de novo assembly

[hakattack]

Hi everyone;

I have pair-end reads (length 26 bases) Illumina fastq files and I want to perform de novo assembly. I have installed ABYss within my local Galaxy instance.... Now I have two questions:

1. When I ran it from within Galaxy I get Errors and here is the error message
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ABYSS -k15 -q3 --coverage-hist=coverage.hist -s abyss-bubbles.fa -o abyss-1.fa /usr/local/galaxy/galaxy-dist/database/files/001/dataset_1857.dat /usr/local/galaxy/galaxy-dist/database/files/001/dataset_1858.dat
ABySS 1.3.5
ABYSS -k15 -q3 --coverage-hist=coverage.hist -s abyss-bubbles.fa -o abyss-1.fa /usr/local/galaxy/galaxy-dist/database/files/001/dataset_1857.dat /usr/local/galaxy/galaxy-dist/database/files/001/dataset_1858.dat
Reading `/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1857.dat'...
Reading `/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1858.dat'...
Loaded 522031 k-mer
Minimum k-mer coverage is 20
Using a coverage threshold of 7...
The median k-mer coverage is 45
The reconstruction is 31830
The k-mer coverage threshold is 6.7082
Setting parameter e (erode) to 7
Setting parameter E (erodeStrand) to 1
Setting parameter c (coverage) to 6.7082
Generating adjacency
Added 1152045 edges.
Eroding tips
Eroded 395857 tips.
Eroded 0 tips.
Pruning tips shorter than 1 bp...
Pruned 11 k-mer in 11 tips.
Pruning tips shorter than 2 bp...
Pruned 6 k-mer in 3 tips.
Pruning tips shorter than 4 bp...
Pruning tips shorter than 8 bp...
Pruned 10 k-mer in 2 tips.
Pruning tips shorter than 15 bp...
Pruned 16 tips in 4 rounds.
Marked 102639 edges of 40809 ambiguous vertices.
Removing low-coverage contigs (mean k-mer coverage < 6.7082)
Found 126130 k-mer in 38312 contigs before removing low-coverage contigs.
Removed 95234 k-mer in 19172 low-coverage contigs.
Split 38343 ambigiuous branches.
Eroding tips
Eroded 715 tips.
Eroded 0 tips.
Pruning tips shorter than 1 bp...
Pruned 54 k-mer in 54 tips.
Pruning tips shorter than 2 bp...
Pruned 28 k-mer in 19 tips.
Pruning tips shorter than 4 bp...
Pruned 69 k-mer in 23 tips.
Pruning tips shorter than 8 bp...
Pruned 67 k-mer in 12 tips.
Pruning tips shorter than 15 bp...
Pruned 110 k-mer in 11 tips.
Pruning tips shorter than 15 bp...
Pruned 119 tips in 5 rounds.
Popping bubbles
Removed 4 bubbles.
Removed 4 bubbles
Marked 18979 edges of 4979 ambiguous vertices.
Left 18 unassembled k-mer in circular contigs.
Assembled 29791 k-mer in 2867 contigs.
Removed 492161 k-mer.
The signal-to-noise ratio (SNR) is -12.1687 dB.
AdjList -k15 -m50 abyss-1.fa >abyss-1.adj
abyss-filtergraph -k15 -g abyss-2.adj abyss-1.adj >abyss-1.path
PopBubbles -j2 -k15 -p0.9 -g abyss-3.adj abyss-1.fa abyss-2.adj >abyss-2.path
MergeContigs -k15 -o abyss-3.fa abyss-1.fa abyss-2.adj abyss-2.path
awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \
abyss-2.path abyss-1.fa >abyss-indel.fa
ln -sf abyss-3.fa abyss-unitigs.fa
abyss-map -j2 -l15 /usr/local/galaxy/galaxy-dist/database/files/001/dataset_1857.dat /usr/local/galaxy/galaxy-dist/database/files/001/dataset_1858.dat abyss-3.fa \
|abyss-fixmate -l15 -h abyss-3.hist \
|sort -snk3 -k4 \
|DistanceEst -j2 -k15 -l15 -s200 -n10 -o abyss-3.dist abyss-3.hist
ABORTING

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If I copy and paste this command and run it from the command line i get no such message....and all output including contig file get generated even though, it seems none of these contigs map to my reference sequence but that is different question.

2. Is there better tool than this? I tried MIRA but got some issues with it but I am thinking of PHRAP too.

Can someone help me with this?

Regards,


Does anyone knows why I am getting an error when I try to use