Problem running PHLAWD, segmentation fault

[Shing]

Dear Stephen,

Thank you for developing this useful method and tool.

I have been trying to learn to use this tool, but I am running into
several bugs.

I think I have successfully created a database using the load_database
python script, since I didn't notice runtime errors.
> python load_database plants pln T

Then, I think I successfully compiled PHLAWD under ./src/.
cd ./src/
mv Makefile.old Makefile # I used the *.old version of the Makefile. I
am using Ubuntu Linux. Please let me know if I should be using this
version.
make clean
make

Without halting and without producing noticeable compilation errors,
PHLAWD was built under ./src/. Then summoning PHLAWD outputs help to
terminal without error:
./PHLAWD

All seems to be well until I actually tried to use PHLAWD.
cd ../
./src/PHLAWD assemble ./example/rbcL.phlawd

Output to terminal:
using sqlite
assembly
number of threads: 1
clade name: Asteraceae
search: rbcL
gene name: rbcL
mad cutoff: 0.0007
coverage: 0.4
identity: 0.2
removing existing files
search number 1
connected to ./blackrim-phlawd-4a276a3/create_database/plants
Found 0 taxon ids:
Segmentation fault

I am not sure why it is hitting a segmentation fault.

Please let me know what I may be doing wrong.

Thank you very much,
Shing

[Stephen Smith]

Dear Shing,
Happy to help. It appears that you are using the example files
correct? It looks to me as though it could be something with the
connection to the database. Could you send along the output of
ls -l blackrim-phlawd-4a276a3/
and
ls -l blackrim-phlawd-4a276a3/create_database
Thanks
Stephen

[Shing]

Hi Stephen,

Thanks for replying so quickly.

ls -l blackrim-phlawd-4a276a3/

-rw-r--r--+ 1 szhan 1424 Oct 24 16:53 CMakeLists.txt
-rw-r--r--+ 1 szhan 18092 Oct 24 16:53 COPYING
drwxr-xr-x+ 2 szhan 77 Jan 9 02:57 create_database
drwxr-xr-x+ 9 szhan 9 Jan 8 18:02 deps
-rw-rw----+ 1 szhan 1298 Jan 8 18:07 EDNAFULL
drwxr-xr-x+ 2 szhan 5 Jan 9 03:08 examples
-rw-r--r--+ 1 szhan 206 Oct 24 16:53 FEATURES_TO_ADD
drwxr-xr-x+ 2 szhan 8 Oct 24 16:53 PHLAWDGU
-rwxr-xr-x+ 1 szhan 19369390 Oct 24 16:53 PHLAWD.LINUX
-rw-r--r--+ 1 szhan 72 Oct 24 16:53 README
drwxr-xr-x+ 2 szhan 7 Oct 24 16:53 release
drwxr-xr-x+ 3 szhan 98 Jan 9 02:55 src
drwxrwx--- 2 szhan 2 Jan 9 03:08 TEMPFILES

