P1.max FASTA file no longer being generated

[Bobby Read]

Hi there!

I have been using BAli-Phy a little bit now to produce some great-looking trees, however, for some reason the P1.max.fasta file that was being produced when running the bp-analyze function is no longer being made.

I had to repeat a tree as i realised there was a sequence included that shouldn't have been! The commands were totally identical so i'm a little confused as to why the bp-analyse function is no longer making the P1.max.fasta file so i can view the alignment. 

I have tried reinstalling Cygwin and Bali-Phy itself, but still encountering the same error. Is there an easy fix or perhaps a separate command that will produce the alignment? 

Thanks in advance!

Ben

[Bobby Read]

Just to add a bit more information... here is what the cygwin console gives back to me when i run bp-analyze

$ bp-analyze ATPPRT_NEW-1/ ATPPRT_NEW-2/ --skip=11500

Renaming 'Results/' to 'Results.1'

Creating new directory Results/ for summary files.

Summarizing distribution of numerical parameters: done.

Analyzing scalar variables: done.

Summarizing topology distribution:  done.

Drawing trees: c50 c66 c80 c90 c95 c99 c100 greedy MAP . done.

Generate mixing diagnostics for topologies ...command: '/usr/bin/R' '--slave' '--vanilla' '--args' 'Results/LOD-table' 'Results/convergence-PP.pdf' < '/home/br33/Applications/bali-phy-3.5.0/lib/bali-phy/libexec/compare-runs.R'

 exit: 126

To clarify, the tree files are still being produced as normal, but the files containing the alignments are not

[Benjamin Redelings]

Hi Ben,

It looks like somehow the bp-analyze script failed before it got to the part where it generates P1.max.fasta

One possibility is that you are trying to skip too many iterations -- i.e. you don't have enough iterations left after 11500.  That is just a guess though.

If you look in the Results directory, there should be a file called `commands.log`.  Does it give any more information on why the compare-runs.R script would have failed?

-BenRI

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[Bobby Read]

Hi Ben 

Thanks for getting back to me. It appears that the program is having issues accessing R as it returns "permission denied" after the compare-runs.R script. I will try re-installing the Cygwin terminal again and make sure that everything has gone fine with the R package install.

Thanks again,

Ben

-----------------------------------------------------------

'statreport' 'ATPPRT_NEW-1/C1.log' 'ATPPRT_NEW-2/C1.log' '--skip=11500' > 'Results/Report'

'trees-consensus' '--map-tree=Results/MAP.PP.tree' '--greedy-consensus=Results/greedy.PP.tree' '--report=Results/consensus' 'ATPPRT_NEW-1/C1.trees' 'ATPPRT_NEW-2/C1.trees' '--support-levels=Results/c-levels.plot' '--skip=11500' '--consensus=0.5:Results/c50.PP.tree,0.66:Results/c66.PP.tree,0.8:Results/c80.PP.tree,0.9:Results/c90.PP.tree,0.95:Results/c95.PP.tree,0.99:Results/c99.PP.tree,1.0:Results/c100.PP.tree'

'tree-tool' 'Results/greedy.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/greedy.tree'

'tree-tool' 'Results/MAP.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/MAP.tree'

'tree-tool' 'Results/c50.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c50.tree'

'tree-tool' 'Results/c66.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c66.tree'

'tree-tool' 'Results/c80.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c80.tree'

'tree-tool' 'Results/c90.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c90.tree'

'tree-tool' 'Results/c95.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c95.tree'

'tree-tool' 'Results/c99.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c99.tree'

'tree-tool' 'Results/c100.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c100.tree'

'draw-tree' 'c50.tree' '--layout=equal-daylight'

'draw-tree' 'c50.tree' '--layout=equal-daylight' '--output=svg'

'draw-tree' 'c66.tree' '--layout=equal-daylight'

'draw-tree' 'c66.tree' '--layout=equal-daylight' '--output=svg'

'draw-tree' 'c80.tree' '--layout=equal-daylight'

'draw-tree' 'c80.tree' '--layout=equal-daylight' '--output=svg'

'draw-tree' 'c90.tree' '--layout=equal-daylight'

'draw-tree' 'c90.tree' '--layout=equal-daylight' '--output=svg'

'draw-tree' 'c95.tree' '--layout=equal-daylight'

'draw-tree' 'c95.tree' '--layout=equal-daylight' '--output=svg'

'draw-tree' 'c99.tree' '--layout=equal-daylight'

'draw-tree' 'c99.tree' '--layout=equal-daylight' '--output=svg'

'draw-tree' 'c100.tree' '--layout=equal-daylight'

'draw-tree' 'c100.tree' '--layout=equal-daylight' '--output=svg'

'draw-tree' 'greedy.tree' '--layout=equal-daylight'

'draw-tree' 'greedy.tree' '--layout=equal-daylight' '--output=svg'

'draw-tree' 'MAP.tree' '--layout=equal-daylight'

'draw-tree' 'MAP.tree' '--layout=equal-daylight' '--output=svg'

'pickout' '--no-header' '--large' 'pi' < 'Results/consensus' > 'Results/partitions'

'trees-bootstrap' '--pred=Results/partitions.pred' '--LOD-table=Results/LOD-table' '--pseudocount=1' 'ATPPRT_NEW-1/C1.trees' 'ATPPRT_NEW-2/C1.trees' '--skip=11500' > 'Results/partitions.bs'

'/usr/bin/R' '--slave' '--vanilla' '--args' 'Results/LOD-table' 'Results/convergence-PP.pdf' < '/home/br33/Applications/bali-phy-3.5.0/lib/bali-phy/libexec/compare-runs.R'

  err: /usr/bin/R: line 271: /usr/lib/R/bin/exec/R: Permission denied

/usr/bin/R: line 271: /usr/lib/R/bin/exec/R: No error

 exit: 126

  err: /usr/bin/R: line 271: /usr/lib/R/bin/exec/R: Permission denied

/usr/bin/R: line 271: /usr/lib/R/bin/exec/R: No error

[Bobby Read]

Hi Ben,

Just an update...it turns out I had the wrong version of R installed! All is fixed now and working perfectly!

[Benjamin Redelings]

Great!  Its good to have these kinds of problems/solutions available on the mailing list archives.

-BenRI

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