Scaff step crashes because of long gzip command

[sturgman]

Hello,

Just wanted to report an issue we are seeing. We are using soap to assemble a plant genome. When the scaff step begins we get:

********************
Scaff
********************

Parameters: scaff -g lithmul -F scaff: invalid option -- 'K'
-m

Files for scaffold construction are OK.

There are 1 grad(s), 629927998 read(s), max read len 150.
Kmer size: 117
There are 13429809 edge(s) in edge file.
Mask contigs with coverage lower than 2.2 or higher than 44.0, and strict length 0.
Average contig coverage is 22, 3187804 contig(s) masked.
Mask contigs shorter than 119, 524656 contig(s) masked.
17899968 arc(s) loaded, average weight is 10.
6714905 contig(s) loaded.
Done loading updated edges.
Time spent on loading updated edges: 60s.

*****************************************************
Start to load paired-end reads information.

Cannot open lithmul.readOnContig. Now exit to system...

We are running the steps like this:

cd ${rundir}

label=lithmul

${exedir}/SOAPdenovo-127mer sparse_pregraph -s ${rundir}/lithmul.config -K 117 -z 1700000000 -p 23 -o ${label}
${exedir}/SOAPdenovo-127mer contig -g ${label} -R -p 23 -K 117 -z 1700000000
${exedir}/SOAPdenovo-127mer map -s ${rundir}/lithmul.config -g ${label} -p 23 -K 117
${exedir}/SOAPdenovo-127mer scaff  -g ${label} -F -K 117 -z 1700000000

Seems like the gunzip command takes too long to finish leading to soap not being able to find the file it needs. I have uncompressed in advance and seems to work as expected except for a warning that it could not decompress the file.

Thanks for a great tool!