Species File Failing in MAKER

Discussions about training AUGUSTUS from various sources of evidence. Not discussed here: BRAKER1 and WebAUGUSTUS!

Moderator: bioinf

Post Reply
hhayleyj
Posts: 1
Joined: Wed Mar 24, 2021 5:57 pm

Species File Failing in MAKER

Post by hhayleyj »

I am trying to use Augustus inside of MAKER with a species folder that I generated using BUSCO. I am using the same workflow on two separate species and am hitting the same error in both cases. I contacted MAKER about it, and it was determined that the most likely problem is that there is an issue with the files in the species folder. Here is a summary of what I have done so far:

Ran BUSCO:
python /home/ec2-user/busco/scripts/run_BUSCO.py -i example.fasta -o example -l /home/ec2-user/eukaryota_odb9/ -m geno -c 1 --long -sp example

I then copied the species file produced by this run onto the compute instance I was using for MAKER. When I try to run MAKER (in this case, on a single scaffold to produce the error), I get this error:

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!!!



The MAKER team tried a run on a random fasta file using the species folder I shared with them and produced this error:


$ augustus --species=BUSCO_hemistictus_3028031324 test.fa

# This output was generated with AUGUSTUS (version 3.3.1).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /uufs/chpc.utah.edu/common/PE/proj_UCGD/apps/redwood.bridges/augustus/3.3.1/config/ ...
# BUSCO_hemistictus_3028031324 version. Using default transition matrix.

augustus: ERROR
Invalid nucleotide '�' encountered.


Have you seen this before? Any guesses what might have happened? I am happy to provide more information about the run or the files involved if helpful.

Thanks!
mehlan
Site Admin
Posts: 5
Joined: Mon Oct 14, 2019 2:24 pm

Re: Species File Failing in MAKER

Post by mehlan »

The line
Invalid nucleotide '�' encountered.
may show that not all input files are in ASCII format.
Please check this for all input files.
For example for the files in the species folder use:

Code: Select all

$ find species -type f -print0 | xargs -0 file 
Post Reply