Closed:Issue using IDBA

Question

[Chvatil]

Hi all, I'm actually trying to assemble a lepidopteran genome (around 1.5 GB) using IDBA-1.1.1 So I cleaned my reads and now I need to assemble my genome. To do so I used this script:

#PBS -S /bin/bash
#PBS -l nodes=1:ppn=16,mem=800gb

# sample name
NAME=ACG-006

# location of IDBA
IDBA='/panhome/TOOLS/idba-1.1.1/' 

INPUT1='/pandata/LEPIWASP/ACG-0006_0027/ACG-006/'$NAME
'_reads1.fq'
INPUT2='/pandata/LEPIWASP/ACG-0006_0027/ACG-006/'$NAME
'_reads2.fq'


###################################################################################
#       assemble
###################################################################################


# run the assembly :
echo 'start assembly' $(date)

$IDBA'bin/idba_ud' -o /pandata/LEPIWASP/ACG-0006_0027/OUT-0006-2 -r $INPUT1'.fa' --num_threads 8

echo 'fin assembly' $(date)

But it seems that it did not work because I did not get any scaffold.fa file as expected.

Here is the log content: bguinet@pbil-deb:/pandata/LEPIWASP/ACG-0006_0027/OUT-0006-2$ more log

number of threads 8
reads 21046740
long reads 0
extra reads 0
read_length 150
kmer 60
kmers 450058700 449335558
merge bubble 51236
contigs: 966412 n50: 521 max: 693523 mean: 376 total length: 363412524 n80: 313
aligned 11731380 reads
confirmed bases: 180509710 correct reads: 2498768 bases: 496649
kmer 20
kmers 429156207 438153552
merge bubble 443732
contigs: 6713235 n50: 111 max: 13059 mean: 56 total length: 382339472 n80: 25
aligned 3873790 reads
confirmed bases: 48377200 correct reads: 939944 bases: 7564
distance mean 355.452 sd 88.0153
seed contigs 410168 local contigs 13426470
kmer 40
kmers 458322670 459803899
merge bubble 106856
contigs: 1770325 n50: 523 max: 391240 mean: 231 total length: 409696606 n80: 175
aligned 10450658 reads
confirmed bases: 158884703 correct reads: 2189497 bases: 29331
distance mean 355.566 sd 79.6245
seed contigs 555168 local contigs 3540650
kmer 60
kmers 446139050 446728022
merge bubble 51370
contigs: 983180 n50: 849 max: 509922 mean: 431 total length: 424617018 n80: 347
aligned 13012094 reads
confirmed bases: 201117239 correct reads: 2500093 bases: 19482
distance mean 356.822 sd 78.8531
seed contigs 526752 local contigs 1966360
kmer 80
kmers 432046876 432221736
merge bubble 28985

and here are all the files in my directory :

-rw-r--r-- 1  gei   223643400 Jul 23 08:36 align-20
-rw-r--r-- 1  gei   460410648 Jul 23 10:33 align-40
-rw-r--r-- 1  gei   552622344 Jul 23 12:19 align-60
-rw-r--r-- 1  gei           0 Jul 23 03:09 begin
-rw-r--r-- 1  gei   670838977 Jul 23 08:37 contig-20.fa
-rw-r--r-- 1  gei   485887526 Jul 23 10:34 contig-40.fa
-rw-r--r-- 1  gei   466896404 Jul 23 12:20 contig-60.fa
-rw-r--r-- 1  gei   976575902 Jul 23 06:12 graph-20.fa
-rw-r--r-- 1  gei   629757249 Jul 23 09:48 graph-40.fa
-rw-r--r-- 1  gei   561943552 Jul 23 11:45 graph-60.fa
-rw-r--r-- 1  gei   517678542 Jul 23 13:29 graph-80.fa
-rw-r--r-- 1  gei 16597208120 Jul 23 05:00 kmer
-rw-r--r-- 1 gei   594964775 Jul 23 08:43 local-contig-20.fa
-rw-r--r-- 1  gei   613166508 Jul 23 10:49 local-contig-40.fa
-rw-r--r-- 1  gei   568846077 Jul 23 12:38 local-contig-60.fa
-rw-r--r-- 1  gei        1231 Jul 23 13:27 log

Does someone know where is the issue?

Thks a lot.