Error: usr/bin/abyss-pe:473: recipe for target 'transabyss-1.fa' failed

[BlrGenomics]

Hi,
I am using Illumina paired end reads. I have used the following command:

./transabyss --pe /mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq --outdir /mnt/storage/Matured_Fruit/transabyss3 --threads 18

I am getting the following error:

/usr/bin/abyss-pe:473: recipe for target 'transabyss-1.fa' failed

The std output is:

Trans-ABySS 1.5.5
CMD: ./transabyss --pe /mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq --outdir /mnt/storage/Matured_Fruit/transabyss3 --threads 18
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Found Trans-ABySS directory at: /home/bgc/Downloads/transabyss-master
Found Trans-ABySS `bin` directory at: /home/bgc/Downloads/transabyss-master/bin
Found script at: /home/bgc/Downloads/transabyss-master/bin/skip_psl_self.awk
Found script at: /home/bgc/Downloads/transabyss-master/bin/skip_psl_self_ss.awk
Found `blat' at /home/bgc/bin/blat
Found `MergeContigs' at /home/bgc/bin/MergeContigs
Found `abyss-filtergraph' at /home/bgc/bin/abyss-filtergraph
Found `abyss-map' at /home/bgc/bin/abyss-map
Found `abyss-pe' at /usr/bin/abyss-pe
Found `abyss-junction' at /home/bgc/bin/abyss-junction
# CPU(s) available:     56
# thread(s) requested:  18
# thread(s) to use:     18
Creating output directory: /mnt/storage/Matured_Fruit/transabyss3
CMD: bash -euo pipefail -c 'abyss-pe --directory=/mnt/storage/Matured_Fruit/transabyss3 k=32 name=transabyss E=0 e=2 c=2 j=18 transabyss-1.fa transabyss-1.adj q=3 se="/mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq"'
make: Entering directory '/mnt/storage/Matured_Fruit/transabyss3'
ABYSS -k32 -q3 -e2 -E0 -c2    --coverage-hist=coverage.hist -s transabyss-bubbles.fa  -o transabyss-1.fa  /mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq
ABySS 1.9.0
ABYSS -k32 -q3 -e2 -E0 -c2 --coverage-hist=coverage.hist -s transabyss-bubbles.fa -o transabyss-1.fa /mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq
Reading `/mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq'...
Reading `/mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq'...
/usr/bin/abyss-pe:473: recipe for target 'transabyss-1.fa' failed

I'll appreciate any help with the error. 

Thankyou for your support!

[Ka Ming Nip]

The current version of Trans-ABySS only works with ABySS 1.5.x, but you are using version 1.9.0.
Please install version ABySS 1.5.2 and try again.

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 BlrGenomics [shelv...@gmail.com]
Sent: January 7, 2017 2:43 AM
To: Trans-ABySS
Subject: Error: usr/bin/abyss-pe:473: recipe for target 'transabyss-1.fa' failed

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[BlrGenomics]

Hi so i downloaded the required version of abyss and I tried running it:

bgc@ubuntu:~/Downloads/transabyss-master$ ./transabyss --pe /mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq --outdir /mnt/storage/Matured_Fruit/transabyss3 --threads 18

Trans-ABySS 1.5.5
CMD: ./transabyss --pe /mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq --outdir /mnt/storage/Matured_Fruit/transabyss3 --threads 18
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Found Trans-ABySS directory at: /home/bgc/Downloads/transabyss-master
Found Trans-ABySS `bin` directory at: /home/bgc/Downloads/transabyss-master/bin
Found script at: /home/bgc/Downloads/transabyss-master/bin/skip_psl_self.awk
Found script at: /home/bgc/Downloads/transabyss-master/bin/skip_psl_self_ss.awk
Found `blat' at /home/bgc/bin/blat
Found `MergeContigs' at /home/bgc/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:     56
# thread(s) requested:  18
# thread(s) to use:     18

CMD: bash -euo pipefail -c 'abyss-pe --directory=/mnt/storage/Matured_Fruit/transabyss3 k=32 name=transabyss E=0 e=2 c=2 j=18 transabyss-1.fa transabyss-1.adj q=3 se="/mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq"'
make: Entering directory '/mnt/storage/Matured_Fruit/transabyss3'
ABYSS -k32 -q3 -e2 -E0 -c2   --coverage-hist=coverage.hist -s transabyss-bubbles.fa  -o transabyss-1.fa  /mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq

ABySS 1.5.2

ABYSS -k32 -q3 -e2 -E0 -c2 --coverage-hist=coverage.hist -s transabyss-bubbles.fa -o transabyss-1.fa /mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq /mnt/storage/Matured_Fruit/MaturedFruit_S7_R2_001_trim.fastq
Reading `/mnt/storage/Matured_Fruit/MaturedFruit_S7_R1_001_trim.fastq'...

I doesn't go past this and no files are made in output folder

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[Ka Ming Nip]

Hi,

I did not see any error messages at all in the log you provided.

Did Trans-ABySS work for our sample dataset?

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 BlrGenomics [shelv...@gmail.com]

Sent: January 19, 2017 2:01 AM
To: Trans-ABySS
Subject: Re: Error: usr/bin/abyss-pe:473: recipe for target 'transabyss-1.fa' failed

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

To unsubscribe from this group and stop receiving emails from it, send an email to trans-abyss...@googlegroups.com<javascript:><mailto:trans-abyss...@googlegroups.com<javascript:>>.

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