[maker-devel] Running SNAP with MAKER

[Carson Holt]

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
> Homepage: www.paulsheridan.net <http://www.paulsheridan.net/>
> Mobile: +81 80 7889 0859
> <maker_opts2.ctl><run.log><maker_opts1.ctl>_______________________________________________
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