abyss-pe:370: recipe for target 'XX.fa' failed on de novo assembly

[etarisal]

Hello!

I am running transAbyss for a de novo assembly using the following script

/home/tefa/Programs/transabyss-1.5.5/transabyss --SS --kmer 32 --pe /home/tefa/Data_CGE/ISAV/Rinonbasal_S1_L001_R1_001.fastq.gz /home/tefa/Data_CGE/ISAV/Rinonbasal_S1_L001
_R2_001.fastq.gz --outdir /home/tefa/APA/ISA/KLEAT/k32 --name HK-Basal --threads 2

However, the assemblies are failing and I am getting the following error:
---
Trans-ABySS 1.5.5
CMD: /home/tefa/Programs/transabyss-1.5.5/transabyss --SS --kmer 32 --pe /home/tefa/Data_CGE/ISAV/Rinonbasal_S1_L001_R1_001.fastq.gz /home/tefa/Data_CGE/ISAV/Rinonbasal_S1_L001
_R2_001.fastq.gz --outdir /home/tefa/APA/ISA/KLEAT/k32 --name HK-Basal --threads 2
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Found Trans-ABySS directory at: /home/tefa/Programs/transabyss-1.5.5
Found Trans-ABySS `bin` directory at: /home/tefa/Programs/transabyss-1.5.5/bin
Found script at: /home/tefa/Programs/transabyss-1.5.5/bin/skip_psl_self.awk
Found script at: /home/tefa/Programs/transabyss-1.5.5/bin/skip_psl_self_ss.awk
Found `blat' at /home/tefa/Programs/blat
Found `MergeContigs' at /usr/local/bin/MergeContigs
Found `abyss-filtergraph' at /usr/local/bin/abyss-filtergraph
Found `abyss-map' at /usr/local/bin/abyss-map
Found `abyss-pe' at /usr/local/bin/abyss-pe
Found `abyss-junction' at /usr/local/bin/abyss-junction
# CPU(s) available:    8
# thread(s) requested:    2
# thread(s) to use:    2
CMD: bash -euo pipefail -c 'abyss-pe --directory=/home/tefa/APA/ISA/KLEAT/k32 k=32 name=HK-Basal E=0 e=2 c=2 j=2 HK-Basal-1.fa HK-Basal-1.adj q=3 SS=--SS se="/home/tefa/Data_CG
E/ISAV/Rinonbasal_S1_L001_R1_001.fastq.gz /home/tefa/Data_CGE/ISAV/Rinonbasal_S1_L001_R2_001.fastq.gz"'
make: Entering directory '/home/tefa/APA/ISA/KLEAT/k32'
ABYSS -k32 -q3 -e2 -E0 -c2  --SS --coverage-hist=coverage.hist -s HK-Basal-bubbles.fa  -o HK-Basal-1.fa  /home/tefa/Data_CGE/ISAV/Rinonbasal_S1_L001_R1_001.fastq.gz /home/tefa/
Data_CGE/ISAV/Rinonbasal_S1_L001_R2_001.fastq.gz
ABySS 1.5.2
ABYSS -k32 -q3 -e2 -E0 -c2 --SS --coverage-hist=coverage.hist -s HK-Basal-bubbles.fa -o HK-Basal-1.fa /home/tefa/Data_CGE/ISAV/Rinonbasal_S1_L001_R1_001.fastq.gz /home/tefa/Dat
a_CGE/ISAV/Rinonbasal_S1_L001_R2_001.fastq.gz
Reading `/home/tefa/Data_CGE/ISAV/Rinonbasal_S1_L001_R1_001.fastq.gz'...
Reading `/home/tefa/Data_CGE/ISAV/Rinonbasal_S1_L001_R2_001.fastq.gz'...
/usr/local/bin/abyss-pe:370: recipe for target 'HK-Basal-1.fa' failed
make: Leaving directory '/home/tefa/APA/ISA/KLEAT/k32'
Elapsed time: 0 h 58 m 40 s
ERROR: CMD ended with status code 2
------

I don't know what to do and I will be very grateful if somebody can help me with this error.

Thanks,

Etarisal

[Ka Ming Nip]

Hi Etarisal,

Are you using ABySS 1.5.X?
And, did Trans-ABySS ever work on the sample data?

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of etarisal [etar...@gmail.com]
Sent: January 6, 2017 12:00 PM
To: Trans-ABySS
Subject: abyss-pe:370: recipe for target 'XX.fa' failed on de novo assembly

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[etarisal]

Hi Ming,

I am using ABySS 1.5.2. After a time, I succeed to run Trans-Abyss on a subset of my data (2M paired-end reads of 180nu).
However, now running the full set (14M) I got the same error.
I guess the problem is about memory, my computer has only 16G and the program uses more than 90%.
What do you think?
Is there any other solution?

Cheers,
Etarisal

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[Ka Ming Nip]

Hi Etarisal,

1. If you haven't done so already, you should consider removing lower quality bases in your reads using the `-Q` option, ie.

trans-abyss -Q 5 --SS --kmer 32 ...

2. You also can lower the memory usage by recompiling ABySS and set its max kmer size to 32, ie.

./configure --enable-maxk=32
make

In this case, you cannot use kmers size larger than 32 anymore.

Hope that helps!

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of etarisal [etar...@gmail.com]

Sent: February 1, 2017 10:20 AM
To: Trans-ABySS
Subject: Re: abyss-pe:370: recipe for target 'XX.fa' failed on de novo assembly

Hi Ming,

I am using ABySS 1.5.2. After a time, I succeed to run Trans-Abyss on a subset of my data (2M paired-end reads of 180nu).
However, now running the full set (14M) I got the same error.
I guess the problem is about memory, my computer has only 16G and the program uses more than 90%.
What do you think?
Is there any other solution?

Cheers,
Etarisal

On Friday, 6 January 2017 17:21:59 UTC-3, Ka Ming Nip wrote:
Hi Etarisal,

Are you using ABySS 1.5.X?
And, did Trans-ABySS ever work on the sample data?

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________

From: trans...@googlegroups.com<javascript:> [trans...@googlegroups.com<javascript:>] On Behalf Of etarisal [etar...@gmail.com<javascript:>]

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