nasira
n00b
Joined: 16 Jun 2005
Posts: 32
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 Posted: Tue May 29, 2007 6:13 pm Post subject: emboss (fdnadist) segmentation fault with multiple matricies |
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I have a replicable segmentation fault problem running fdnadist, part of the Emboss molecular biology package.
If I run the following command;
| Quote: | | fneighbor -datafile tinytest.dat -replicates y -outfile filefrom.fnb |
using a tinytest.dat file containing;
| Code: | 3
1187Aquife 0.000000 0.368385 0.404489
BB213b06 0.368385 0.000000 0.151182
BB269b06 0.404489 0.151182 0.000000
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then everything works.
If, however, my tinytest.phy contains two similarity matricies (or, for that matter, the one hundred bootstrap replicates written by fdnadist by default), like this;
| Code: | 3
1187Aquife 0.000000 0.368385 0.404489
BB213b06 0.368385 0.000000 0.151182
BB269b06 0.404489 0.151182 0.000000
3
1187Aquife 0.000000 0.368385 0.404489
BB213b06 0.368385 0.000000 0.151182
BB269b06 0.404489 0.151182 0.000000
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then fdnadist returns;
| Quote: | Phylogenies from distance matrix by N-J or UPGMA method
Segmentation fault
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The fault remains regardless of the "-replicates" setting.
I am not familiar with the Emboss program; I am attempting to translate a Phylip algorhythm. It is possible that I am simply misusing fdnadist by treating it as I did Phylip's dnadist.
This has been cross-posted to the Emboss mailing list ; I'll also cross-post the fix.
Thank you for your time.
UPDATE:
Peter Rice, one of the developers, has been very helpful and this fault is now being fixed. See the EMBOSS list for May 2007 onwards, the thread titled "Segmentation fault with multiple similarity matricies [sic] in fdnadist". I'll post updates/major developments here. |
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