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!
Species File Failing in MAKER
Moderator: bioinf
Re: Species File Failing in MAKER
The line
Please check this for all input files.
For example for the files in the species folder use:
may show that not all input files are in ASCII format.Invalid nucleotide '�' encountered.
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