Problem with SSCOPE

[ndeshpan]

Hi,

I am using SSCOPE for putting together my contigs, assembled by SOAPdenovo.

The tool looks very promising ..however I am having a very peculiar problem..

My shell script looks like this:
======================

#!/bin/bash
#PBS -q normal
#PBS -l walltime=100:00:00,vmem=10GB
#PBS -j oe
#PBS -l ncpus=16
#PBS -A a07
#PBS -M [email protected]
#PBS -m be
cd "$PBS_O_WORKDIR"
cat ${PBS_NODEFILE} > pbsnodes.txt
ulimit -s unlimited


perl /project/flauro/ndeshpan/fly_March_2011/April_13_2011/assembly/SOAPdenovo/scaffolding/SSPACE-1.1_linux-x86_64/SSPACE_v1-1.pl -u /project/flauro/ndeshpan/fly_March_2011/April_13_2011/assembly/SOAPdenovo/trimmed_files/using_illuminaTrimmer/mate_paired/s_78_sequence.txt.trimmed.singl -l curretn_library.txt -b scaffold3 -p 1 -s /project/flauro/ndeshpan/fly_March_2011/April_13_2011/assembly/SOAPdenovo/raw_files/using_all_3_raws/61/using_bigger_insertSize/insert300/contigs_bigger210bp2_gHeaders.fasta

=================
My library file (curretn_library.txt) contains the follwing details

m7 /project/flauro/ndeshpan/fly_March_2011/April_13_2011/assembly/SOAPdenovo/trimmed_files/using_illuminaTrimmer/mate_paired/s_7_1_sequence.txt.trimmed.paired1 /project/flauro/ndeshpan/fly_March_2011/April_13_2011/assembly/SOAPdenovo/trimmed_files/using_illuminaTrimmer/mate_paired/s_7_1_sequence.txt.trimmed.paired2 5000 0.2 1
m8 /project/flauro/ndeshpan/fly_March_2011/April_13_2011/assembly/SOAPdenovo/trimmed_files/using_illuminaTrimmer/mate_paired/s_8_1_sequence.txt.trimmed.paired1 /project/flauro/ndeshpan/fly_March_2011/April_13_2011/assembly/SOAPdenovo/trimmed_files/using_illuminaTrimmer/mate_paired/s_8_1_sequence.txt.trimmed.paired2 5000 0.2 1
=================================

However the final files/folders created seem to be using only the first library "m7"..this is what my working folder looks like:


S3cfold.sh
-rw-r----- 1 ndeshpan flauro 21692018 May 24 15:28 S3cfold.sh.o148310
drwxr-sr-x 2 ndeshpan flauro 16384 May 24 13:28 bowtieoutput
-rw-r----- 1 ndeshpan flauro 328 May 24 12:19 curretn_library.txt
drwxr-sr-x 3 ndeshpan flauro 16384 May 24 16:34 intermediate_results
drwxr-sr-x 2 ndeshpan flauro 84 May 24 16:26 pairinfo
-rw-r--r-- 1 ndeshpan flauro 128 May 24 12:25 pbsnodes.txt
drwxr-sr-x 2 ndeshpan flauro 100 May 24 14:13 reads
-rw-r--r-- 1 ndeshpan flauro 1397 May 24 15:27 scaffold3.logfile.txt
-rw-r--r-- 1 ndeshpan flauro 1752 May 24 14:45 scaffold3.summaryfile.txt
drwxr-sr-x 2 ndeshpan flauro 54 May 24 14:07 tmp.scaffold3


The intermediate_results folder contains

drwxr-sr-x 3 ndeshpan flauro 16384 May 24 16:34 .
drwxr-sr-x 7 ndeshpan flauro 16384 May 24 17:48 ..
-rw-r--r-- 1 ndeshpan flauro 253 May 24 16:04 formatdb.log
-rw-r--r-- 1 ndeshpan flauro 528218253 May 24 12:43 scaffold3.formattedcontigs.fasta
-rw-r--r-- 1 ndeshpan flauro 118989 May 24 14:45 scaffold3.m7.repeats
-rw-r--r-- 1 ndeshpan flauro 29694740 May 24 15:27 scaffold3.m7.scaffolds
-rw-r--r-- 1 ndeshpan flauro 17874944 May 24 15:27 scaffold3.m7.scaffolds.evidence
-rw-r--r-- 1 ndeshpan flauro 569724928 May 24 15:28 scaffold3.m7.scaffolds.fasta


and does contain scaffolds files ..However I am wondering if I am doing anything wrong for the program to not use m8 library?

Appreciate any replies,

cheers,

Nandan

[boetsie]

Hi ndeshpan,

I think you mean the program SSPACE, not SSCOPE?

Anyway, you might have a look at the scaffold3.logfile.txt and scaffold3.summaryfile.txt. Maybe this indicates that there went something wrong. Because i don't see anything strange in your library file and your parameters.

Boetsie

[ndeshpan]

Thanks Boetsie