[maker-devel] Maker Error : Thread 1 terminated abnormally..

[André Machado]

Hi ,


First of all thanks for your efforts in Maker pipeline. Its a tremendous
help for the people that works with genomes.

In the last 4 days i have broke my head.. with an error .. but still
without a solution.

I found this old thread:
https://groups.google.com/forum/#!msg/maker-devel/X2-76BH9gvg/rU4kLJ3B6tsJ

Seems to be a quite similar... but don't point to a specific solution.

I have run maker with the data test and all runned ok. Maker finalize the
entire process without errors.

Recently, i’m trying to aplly my own data on MPI cluster. But this error,
frequently occurred.

Thread 1 terminated abnormally:
../dna.maker.output/mpi_blastdb/dna%2Efa.mpi.1/dna%2Efa.mpi.1.0

--> rank=8, hostname=compute-0-1.local, at ../Analysis/Geno/maker/bin/maker
line 1451 thread 1.

--> rank=8, hostname=compute-0-1.local

deleted:0 hits

deleted:0 hits

preparing ab-inits

deleted:0 hits

deleted:0 hits

FATAL: Thread terminated, causing all processes to fail

--> rank=8, hostname=compute-0-1.local

deleted:0 hits


Basically im tring to run a maker with dna.fa, rna.fa, prot.fa and
my_custom_lib_of_repeats.fa, to produce raw genes models which will be used
to train SNAP.


I already used several command lines and all gave me the same error.. The
only change between different tests was the local of the error, sometimes
happened in compute-0-1.local other time in compute-0-4.local or in another
one.

mpiexec -n 63 --hostfile Host maker 1>1.log 2>2.err

mpiexec --hostfile Host maker 1>1.log 2>2.err

mpiexec -mca btl ^openib -n 63 --hostfile Host maker 1>1.log 2>2.err

nohup mpiexec -mca btl ^openib -n 63 --hostfile Host maker -a 1>1.log
2>2.err


The log file as well the option files are provided below.


Many thanks in advance,


André
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20180626/7b74d074/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 2.log
Type: text/x-log
Size: 38655 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20180626/7b74d074/attachment-0002.log>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: maker_exe.ctl
Type: application/octet-stream
Size: 1224 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20180626/7b74d074/attachment-0006.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: maker_opts.ctl
Type: application/octet-stream
Size: 4548 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20180626/7b74d074/attachment-0007.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: maker_bopts.ctl
Type: application/octet-stream
Size: 1413 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20180626/7b74d074/attachment-0008.obj>