Running SNAP with MAKER

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

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
Mobile: +81 80 7889 0859

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

maker_opts2.ctl (6K) Download Attachment
run.log (3K) Download Attachment
maker_opts1.ctl (6K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: Running SNAP with MAKER

Carson Holt-2
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.


—Carson


On Apr 4, 2019, at 4:46 PM, Paul Sheridan <[hidden email]> 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
Mobile: +81 80 7889 0859
<maker_opts2.ctl><run.log><maker_opts1.ctl>_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: 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 <[hidden email]> 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.


—Carson


On Apr 4, 2019, at 4:46 PM, Paul Sheridan <[hidden email]> 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
Mobile: +81 80 7889 0859
<maker_opts2.ctl><run.log><maker_opts1.ctl>_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



--
CSO at Tupac Bio
Mobile: +81 80 7889 0859

_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org