[maker-devel] MAKER Commercial User -- Question

Tue Mar 9 12:17:10 MST 2021

Hi Carson,

Unfortunately, it looks like I am running MPICH version 3.0.4, so that
doesn't explain the problem. I regenerated the error for you:

STATUS: Parsing control files...

STATUS: Processing and indexing input FASTA files...

STATUS: Setting up database for any GFF3 input...

A data structure will be created for you at:

/home/ubuntu/PGScratch/scaff1/scaff0.maker.output/scaff0_datastore

To access files for individual sequences use the datastore index:

/home/ubuntu/PGScratch/scaff1/scaff0.maker.output/scaff0_master_datastore_index.log

STATUS: Now running MAKER...

examining contents of the fasta file and run log

--Next Contig--

Processing run.log file...

MAKER WARNING: The file
scaff0.maker.output/scaff0_datastore/0B/6F/PGA_scaffold0__8_contigs__length_34808196//theVoid.PGA_scaffold0__8_contigs__length_34808196/PGA_scaffold0__8_contigs__length_34808196.abinit_masked.1.BUSCO_hemistictus_3028031324.augustus

did not finish on the last run and must be erased

MAKER WARNING: The file
scaff0.maker.output/scaff0_datastore/0B/6F/PGA_scaffold0__8_contigs__length_34808196//theVoid.PGA_scaffold0__8_contigs__length_34808196/PGA_scaffold0__8_contigs__length_34808196.abinit_masked.0.BUSCO_hemistictus_3028031324.augustus

did not finish on the last run and must be erased

MAKER WARNING: The file
scaff0.maker.output/scaff0_datastore/0B/6F/PGA_scaffold0__8_contigs__length_34808196//theVoid.PGA_scaffold0__8_contigs__length_34808196/PGA_scaffold0__8_contigs__length_34808196.abinit_masked.2.BUSCO_hemistictus_3028031324.augustus

did not finish on the last run and must be erased

#---------------------------------------------------------------------

Now retrying the contig!!

SeqID: PGA_scaffold0__8_contigs__length_34808196

Length: 34808196

Tries: 2!!

#---------------------------------------------------------------------

setting up GFF3 output and fasta chunks

preparing ab-inits

running  augustus.

#--------- command -------------#

Widget::augustus:

/home/ubuntu/PGTools/Augustus/bin/augustus
--species=BUSCO_hemistictus_3028031324 --UTR=off
/tmp/maker_pzUjBq/PGA_scaffold0__8_contigs__length_34808196.abinit_masked.0
>
/tmp/maker_pzUjBq/PGA_scaffold0__8_contigs__length_34808196.abinit_masked.0.BUSCO_hemistictus_3028031324.augustus

#-------------------------------#

/home/ubuntu/PGTools/Augustus/bin/augustus: ERROR

Invalid nucleotide '' encountered.

/home/ubuntu/PGTools/Augustus/bin/augustus: ERROR

Invalid nucleotide '?' encountered.

ERROR: Augustus failed

--> rank=NA, hostname=ip-172-31-14-148

ERROR: Failed while preparing ab-inits

ERROR: Chunk failed at level:0, tier_type:2

FAILED CONTIG:PGA_scaffold0__8_contigs__length_34808196

ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:PGA_scaffold0__8_contigs__length_34808196

examining contents of the fasta file and run log

--Next Contig--

Processing run.log file...

MAKER WARNING: The file
scaff0.maker.output/scaff0_datastore/0B/6F/PGA_scaffold0__8_contigs__length_34808196//theVoid.PGA_scaffold0__8_contigs__length_34808196/PGA_scaffold0__8_contigs__length_34808196.abinit_masked.0.BUSCO_hemistictus_3028031324.augustus

did not finish on the last run and must be erased

Maker is now finished!!!

Start_time: 1615317386

End_time:   1615317388

Elapsed:    2

On Fri, Mar 5, 2021 at 7:41 PM Carson Holt <carsonhh at gmail.com> wrote:

> Hi Hayley,
>
> Which flavor of MPI are you using? OpenMPI, MVAPICH2, MPICH, or Intel
> MPI?  There is a known issue with infiniband network cards that causes them
> to freeze on certain system calls, and I bet that is what you are seeing.
> It is not a MAKER issue, but a limitation in order to allow performance
> benefits elsewhere with MPI.  You need to add extra command line flags to
> tell MPI to communicate a bit differently to get around it. You can find
> multiple threads with more info in the maker-devel archives here —>
> https://groups.google.com/g/maker-devel
>
>
> For OpenMPI you may need to add these flags to the mpiexec command line
> —> --mca btl vader,tcp,self --mca btl_tcp_if_include ib0 --mca
> btl_openib_want_fork_support 1 --mca mpi_warn_on_fork 0
>
> For intel MPI set the environmental variable I_MPI_FABRICS=shm:tcp before
> running mpiexec
>
> For MPICH, no modifications should be needed (it doesn’t experience the
> issue).
>
> For MVAPICH2, there is no work around and you just need to use one of the
> other MPI flavors.
>
>
> For the second failure, if you can regenerate it, send me the STDERR and I
> will take a look.
>
> Thanks,
> Carson
>
>
>
>
> *From:* Hayley Mangelson <hayley at phasegenomics.com>
> *Sent:* Thursday, March 4, 2021 12:03 PM
> *To:* AARON A DUFFY <aaron.duffy at utah.edu>
> *Cc:* Mary Wood <mary at phasegenomics.com>
> *Subject:* MAKER Commercial User -- Question
>
> Hi Aaron,
>
> Mary and I are bioinformaticians at Phase Genomics, and we are using the
> MAKER software (for which Phase purchased a licence) to annotate a couple
> of genomes. We are using the same workflow that I used for a previous
> project, but are having the same issues while working on separate projects.
> I am hoping you could help us out or direct us to someone who can help!
>
> Here is some background. I am trying to get it to run using *mpiexec* for
> parallelization. I let it run for about a week and all processes remained
> “active”, but no new output seemed to be generated. It was hung up on
> “prepare section files” for nearly the whole 1-week period. I canceled the
> run, then tried running again without parallelization (in the same folder
> as the failed run). I got an error about each contig failing, and something
> about Augustus. Unfortunately, I didn’t save the error message. I tried to
> regenerate the error, but it looks like I would probably need to completely
> rerun… this is the error message now (repeated for each contig), if I run
> in the same folder again.
>
>
>
>
>
>
> *The contig failed 2 times!!Maker will not try again!!The contig will be
> stored in a fasta file that you can use for debugging.SeqID:
> PGA_scaffold4__8_contigs__length_31799528Length: 31799528FASTA:
> /home/ubuntu/PGScratch/chunk1/chunk1.maker.output/chunk1_datastore/10/91/PGA_scaffold4__8_contigs__length_31799528//PGA_scaffold4__8_contigs__length_31799528.died.fasta*
>
> Any thoughts about why *mpiexec *seems unable to finish? I tried a run on
> the test data using parallelization, and it completed in under a minute.
>
> Thanks!
>
> Hayley
> --
> Hayley Mangelson
> Bioinformatics Scientist
> Phase Genomics, Inc
>
>
>

-- 
Hayley Mangelson
Bioinformatics Scientist
Phase Genomics, Inc
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