[maker-devel] Ask for help about the collapse of Maker (version 2.31.9) when annotated with Fgenesh

[史俊鹏]

Dear Carson,

First of all, I must apologize that I could't post my questions in Google group since I can't get access to Google in mainland China.

I am using Maker (version 2.31.9) to annotate several foxtail millet genomes. I combined Augustus and Fgenesh (v.3.1.1) for the de novo annotation of these genomes.

The majority of contigs were anotated well with maker pipeline. While, several contigs failed when annotated with Fgenesh with the following error information:

#--------- command -------------#
Widget::fgenesh:
/NAS7/home/shijunpeng/software/maker/bin/../lib/Widget/fgenesh/fgenesh_wrap /NAS7/home/shijunpeng/software/fgenesh/fgenesh /NAS7/home/shijunpeng/software/fgenesh/Monocots /tmp/43438.1.all.q/maker_8zLUxB/0/108_0.4597215-4597401.Monocots.auto_annotator.fgenesh.fasta -exon_table:/tmp/43438.1.all.q/maker_8zLUxB/0/108_0.4597215-4597401.Monocots.auto_annotator.xdef.fgenesh > /tmp/43438.1.all.q/maker_8zLUxB/0/108_0.4597215-
#-------------------------------#
ERROR: FgenesH failed
--> rank=NA, hostname=bioinfor3.local
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:scaffold_1

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:scaffold_1
###############################################################################################################################################

A system core file generated after this collapse. I checked the temperate fasta file 108_0.4597215-4597401.Monocots.auto_annotator.fgenesh.fasta to be normal about ~300 bp.

I also checked my original sequence file and confirmed no problem (A,T,C,G and N). I also tried to set the pred_flank option from 200 (original) to 0 and the error still exists.

I ran the Maker pipeline in a single node with 16 processors and 256 Gb RAMs, so it may be not due to the MPI problems.

Below were my detailed maker bahavior options:
#-----MAKER Behavior Options
max_dna_len=300000 #length for dividing up contigs into chunks (increases/decreases memory usage)
min_contig=10000 #skip genome contigs below this length (under 10kb are often useless)

pred_flank=0 #flank for extending evidence clusters sent to gene predictors
pred_stats=1 #report AED and QI statistics for all predictions as well as models
AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)
min_protein=0 #require at least this many amino acids in predicted proteins
alt_splice=1 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no
always_complete=1 #extra steps to force start and stop codons, 1 = yes, 0 = no
map_forward=1 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no
keep_preds=0 #Concordance threshold to add unsupported gene prediction (bound by 0 and 1)

split_hit=10000 #length for the splitting of hits (expected max intron size for evidence alignments)
single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no
single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'
correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes

tries=5 #number of times to try a contig if there is a failure for some reason
clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0 = no
clean_up=0 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no
TMP= #specify a directory other than the system default temporary directory for temporary files 

Could you please help me to solve this error? I am looking forward to hearing from you.

Sincerely, 
Junpeng

--
Junpeng Shi, PhD
State Key Lab For Agrobiotech, China Agricultural University
National Maize Improvement Center of China 
Center For Life Science, NO.2, 
The West Street of Yuanmingyuan Park, Beijing, P.R.China 
Tel：+86-13581863941