[maker-devel] [EXTERNAL] Troubleshooting Maker failure

Wed Sep 22 10:21:29 MDT 2021

I’d have to see the GFF, but in general you should organize sequence alignments as match/match_part features.

Here is n example from the GFF3 format specification:

ctg123 . cDNA_match  1200  9000  .        .  .    ID=cDNA00001
ctg123 . match_part  1200  3200  2.2e-30  +  .    ID=match00002;Parent=cDNA00001;Target=mjm1123.5 5 506;Gap=M301 D1499 M201
ctg123 . match_part  7000  9000  7.4e-32  -  .    ID=match00003;Parent=cDNA00001;Target=mjm1123.3 1 502;Gap=M101 D1499 M401

Also make sure you are not inadvertently using GFF2 or GTF. They are not backwards compatible with GFF3.

—Carson

> On Sep 22, 2021, at 8:06 AM, Kevin Kocot <kmkocot at ua.edu> wrote:
> 
> Thanks Carson,
> 
> I think I see the problem now. Here's what I'm getting:
> 
> -----
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> A data structure will be created for you at:
> /home/wirenia/Desktop/2021-08-11_MAKER_Dreissena_rostriformis/PGA_assembly_shortened_headers.fasta.maker.output/PGA_assembly_shortened_headers.fasta_datastore
> 
> To access files for individual sequences use the datastore index:
> /home/wirenia/Desktop/2021-08-11_MAKER_Dreissena_rostriformis/PGA_assembly_shortened_headers.fasta.maker.output/PGA_assembly_shortened_headers.fasta_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> #---------------------------------------------------------------------
> Now retrying the contig!!
> SeqID: PGA_scaffold0
> Length: 141759199
> Tries: 5!!
> #---------------------------------------------------------------------
> 
> 
> setting up GFF3 output and fasta chunks
> prepare section files
> Gathering GFF3 input into hits - chunk:0
> ERROR: Non-unique top level ID for match.19561.56
> While this is technically legal in GFF3, it usually
> indicates a poorly fomatted GFF3 file (perhaps you
> tried to merge two GFF3 files without accounting for
> unique IDs).  MAKER will not handle these correctly.
> 
> --> rank=NA, hostname=wirenia
> ERROR: Failed while prepare section files
> ERROR: Chunk failed at level:12, tier_type:3
> FAILED CONTIG:PGA_scaffold0
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:PGA_scaffold0
> 
> examining contents of the fasta file and run log
> -----
> 
> It looks like maker doesn't like the format of the exonerate gff3 I am using. I tried 'fixing' it with agat_convert_sp_gxf2gxf.pl, which seemed to work on my Braker output, but that just produced an empty gff3 file for both my exonerate and PASA gff3 files. Any advice on how to prepare exonerate or PASA gff3 files for Maker?
> 
> Thanks!
> Kevin
> From: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Sent: Monday, September 20, 2021 8:06 AM
> To: Kevin Kocot <kmkocot at ua.edu <mailto:kmkocot at ua.edu>>
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure
>  
> Hi Kevin,
> 
> The files are already being skipped because of previous failures. Can you increase the try count (-t on the command line) to something like 6, and send me the STDERR after it generates a new failure.
> 
> —Carson 
> 
> Sent from my iPhone
> 
>> On Sep 20, 2021, at 4:56 AM, Kevin Kocot <kmkocot at ua.edu <mailto:kmkocot at ua.edu>> wrote:
>> 
>> 
>> Thanks Carson! I've uploaded that file here:
>> http://genomes.ua.edu/Kocot/2021-09-10_Maker/round1_run_maker_try2.log <http://genomes.ua.edu/Kocot/2021-09-10_Maker/round1_run_maker_try2.log>
>> 
>> 
>> From: Carson Holt
>> Sent: Tuesday, September 14, 2021 9:51 PM
>> To: Kevin Kocot
>> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>> Subject: [EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure
>> 
>> What I really need is the captured STDERR from the failed run.
>> 
>> —Carson
>> 
>>> On Sep 10, 2021, at 9:19 AM, Kevin Kocot <kmkocot at ua.edu <mailto:kmkocot at ua.edu>> wrote:
>>> 
>>> Hi Carson and all,
>>>  
>>> I ran Maker 3.01.03 on a chromosome-level mollusc genome assembly using some evidence I previously generated with Funannotate and BRAKER2, but Maker is not completing successfully. Every scaffold in the datastore_index.log file has both STARTED and FAILED statuses. I can't figure out where the problem lies, though. Running ./Build status indicates all the dependencies are there (I’m not using MPI). The run.log files just ends with "DIED RANK 0" and "DIED COUNT 3." Is there a way to tell which (if any) of the dependencies is misbehaving here (they all seem to run fine independently) or if my evidence .gff3 files are not correctly formatted?
>>>  
>>> I’ve uploaded a zipped sample output folder as well as my config files and the datastore.log file here: http://genomes.ua.edu/Kocot/2021-09-10_Maker/ <http://genomes.ua.edu/Kocot/2021-09-10_Maker/>
>>>  
>>> Any guidance on what might be the issue would be greatly appreciated.
>>>  
>>> Thanks!
>>> Kevin
>>>  
>>> Kevin M. Kocot
>>> he/him/his
>>> Associate Professor & Curator of Invertebrates
>>> Department of Biological Sciences & Alabama Museum of Natural History
>>> The University of Alabama <https://www.ua.edu/> 
>>> 307 Mary Harmon Bryant Hall
>>> Box 870344
>>> Tuscaloosa, AL 35487
>>> phone 205-348-4052 <tel:205-348-4052> | fax 205-348-4039 
>>> kmkocot at ua.edu <mailto:kmkocot at ua.edu> | www.kocotlab.com <https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kocotlab.com%2F&data=04%7C01%7Ckmkocot%40ua.edu%7C076240cd4e344ea3edca08d97c377b07%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637677400014541339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ZaHL3%2FTQBgdYkf6B7N%2FUKwrwOObDQk%2Fh5O4sd%2FTkAoQ%3D&reserved=0>
>>> https://uasystem.zoom.us/j/3755490727 <https://uasystem.zoom.us/j/3755490727>
>>>  
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