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Segmentation fault (core dumped) while running Augustus gene finder on Ubuntu

Hi am Latha,am running Augustus using plant genome contigs. Though memory and space on my computer are sufficient for running this tool, am getting the below error:-

kulaganathan@kulab:~/busco-master/augustus.2.5.5$ augustus --strand=both --species=rice --maxDNAPieceSize=20000000 sandalnew.fa >output1.gff
replaced tx with 0 MEA txs
replaced tx with 1 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
Segmentation fault (core dumped)
kulaganathan@kulab:~/busco-master/augustus.2.5.5$ augustus --strand=both --species=rice --maxDNAPieceSize=50000000 sandalnewmasked.fa >output1.gff
replaced tx with 1 MEA txs
replaced tx with 1 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
Segmentation fault (core dumped)
kulaganathan@kulab:~/busco-master/augustus.2.5.5$ augustus --strand=both --species=rice  sandalnew.fa >output1.gff
replaced tx with 0 MEA txs
replaced tx with 1 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
replaced tx with 0 MEA txs
Segmentation fault (core dumped)

Can someone help me to solve this....thanku in advance

software error next-gen genome
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updated by Felipe • Felipe • written by latha.battu24 • latha.battu24

Hello, did you manage to solve this problem? the same thing happened to me and couldn't fix it

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written by Felipe • Felipe

1 answer

Things I would try:

  • check whether the input file is broken (use tail to check the end)

  • remove small contigs from the assembly (for example, bioawk -c fastx '{ if(length($seq) > 1000) { print ">"$name; print $seq }}' sandalnew.fa > filtered_sandalnew.fa )

  • recompile augustus via ./configure and make

  • recompile the auxiliary programs in the 'auxprogs' folder (bam2hints etc.) - each one has its own Makefile!

  • install augustus via bioconda, or linuxbrew

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written by Philipp Bayer Philipp Bayer

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