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