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

Question

[latha.battu24]

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

[Felipe]

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

Answer 1

[Philipp Bayer]

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