ls -l blackrim-phlawd-4a276a3/create_database/

-rw-r-----+ 1 szhan 9420786 Jan 8 16:20 citations.dmp
-rw-r-----+ 1 szhan 2288041 Jan 8 16:20 delnodes.dmp
-rw-r-----+ 1 szhan 419 Jan 8 16:20 division.dmp
-rw-r--r--+ 1 szhan 1772 Oct 24 16:53 enter_names_dmp_pysqlite
-rw-rw----+ 1 szhan 212 Jan 8 17:28 err.txt
-rw-r-----+ 1 szhan 0 Jan 9 02:57 gbpln
-rw-rw----+ 1 szhan 250000036 Dec 17 22:55 gbpln10.seq
-rw-rw----+ 1 szhan 249995940 Dec 17 22:55 gbpln11.seq
-rw-rw----+ 1 szhan 249894997 Dec 17 22:55 gbpln12.seq
-rw-rw----+ 1 szhan 214538339 Dec 17 22:55 gbpln13.seq
-rw-rw----+ 1 szhan 249998215 Dec 17 22:55 gbpln14.seq
-rw-rw----+ 1 szhan 249985349 Dec 17 22:55 gbpln15.seq
-rw-rw----+ 1 szhan 249996352 Dec 17 22:55 gbpln16.seq
-rw-rw----+ 1 szhan 249429028 Dec 17 22:55 gbpln17.seq
-rw-rw----+ 1 szhan 249983070 Dec 17 22:55 gbpln18.seq
-rw-rw----+ 1 szhan 249606536 Dec 17 22:55 gbpln19.seq
-rw-rw----+ 1 szhan 249997909 Dec 17 22:55 gbpln1.seq
-rw-rw----+ 1 szhan 249999605 Dec 17 22:55 gbpln20.seq
-rw-rw----+ 1 szhan 33446710 Dec 17 22:55 gbpln21.seq
-rw-rw----+ 1 szhan 249999308 Dec 17 22:55 gbpln22.seq
-rw-rw----+ 1 szhan 97584419 Dec 17 22:55 gbpln23.seq
-rw-rw----+ 1 szhan 249999270 Dec 17 22:55 gbpln24.seq
-rw-rw----+ 1 szhan 249998346 Dec 17 22:55 gbpln25.seq
-rw-rw----+ 1 szhan 249390857 Dec 17 22:55 gbpln26.seq
-rw-rw----+ 1 szhan 221100868 Dec 17 22:55 gbpln27.seq
-rw-rw----+ 1 szhan 247981553 Dec 17 22:55 gbpln28.seq
-rw-rw----+ 1 szhan 249923572 Dec 17 22:55 gbpln29.seq
-rw-rw----+ 1 szhan 249853654 Dec 17 22:55 gbpln2.seq
-rw-rw----+ 1 szhan 249856103 Dec 17 22:55 gbpln30.seq
-rw-rw----+ 1 szhan 249998570 Dec 17 22:55 gbpln31.seq
-rw-rw----+ 1 szhan 249999030 Dec 17 22:55 gbpln32.seq
-rw-rw----+ 1 szhan 217495983 Dec 17 22:55 gbpln33.seq
-rw-rw----+ 1 szhan 249999653 Dec 17 22:55 gbpln34.seq
-rw-rw----+ 1 szhan 249998807 Dec 17 22:55 gbpln35.seq
-rw-rw----+ 1 szhan 249999225 Dec 17 22:55 gbpln36.seq
-rw-rw----+ 1 szhan 249998322 Dec 17 22:55 gbpln37.seq
-rw-rw----+ 1 szhan 135929383 Dec 17 22:55 gbpln38.seq
-rw-rw----+ 1 szhan 249972413 Dec 17 22:55 gbpln39.seq
-rw-rw----+ 1 szhan 249925094 Dec 17 22:55 gbpln3.seq
-rw-rw----+ 1 szhan 249999846 Dec 17 22:55 gbpln40.seq
-rw-rw----+ 1 szhan 248401991 Dec 17 22:55 gbpln41.seq
-rw-rw----+ 1 szhan 249998841 Dec 17 22:55 gbpln42.seq
-rw-rw----+ 1 szhan 249994533 Dec 17 22:55 gbpln43.seq
-rw-rw----+ 1 szhan 221073128 Dec 17 22:55 gbpln44.seq
-rw-rw----+ 1 szhan 249999800 Dec 17 22:55 gbpln45.seq
-rw-rw----+ 1 szhan 246763278 Dec 17 22:55 gbpln46.seq
-rw-rw----+ 1 szhan 249998557 Dec 17 22:55 gbpln47.seq
-rw-rw----+ 1 szhan 249998324 Dec 17 22:55 gbpln48.seq
-rw-rw----+ 1 szhan 249996347 Dec 17 22:55 gbpln49.seq
-rw-rw----+ 1 szhan 249899590 Dec 17 22:55 gbpln4.seq
-rw-rw----+ 1 szhan 249997469 Dec 17 22:55 gbpln50.seq
-rw-rw----+ 1 szhan 249995929 Dec 17 22:55 gbpln51.seq
-rw-rw----+ 1 szhan 152739715 Dec 17 22:55 gbpln52.seq
-rw-rw----+ 1 szhan 249875917 Dec 17 22:55 gbpln5.seq
-rw-rw----+ 1 szhan 249935469 Dec 17 22:55 gbpln6.seq
-rw-rw----+ 1 szhan 249999166 Dec 17 22:55 gbpln7.seq
-rw-rw----+ 1 szhan 223220687 Dec 17 22:55 gbpln8.seq
-rw-rw----+ 1 szhan 249998292 Dec 17 22:55 gbpln9.seq
-rw-r-----+ 1 szhan 11099 Jan 8 16:20 gc.prt
-rw-r-----+ 1 szhan 3377 Jan 8 16:20 gencode.dmp
-rw-r--r--+ 1 szhan 2647 Jan 8 16:37 load_database
-rw-r--r--+ 1 szhan 1650 Oct 24 16:53 load_gb_file_pysqlite.py
-rw-r-----+ 1 szhan 396018 Jan 8 16:20 merged.dmp
-rw-r--r--+ 1 szhan 1034 Oct 24 16:53
merge_old_names_in_sequences
-rw-r-----+ 1 szhan 69930790 Jan 8 16:20 names.dmp
-rw-r-----+ 1 szhan 57884516 Jan 8 16:20 nodes.dmp
-rw-r-----+ 1 szhan 14336 Jan 8 16:15 plants
-rw-r-----+ 1 szhan 0 Jan 9 02:56 pln
-rw-rw----+ 1 szhan 2652 Jun 13 2006 readme.txt
-rw-r--r--+ 1 szhan 1582 Oct 24 16:53 rebuild_tree_pysqlite
-rw-rw----+ 1 szhan 21108636 Jan 8 16:16 taxdump.tar.gz
-rw-r--r--+ 1 szhan 486 Oct 24 16:53
ungz_send_to_load_all_gb_files
-rw-r--r--+ 1 szhan 488 Oct 24 16:53
ungz_send_to_update_all_gb_files
-rw-r--r--+ 1 szhan 1302 Oct 24 16:53 update_database
-rw-r--r--+ 1 szhan 1867 Oct 24 16:53 update_names_dmp_pysqlite

