[maker-devel] Running SNAP with MAKER

[Paul Sheridan]

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
Mobile: +81 80 7889 0859
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20190405/f5d53d95/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: maker_opts2.ctl
Type: application/octet-stream
Size: 4728 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20190405/f5d53d95/attachment-0006.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: run.log
Type: application/octet-stream
Size: 2366 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20190405/f5d53d95/attachment-0007.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: maker_opts1.ctl
Type: application/octet-stream
Size: 4515 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20190405/f5d53d95/attachment-0008.obj>