[maker-devel] Running SNAP with MAKER

[Paul Sheridan]

Hi Carson,

Indeed, I did generate the hmm file immediately previously to my second
run. I redid the process by following these commands from the link you
supplied:

mkdir snap
cd snap
gff3_merge -d
/root/tuna-round-2/genome.maker.output/genome_master_datastore_index.log
maker2zff genome.all.gff
fathom -categorize 1000 genome.ann genome.dna
fathom -export 1000 -plus uni.ann uni.dna
forge export.ann export.dna
hmm-assembler.pl genome . > ../genome1.hmm

I didn't find any errors generated by Snap during training. But when I
reran MAKER, I got errors of this variety:

processing all repeats
processing all repeats
error: unknown command
"/root/tuna-round-2/genome.maker.output/genome1.hmm", see 'snap help'
error: unknown command
"/root/tuna-round-2/genome.maker.output/genome1.hmm", see 'snap help'
preparing masked sequence
processing all repeats
collecting blastx repeatmasking
preparing masked sequence
collecting blastx repeatmasking
collecting blastx repeatmasking
processing all repeats
processing all repeats
processing all repeats
processing all repeats
preparing masked sequence
collecting blastx repeatmasking
ERROR: Snap failed
--> rank=21, hostname=localhost
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:scf7180000008536_pilon_pilon

ERROR: Snap failed
--> rank=5, hostname=localhost
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:scf7180000008522_pilon_pilon

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scf7180000008536_pilon_pilon

preparing masked sequence
ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scf7180000008522_pilon_pilon

Do you have any other suggestions?

Thanks in Advance,

Paul

On Sun, Apr 7, 2019 at 6:00 AM Carson Holt <carsonhh at gmail.com> wrote:

> The error is being thrown by snap itself. Perhaps there is an issue with
> the genome.hmm file. Did you generate the file immediately previously to
> this run? Perhaps you can redo that process, and review any errors that
> come up during training.
>
> Some details on training SNAP from the wiki —>
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Training_ab_initio_Gene_Predictors
>
> —Carson
>
>
> On Apr 4, 2019, at 4:46 PM, Paul Sheridan <paul at tupac.bio> wrote:
>
> Dear MAKER Team,
>
> I am running MAKER 2.31.10 a 32 core instance. My first pass completed
> successfully. However, my second pass using SNAP and Augustus trained ab
> initio gene predictions failed. Here is some example output which
> illustrates the problem:
>
> MAKER WARNING: Changes in control files make re-use of all old data
> impossible
> All old files will be erased before continuing
> processing all repeats
> doing repeat masking
> doing repeat masking
> #---------------------------------------------------------------------
> Now starting the contig!!
> SeqID: scf7180000008677_pilon_pilon
> Length: 49996
> #---------------------------------------------------------------------
>
> doing repeat masking
> preparing ab-inits
> running  snap.
> #--------- command -------------#
> Widget::snap:
> /usr/bin/snap
> /root/tuna-round-2/genome.maker.output/snap/round1/genome.hmm
> /tmp/maker_8RuX8Z/scf718
> 0000006915_pilon_pilon.abinit_masked.0 >
> /tmp/maker_8RuX8Z/scf7180000006915_pilon_pilon.abinit_maske
> d.0.genome%2Ehmm.snap
> #-------------------------------#
> setting up GFF3 output and fasta chunks
> processing all repeats
> doing repeat masking
> in cluster::shadow_cluster...
> ...finished clustering.
> error: unknown command
> "/root/tuna-round-2/genome.maker.output/snap/round1/genome.hmm", see 'snap
> help'
> ERROR: Snap failed
> --> rank=21, hostname=localhost
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> FAILED CONTIG:scf7180000007575_pilon_pilon
>
> I confirmed that the path to genome.hmm is correct. In addition, run.log
> contains the following kind of output:
>
> STARTED
> genome.maker.output/genome_datastore/00/6E/scf7180000008677_pilon_pilon//theVoid.scf7180000008677_pilon_pilon/scf7180000008677_pilon_pilon.abinit_m
> asked.0.genome%2Ehmm.snap
> DIED RANK 30:4:0:0
> DIED COUNT 2
> DIED RANK 30
> DIED COUNT 2
>
> How can I resolve this issue?
>
> Also, is the warning about it being impossible to use the old data to be
> expected?
>
> Attached files:
> - maker_otps1.ctl: first pass control file
> - maker_opts2.ctl: second pass control file
> - run.log: log file for an example contig
>
> Thanks in Advance,
>
> Paul Sheridan
>
> --
> CSO at Tupac Bio
> Email: paul at tupac.bio <paul at tupac.bio>
> Homepage: www.paulsheridan.net
> Mobile: +81 80 7889 0859
> <maker_opts2.ctl><run.log><maker_opts1.ctl>
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>
>
>

-- 
CSO at Tupac Bio
Email: paul at tupac.bio
Homepage: www.paulsheridan.net
Mobile: +81 80 7889 0859
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