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

[Carson Holt]

It’s failing when given hints. It’s possible there is more detail further back (try running just the failing contig and collecting the entire STDERR to send). Fgenesh is hard for me to test since we don’t have a license to run it anymore. But if it is MAKER that fails, then you would get a more informative error. If it’s FGENESH that fails directly (non-zero exit status), it could kill everything and it all depends on whether they report something useful. Try collecting the full STDERR for the contig first. If that doesn’t work I can help you to collect the files used and command line used so you can run FGENESH all by itself (outside of MAEKR) and send a test dataset to the developers if necessary.

—Carson


> On Jul 14, 2018, at 2:04 AM, 史俊鹏 <shijunpeng at cau.edu.cn> wrote:
> 
> 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