Ask for help for running Trans-abyss 1.3.5

[mmcniu]

Dear sir/madam；
I'm trying to locally run Trans-ABySS version_1.3.5. The first time I run the stage 0 separately, the code and the output showed as follow:

<TOPDIR>:/home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST
<INPUT>:/home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1
<ASSEMBLY>:/home/wangsheng/rnaseq/ABYSS_LIB
<LIBRARY>:ABYSS_LIB
<YOUR_PROJECT_NAME>:ABYSS_TEST1

STAGE 0

STEP1：
INPUT:
/home/wangsheng/rnaseq/trans-ABySS-v1.3.5
wrappers/setup.pl /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -make_dir
OUTPUT:
/home/wangsheng/rnaseq/trans-ABySS-v1.3.5
topdir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB; reference: none
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Reads_to_genome
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
ln -s abyss-1.3.5 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/current
ln -s /home/wangsheng/rnaseq/ABYSS_LIB /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/source
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k52
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k54
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k58
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k62
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k64
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge/cluster
chmod a+w /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge/cluster
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/fusions
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/tracks
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/reads_to_contigs
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/novelty
mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/snv


STEP2:
INPUT:
[~/rnaseq/trans-ABySS-v1.3.5]
wangsheng@Venus $ wrappers/setup.pl /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -get_reads
OUTPUT:
/home/wangsheng/rnaseq/trans-ABySS-v1.3.5
topdir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB; reference: none
Reads files are ready.


STEP3:
~/rnaseq/trans-ABySS-v1.3.5/wrappers/setup.pl /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -fem
INPUT:
[~/rnaseq/trans-ABySS-v1.3.5]
wangsheng@Venus $ wrappers/setup.pl /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -fem
OUTPUT:
……
Venus
====================================
library: ABYSS_LIB
kmer size: 52
island size: 151
working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k52
output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k52
output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k52/ABYSS_LIB-contigs.fa
task: Extend junction contigs and indel-bubbles.
====================================
====================================
library: ABYSS_LIB
kmer size: 54
island size: 151
working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k54
output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k54
output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k54/ABYSS_LIB-contigs.fa
task: Extend junction contigs and indel-bubbles.
====================================
====================================
library: ABYSS_LIB
kmer size: 58
island size: 151
working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k58
output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k58
output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k58/ABYSS_LIB-contigs.fa
task: Extend junction contigs and indel-bubbles.
====================================
====================================
library: ABYSS_LIB
kmer size: 62
island size: 151
working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k62
output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k62
output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k62/ABYSS_LIB-contigs.fa
task: Extend junction contigs and indel-bubbles.
====================================
====================================
library: ABYSS_LIB
kmer size: 64
island size: 151
working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k64
output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k64
output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k64/ABYSS_LIB-contigs.fa
task: Extend junction contigs and indel-bubbles.
====================================
====================================
library: ABYSS_LIB
input: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
input type: DIR
working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge
threads: 8
output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge/ABYSS_LIB-contigs.fa
task: Merge both contigs and indel-bubbles.
but when I try to run stage 2 the programme it shows me the following:
INPUT:
/home/wangsheng/rnaseq/trans-ABySS-v1.3.5/wrappers/trans-abyss.sh -i /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -2
OUTPUT:
input: /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1
Option cluster requires an argument
input:/home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1
ABYSS_LIB
sh: 1: source: not found
ERROR: Cannot find contigs fasta file, /home/wangsheng/rnaseq/ABYSS_ABYSS_LIB/TOPDIR_TEST/ABYSS_ABYSS_LIB/Assembly/abyss-1.3.5/merge/ABYSS_ABYSS_LIB-contigs.fa

I think it try to find the contigs fasta file in a wrong path, the correct path should be “/home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge/ABYSS_LIB-contigs.fa” instead of “/home/wangsheng/rnaseq/ABYSS_ABYSS_LIB/TOPDIR_TEST/ABYSS_ABYSS_LIB/Assembly/abyss-1.3.5/merge/ABYSS_ABYSS_LIB-contigs.fa”. I don’t how could it happened and what should I do to correct the path.

Moreover, there is another warning “sh: 1: source: not found” appeared. Would you please tell me what does this warning mean? And does it matter?

I really hope you could help.

Best regards

Wangsheng
2013-08-09