Please let me know what you think.

Thank you,
Shing

[Stephen Smith]

If plants is the name of the database from running load_database, it
appears as though it didn't successfully load the database. Did you
receive any error messages when you tried to run that?
Stephen

[Shing]

Hi Stephen,

I re-ran load_database, and I am quite certain that the database was
properly. I got further this time.
And then I ran ./src/PHLAWD assemble examples/rbcL.phlawd.

using sqlite
assembly
number of threads: 1

clade name: Gunnera

search: rbcL
gene name: rbcL

mad cutoff: 0.007

coverage: 0.4
identity: 0.2
removing existing files

search number 67391
connected to /projects/bin//blackrim-phlawd-4a276a3/create_database/
plants.db
Found 1 taxon ids:
24956
Will be using 24956
first: 34
blasted: 0
dups: 0
leftovers: 0
picking where leftovers should go
removing existing files
getting file names
getting file names
Segmentation fault

It seems to be doing fine until it is retrieving file names (GenBank
files?). I am not sure what is causing the segmentation fault.

Please let me know when you think.

Thanks,
Shing

On Jan 10, 10:40 am, Stephen Smith <black...@gmail.com> wrote:
> If plants is the name of the database from running load_database, it
> appears as though it didn't successfully load the database. Did you
> receive any error messages when you tried to run that?
> Stephen
>

[Stephen Smith]

Hi Shing,
Do you have a line in the rbcL.phlawd file that looks like
knownfile = rbcL.keep
?

Stephen

[Miao Sun]

Hi,

Is this problem solved?

I have the same story:

assembly

number of threads: 4

clade name: rosids

search: (description LIKE '%ITS%' OR description LIKE '%internal%' OR description LIKE '%5.8S%') AND NOT (description LIKE '%18S%' OR description LIKE '%26S%')

gene name: ITS

gene database: ITS.db

mad cutoff: 0.01

coverage: 0.2

identity: 0.2

connected to ITS.db

database created

search number 298979

connected to /scratch/lfs/cactus/Script/pln.db

Found 1 taxon ids:

71275

Will be using 71275

first: 41895

Starting cover/ident calculations

Segmentation fault

Any advice will be insightful!

Thanks!

Miao

在 2012年1月8日星期日 UTC-5下午8:48:54，Shing写道：

[Cody Hinchliff]

Usually that means you have errors (like indels) in your reference (a.k.a. 'keep') sequences

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[cactusre...@gmail.com]

Thanks Cody!

I downloaded the reference from NCBI. Would you please send me a example of ITS as reference?

Gratitude!

Miao

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