run_BUSCO.py fails with segmentation fault with -c option

Question

[lakhujanivijay]

Note: I am cross posting this on biostars from here just to get more visibility (I am in a hurry)

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I am working with BUSCO 3.0.2. See below command

## checking the version
[user@node]$ /opt/app/python-2.7.9/bin/python2.7 /opt/app/busco-master/scripts/run_BUSCO.py -v
>BUSCO 3.0.2

Now, I am trying to run following commands (with 30 threads, -c 30) to train augustus and it fails with segmentation fault:

## Running the command
[user@node]$ date && time /opt/app/python-2.7.9/bin/python2.7 /opt/app/busco-master/scripts/run_BUSCO.py -i v.genome_final_assembly_master_datastore_index.maker.transcripts1000.fasta  -o v.genome_final_assembly_maker -l embryophyta_odb9/ -m genome -c 30 --long -sp tomato -z --augustus_parameters='--progress=true'
Sat Jan 27 17:06:19 IST 2018
WARNING An augustus species is mentioned in the config file, dataset default species (arabidopsis) will be ignored
INFO    ****************** Start a BUSCO 3.0.2 analysis, current time: 01/27/2018 17:06:19 ******************
INFO    Configuration loaded from /opt/app/busco-master/scripts/../config/config.ini
INFO    Init tools...
INFO    Check dependencies...
INFO    Check input file...
INFO    To reproduce this run: python /opt/app/busco-master/scripts/run_BUSCO.py -i v.mygenome_final_assembly_master_datastore_index.maker.transcripts1000.fasta -o v.genome_final_assembly_maker -l embryophyta_odb9/ -m genome -c 30 --long -z -sp tomato --augustus_parameters '--progress=true'
INFO    Mode is: genome
INFO    The lineage dataset is: embryophyta_odb9 (eukaryota)
INFO    Temp directory is ./tmp/
INFO    ****** Phase 1 of 2, initial predictions ******
INFO    ****** Step 1/3, current time: 01/27/2018 17:06:20 ******
INFO    Create blast database...
INFO    [makeblastdb]   Building a new DB, current time: 01/27/2018 17:06:20
INFO    [makeblastdb]   New DB name:   ./tmp/v.genome_final_assembly_maker_3973892503
INFO    [makeblastdb]   New DB title:  v.genome_final_assembly_master_datastore_index.maker.transcripts1000.fasta
INFO    [makeblastdb]   Sequence type: Nucleotide
INFO    [makeblastdb]   Keep Linkouts: T
INFO    [makeblastdb]   Keep MBits: T
INFO    [makeblastdb]   Maximum file size: 1000000000B
INFO    [makeblastdb]   Adding sequences from FASTA; added 31324 sequences in 3.41523 seconds.
INFO    [makeblastdb]   1 of 1 task(s) completed at 01/27/2018 17:06:24
INFO    Running tblastn, writing output to /test/v.genome_final_assembly.maker.output/training_augustus/run_v.genome_final_assembly_maker/blast_output/tblastn_v.genome_final_assembly_maker.tsv...
INFO    [tblastn]   1 of 1 task(s) completed at 01/27/2018 17:14:49
INFO    ****** Step 2/3, current time: 01/27/2018 17:14:49 ******
INFO    Maximum number of candidate contig per BUSCO limited to: 3
INFO    Getting coordinates for candidate regions...
INFO    Pre-Augustus scaffold extraction...
INFO    Running Augustus prediction using tomato as species:
INFO    Additional parameters for Augustus are --progress=true: 
INFO    [augustus]  Please find all logs related to Augustus errors here: /test/v.genome_final_assembly.maker.output/training_augustus/run_v.genome_final_assembly_maker/augustus_output/augustus.log
INFO    [augustus]  466 of 2327 task(s) completed at 01/27/2018 17:16:21
INFO    [augustus]  699 of 2327 task(s) completed at 01/27/2018 17:17:02
INFO    [augustus]  931 of 2327 task(s) completed at 01/27/2018 17:17:38
INFO    [augustus]  1164 of 2327 task(s) completed at 01/27/2018 17:18:20
INFO    [augustus]  1397 of 2327 task(s) completed at 01/27/2018 17:19:04
INFO    [augustus]  1629 of 2327 task(s) completed at 01/27/2018 17:19:35
INFO    [augustus]  1862 of 2327 task(s) completed at 01/27/2018 17:20:08
INFO    [augustus]  2095 of 2327 task(s) completed at 01/27/2018 17:20:46
INFO    [augustus]  2327 of 2327 task(s) completed at 01/27/2018 17:21:31
INFO    Extracting predicted proteins...
INFO    ****** Step 3/3, current time: 01/27/2018 17:22:38 ******
INFO    Running HMMER to confirm orthology of predicted proteins:
Segmentation fault (core dumped)

I noticed that when I use more threads, it fails, however, it is working without the -c option. But, then it is very very slow and working for days now.

How can I solve this problem?

[Matteo Schiavinato]

how big is your benchmarking set?