Trans-Abyss output error

[Yogeshwar Dhar]

I am running trans abyss 1.5.3 for my data, using this command ./transabyss --threads 10 -k 32 --pe /home/nbri/YVD/A_R1.fastq /home/nbri/YVD/A_R2.fastq --outdir /home/nbri/YVD/Out-Trans. But after running the whole job it is generating empty output files.

Kindly me in troubleshoot of this problem.

Thanks & Regards 

[Ka Ming Nip]

Hi,

Sorry for the late reply.
Was there any error messages at all?

Thanks,
Ka Ming

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Yogeshwar Dhar [yogi.b...@gmail.com]
Sent: April 24, 2016 11:17 PM
To: Trans-ABySS
Subject: Trans-Abyss output error

I am running trans abyss 1.5.3 for my data, using this command ./transabyss --threads 10 -k 32 --pe /home/nbri/YVD/A_R1.fastq /home/nbri/YVD/A_R2.fastq --outdir /home/nbri/YVD/Out-Trans. But after running the whole job it is generating empty output files.
Kindly me in troubleshoot of this problem.




Thanks & Regards

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[Yogeshwar Dhar]

Dear Sir , 

Thanks for your reply. During the trans abyss job run or after the run we didn't get any error messages. What we get, are only empty files instead proper output files. 

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Yogeshwar Vikram Dhar

Research Student

C/O Dr.Mehar H Asif 

Computational Biology Lab

CPMB DIVISON

CSIR-National Botanical Research Institute

Lucknow-226001

Contact-+91-9452061958

[Ka Ming Nip]

Hi,

Can you tell me a bit more about your input data? (number of reads, read length, etc.)
Do you see an empty file `*.FINAL.COMPLETE`?
Was the file `coverage.hist' empty?

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

Sent: May 2, 2016 10:42 AM
To: trans...@googlegroups.com
Subject: Re: Trans-Abyss output error

Dear Sir ,

Thanks for your reply. During the trans abyss job run or after the run we didn't get any error messages. What we get, are only empty files instead proper output files.

On Mon, May 2, 2016 at 9:46 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca>> wrote:
Hi,

Sorry for the late reply.
Was there any error messages at all?

Thanks,
Ka Ming

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

From: trans...@googlegroups.com<mailto:trans...@googlegroups.com> [trans...@googlegroups.com<mailto:trans...@googlegroups.com>] On Behalf Of Yogeshwar Dhar [yogi.b...@gmail.com<mailto:yogi.b...@gmail.com>]

Sent: April 24, 2016 11:17 PM
To: Trans-ABySS
Subject: Trans-Abyss output error

I am running trans abyss 1.5.3 for my data, using this command ./transabyss --threads 10 -k 32 --pe /home/nbri/YVD/A_R1.fastq /home/nbri/YVD/A_R2.fastq --outdir /home/nbri/YVD/Out-Trans. But after running the whole job it is generating empty output files.
Kindly me in troubleshoot of this problem.




Thanks & Regards

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Yogeshwar Vikram Dhar
Research Student
C/O Dr.Mehar H Asif
Computational Biology Lab
CPMB DIVISON
CSIR-National Botanical Research Institute
Lucknow-226001
Contact-+91-9452061958

[Yogeshwar Dhar]

Dear Sir,

There are 4 paired end data files (total 8 files), having approx 28055790 number of reads with read length of 101 bp, i am running it on ubuntu enable machine , dependency of abyss is version 1.3.6. 

command line is  

./transabyss --threads 10 -k 32 --pe /home/nbri/transabyss-1.5.3/C/A_R1_filtered.fastq /home/nbri/transabyss-1.5.3/C/A_R2_filtered.fastq /home/nbri/transabyss-1.5.3/C/B_R1_filtered.fastq /home/nbri/transabyss-1.5.3/C/B_R2_filtered.fastq  --outdir /home/nbri/transabyss-1.5.3/C/transabyss-out/

Getting empty *.FINAL.COMPLETE' file. coverage hist file is attached 

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[Ka Ming Nip]

Trans-ABySS depends on ABySS 1.5.2. You can get it here:
https://github.com/bcgsc/abyss/releases/tag/1.5.2

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

Sent: May 3, 2016 5:42 AM

To: trans...@googlegroups.com
Subject: Re: Trans-Abyss output error

Dear Sir,

There are 4 paired end data files (total 8 files), having approx 28055790 number of reads with read length of 101 bp, i am running it on ubuntu enable machine , dependency of abyss is version 1.3.6.

command line is

./transabyss --threads 10 -k 32 --pe /home/nbri/transabyss-1.5.3/C/A_R1_filtered.fastq /home/nbri/transabyss-1.5.3/C/A_R2_filtered.fastq /home/nbri/transabyss-1.5.3/C/B_R1_filtered.fastq /home/nbri/transabyss-1.5.3/C/B_R2_filtered.fastq --outdir /home/nbri/transabyss-1.5.3/C/transabyss-out/

Getting empty *.FINAL.COMPLETE' file. coverage hist file is attached





On Tue, May 3, 2016 at 3:30 AM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca>> wrote:
Hi,

Can you tell me a bit more about your input data? (number of reads, read length, etc.)
Do you see an empty file `*.FINAL.COMPLETE`?
Was the file `coverage.hist' empty?

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

From: trans...@googlegroups.com<mailto:trans...@googlegroups.com> [trans...@googlegroups.com<mailto:trans...@googlegroups.com>] On Behalf Of Yogeshwar Dhar [yogi.b...@gmail.com<mailto:yogi.b...@gmail.com>]

Sent: May 2, 2016 10:42 AM

To: trans...@googlegroups.com<mailto:trans...@googlegroups.com>

Subject: Re: Trans-Abyss output error

Dear Sir ,

Thanks for your reply. During the trans abyss job run or after the run we didn't get any error messages. What we get, are only empty files instead proper output files.

On Mon, May 2, 2016 at 9:46 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>>> wrote:
Hi,

Sorry for the late reply.
Was there any error messages at all?

Thanks,
Ka Ming

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

From: trans...@googlegroups.com<mailto:trans...@googlegroups.com><mailto:trans...@googlegroups.com<mailto:trans...@googlegroups.com>> [trans...@googlegroups.com<mailto:trans...@googlegroups.com><mailto:trans...@googlegroups.com<mailto:trans...@googlegroups.com>>] On Behalf Of Yogeshwar Dhar [yogi.b...@gmail.com<mailto:yogi.b...@gmail.com><mailto:yogi.b...@gmail.com<mailto:yogi.b...@gmail.com>>]

Sent: April 24, 2016 11:17 PM
To: Trans-ABySS
Subject: Trans-Abyss output error

I am running trans abyss 1.5.3 for my data, using this command ./transabyss --threads 10 -k 32 --pe /home/nbri/YVD/A_R1.fastq /home/nbri/YVD/A_R2.fastq --outdir /home/nbri/YVD/Out-Trans. But after running the whole job it is generating empty output files.
Kindly me in troubleshoot of this problem.




Thanks & Regards

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[Yogeshwar Dhar]

Thank u sir :) 

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