandsBaysedimentmicrobiome and ApalachicolaBayAgglutinansmicrobiome…

Segmentation fault: 11

At the command prompt (outside of mothur), can you run…

cut -f 2 stability.opti_mcc.0.03.subsample.shared

And then post the output?

Lexas-MacBook-Air:MiSeq_SOP Lexa$ cut -f 2 stability.opti_mcc.0.03.subsample.shared

Group

FAB4

FAB5

FAB6

FAB7

FNLB

FNLC

SAB1

SAB3

SAB4

SAB5

SAB6

SAB7

SAB8

SAB9

SNLA

SNLB

SNLD

Undetermined

Lexas-MacBook-Air:MiSeq_SOP Lexa$

Could you send your shared, design and logfile to mothur.bugs@gmail.com so I can track down the issue for you?

Hi Lexa,
Thanks for sending the additional files. There are several things causing the issue with the metastats command.

  1. File mismatch - Your shared file contains a group not present in your design file.
    Extra group in shared file - Undetermined

  2. File mismatch - Your design file contains groups not present in your shared file.
    Extra groups in the design file:
    SAB2 ApalachicolaBaysedimentmicrobiome
    SNLC NetherlandsBaysedimentmicrobiome
    WAB1 ApalachicolaBaywatermicrobiome
    WAB2 ApalachicolaBaywatermicrobiome
    WAB3 ApalachicolaBaywatermicrobiome
    WAB4 ApalachicolaBaywatermicrobiome
    WAB5 ApalachicolaBaywatermicrobiome
    WAB6 ApalachicolaBaywatermicrobiome
    WAB7 ApalachicolaBaywatermicrobiome
    WAB8 ApalachicolaBaywatermicrobiome
    WAB9 ApalachicolaBaywatermicrobiome
    FNLA NetherlandsBayAmmoniamicrobiome
    FNLD NetherlandsBayAmmoniamicrobiome

  3. The shared file has very low abundances / number of OTUs. This means for many treatment comparisons, the abundance of the treatment for most OTUs is 0. The total number of sequences in the shared file is 17, with 12 of the 14 OTUs being singletons. This doesn’t seem right. Did you have issues during the preprocessing of your dataset?

This unusual dataset helped me find a small bug in mothur that was causing a segfault. I have corrected the problem and the fix will be part of our next release.

Kindly,
Sarah

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