Question: Segmentation fault (core dumped) while running Augustus gene finder on Ubuntu
0
gravatar for latha.battu24
10 months ago by
latha.battu240 wrote:

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

ADD COMMENTlink modified 10 months ago by Philipp Bayer6.1k • written 10 months ago by latha.battu240
1
gravatar for Philipp Bayer
10 months ago by
Philipp Bayer6.1k
Australia/Perth/UWA
Philipp Bayer6.1k wrote:

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

ADD COMMENTlink written 10 months ago by Philipp Bayer6.1k
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