Using SSPACE: Process 'extend/format contigs' failed when using -x extension option

Question

[freuv]

Hi,

The scaffolder SSPACE fails with the following error when using the contig extension step. Runs fine without extension step.

Process 'extend/format contigs' failed

Any guidance would be much appreciated.

freuv

[graham.etherington]

Could you provide the full command line and errors so that we can see what might be going wrong. Please read the posting guidelines in order to phrase a good question that someone might be able to answer: How To Ask Good Questions On Technical And Scientific Forums

Answer 1

[xunshengbu]

Same issue here.

SSPACE_Standard_v3.0.pl -l libraries.txt -s genome.scf.fasta -x 1 -T 36 -b sspace1 >& log_sspace1.txt &

Required inputs: -l = libraries.txt Number of paired files = 24 -s = genome.scf.fasta -b = sspace1

Optional inputs: -x = 1 -z = 0 -k = 5 -g = 0 -a = 0.7 -n = 15 -T = 36 -p = 0

Contig extension inputs: -o = 20 -m = 32 -r = 0.9

=>Wed May 2 14:59:26 2018: Reading, filtering and converting input sequences of library file initiated

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=>Wed May 2 15:17:06 2018: Extending of contigs with unmapped reads

=>Wed May 2 15:17:06 2018: Building BWA index for contigs [bwt_gen] Finished constructing BWT in 229 iterations.

=>Wed May 2 15:31:21 2018: Mapping reads to contigs with BWA

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Process 'extend/format contigs' failed on Thu May 3 08:38:18 2018