pxrmt Segmentation fault with multiple OGs, and failed to redirect via pipe issues

[Cactusolo]

I have two issues with pxrmt function:

1. When outgroup more than one, then raising "Segmentation fault (core dumped)"

   [cactus]$ pxrmt -t tmp.tre -n 4400,63358,63359,63360 -o test.tre
   Segmentation fault (core dumped)

2. Output to a file failed and always STOUT

   [cactus]$ pxrr -t RAxML_bipartitions.Zygophyllales_2run -g 690755,690812,690814,690816,690824 || pxrmt -n 690755,690812,690814,690816,690824 -o test.tre
   ((690755:0.0309192250234428,(690812:0.0158617919125023,.....);

   The tree file was print to terminal screen and out file "test.tre" is empty. and I also tried with redirect >test.tre also empty.

Please help and me know if you need a test data. Not sure, if I need to update to the recent version, current is v1.1.0.

Thanks!

Miao

[josephwb]

Sorry for the trouble. That version is a bit old (latest release is v1.2.1, and the master branch is v1.3). So please try upgrading. If it still fails, please provide input that we can troubleshoot.

[Cactusolo]

@josephwb it resolved after upgrade to v.1.3. Many thanks!

One small comment that, I found that the tip names in the output tree file containing single quote [ ' ], which may cause problem for downstream tip manipulation. For example, it won't work for relabel the tips, unless I remove all the single quote [don't have this my original tree file], or providing correspond name mapping file with tips in single quote.

[josephwb]

Hrm could you please provide an example (input, output, and example of a problematic label)? Quotes are only ever introduced if a label contains a newick-illegal character. But such labels should (almost) always have 2 quotes.

[Cactusolo]

Hrm could you please provide an example (input, output, and example of a problematic label)? Quotes are only ever introduced if a label contains a newick-illegal character. But such labels should (almost) always have 2 quotes.

# original tree
[cactus@test]$ cat test.tre
(454434-az:0.00225757676750129024,((4288:0.00095317223035216254,1197917:0.00000100000050002909):0.08510136778879195951,454421-az:0.00608116695325890220):0.00528080745550952267,454597-az:0.00112679728728448366):0.0;

# stdout output
[cactus@test]$ pxrr -t test.tre  -g 1197917,4288
((4288:0.0009531722303522,1197917:0.0000010000005):0.042550683894396,('454421-az':0.0060811669532589,('454434-az':0.0022575767675013,'454597-az':0.0011267972872845):0.0052808074555095):0.042550683894396);

# output to a `test_out.tre` file
[cactus@test]$ pxrr -t RAxML_bestTree.Vahliales_2run  -g 1197917,4288 -o test_out.tre

# single quote remains
[cactus@test]$ cat test_out.tre
((4288:0.0009531722303522,1197917:0.0000010000005):0.042550683894396,('454421-az':0.0060811669532589,('454434-az':0.0022575767675013,'454597-az':0.0011267972872845):0.0052808074555095):0.042550683894396);

#original tips
[cactus@test]$ pxlstr -t test.tre -i
1197917
4288
454421-az
454434-az
454597-az

[josephwb]

Thanks for that. ATM we are quoting any label that contains a non-compliant Nexus character. - happens to be illegal for Nexus, but not for newick. I see your point about matching labels downstream. I will figure out how to handle things more accurately.

[josephwb]

@Cactusolo Ok things should work for you now. I may take out the compliancy-quoting, since almost no users will be aware of which characters are illegal.

FWIW:

nexus_illegal = ()[]{}/\,;:=*'"`+-<>
newick_illegal = ()[]\':;,