SSPACE_Basic_v2.0.pl bug?

[mxr1895]

Hi,
I've been trying to extend a denovo yeast assembly using SSPACE. Ive got a ~5000 contig de novo assembly (454+illumina data) that I want to scaffold using illumina PE data ( 123708624 reads, 100bp, trimmed to 30bp on one file).

$/SSPACE_Basic_v2.0.pl -l F15.library -s F15_out.padded.fasta -x 1 -T 6 -m 28 -o 15 -k 7 -a 0.5 -n 10


I get an the following error:
=>Fri May 24 14:35:25 2013: Mapping reads to contigs. Reading bowtie output and pairing contigs

=>Fri May 24 14:35:42 2013: Building scaffolds file

=>Fri May 24 14:35:42 2013: Merging contigs and creating fasta file of scaffolds
Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE TCT*CGA*A*GGCATAT*AGTTGAAGTATCTCTATT/ at /home/mron003/Programs/SSPACE-BASIC-2.0_linux-x86_64/SSPACE_Basic_v2.0.pl line 447, <IN> line 68.

Playing around with the input read files I found the following:
-the program runs fine if I subset my input fastq files to <= 4247288 lines
-different sizes of input fastq larger than 4247288 result in the same error type but they differ in the sequence of the error, the SSPACE_Basic_v2.0.pl line #, and the <IN> line #

any help would be much appreciated.
Cheers,

Miguel

Miguel

[bionet]

Just another related question
in the same script I got this message:
for each library cannot stat initial working directory for <Dir> at SSPACE_Basic_v2.0.pl line 303
where <Dir> has the path of the directory I am using.
Any ideas what might be happening? I run SSPACE v2.0 before but haven't encounter this message before.
thx