denovo assembly collapsed with error " "ERROR: CMD ended with status code 2"

[bilal....@cemb.edu.pk]

Hello all 

i am trying to assemble my RNA-seq data by using trans-Abyss 1.5.5 version while abyss version is 2.0.2. I used the following command

transabyss --pe all.left.reads.1.fq all.right.reads.2.fr -k 25 --name 25-merassembely --outdir ..../...

I setup 4 different commands on the server with different K mer size (25-31), but all collapsed after ~12h of running with following error. "ERROR: CMD ended with status code 2"

for further information please find the snap of terminal here with also.

please help me in this regard. how to fix this problem 

 

Popping bubbles

Removed 229509 bubbles.

Removed 229509 bubbles

Marked 14705656 edges of 6117867 ambiguous vertices.

Left 168831 unassembled k-mer in circular contigs.

Assembled 208633800 k-mer in 6458730 contigs.

Removed 621735446 k-mer.

The signal-to-noise ratio (SNR) is -4.53654 dB.

make: *** No rule to make target `37mer_assembly-1.adj'.  Stop.

make: Leaving directory `/data/storage_green/mbil/compressed_file/trnas-abyss37'

Elapsed time: 12 h 12 m 28 s

"ERROR: CMD ended with status code 2"

 

[Ka Ming Nip]

Hi,

As outlined on GitHub, Trans-ABySS 1.5.5 only works with ABySS 1.5.2:
https://github.com/bcgsc/transabyss

Hope that help!

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 bilal....@cemb.edu.pk [bilal....@cemb.edu.pk]
Sent: November 14, 2016 2:13 AM
To: Trans-ABySS
Subject: denovo assembly collapsed with error " "ERROR: CMD ended with status code 2"

Hello all

i am trying to assemble my RNA-seq data by using trans-Abyss 1.5.5 version while abyss version is 2.0.2. I used the following command

transabyss --pe all.left.reads.1.fq all.right.reads.2.fr -k 25 --name 25-merassembely --outdir ..../...

I setup 4 different commands on the server with different K mer size (25-31), but all collapsed after ~12h of running with following error. "ERROR: CMD ended with status code 2"
for further information please find the snap of terminal here with also.

[https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s320/Capture.PNG]<https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s1600/Capture.PNG>

please help me in this regard. how to fix this problem



Popping bubbles
Removed 229509 bubbles.
Removed 229509 bubbles
Marked 14705656 edges of 6117867 ambiguous vertices.
Left 168831 unassembled k-mer in circular contigs.
Assembled 208633800 k-mer in 6458730 contigs.
Removed 621735446 k-mer.
The signal-to-noise ratio (SNR) is -4.53654 dB.
make: *** No rule to make target `37mer_assembly-1.adj'. Stop.
make: Leaving directory `/data/storage_green/mbil/compressed_file/trnas-abyss37'
Elapsed time: 12 h 12 m 28 s
"ERROR: CMD ended with status code 2"

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[dario.ka...@googlemail.com]

Hello everybody,

I am experiencing a similar problem despite having installed Trans-ABySS 1.5.5 and ABySS 1.5.2.

I'm attaching a screenshot of the message I am getting.

Any ideas how to fix this?

Cheers, Dario

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

[Muhammad Bilal Sarwar]

 Dear Dario

As outlined on GitHub, Trans-ABySS 1.5.5 only works with ABySS 1.5.2:
https://github.com/bcgsc/transabyss

Hope that help!

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With best Regards

Muhammad Bilal Sarwar

Ph.D. Research Fellow

Plant Genomic Lab

National Center of Excellence in Molecular Biology

University of The Punjab, Lahore

bilal....@cemb.edu.pk

bilal_...@yahoo.com

Ph # +92 (323) 6409666 

[dario.ka...@googlemail.com]

Hello Muhammad,

as I wrote before: I have Trans–ABySS 1.5.5 and ABySS 1.5.2 installed on my cluster.

That's why I am confused by this error.

Cheers, Dario

To unsubscribe from this group and all its topics, send an email to trans-abyss...@googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[Ka Ming Nip]

Trans-ABySS has a very tiny sample dataset under the `sample_dataset` directory. Were you able to process that?

ABySS itself also has a test dataset as well.
https://github.com/bcgsc/abyss#assemble-a-small-synthetic-data-set
Were you able to process that, too?

Ka Ming
--
Ka Ming Nip

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

From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com]
Sent: February 13, 2017 5:35 AM
To: Trans-ABySS
Subject: Re: denovo assembly collapsed with error " "ERROR: CMD ended with status code 2"

Hello Muhammad,

as I wrote before: I have Trans–ABySS 1.5.5 and ABySS 1.5.2 installed on my cluster.

That's why I am confused by this error.

Cheers, Dario



Am Freitag, 10. Februar 2017 15:28:57 UTC+1 schrieb Muhammad Bilal Sarwar:
Dear Dario

As outlined on GitHub, Trans-ABySS 1.5.5 only works with ABySS 1.5.2:
https://github.com/bcgsc/transabyss

Hope that help!

On Fri, Feb 10, 2017 at 2:10 PM, dario.karmeinski via Trans-ABySS <trans...@googlegroups.com<javascript:>> wrote:
Hello everybody,

I am experiencing a similar problem despite having installed Trans-ABySS 1.5.5 and ABySS 1.5.2.
I'm attaching a screenshot of the message I am getting.

Any ideas how to fix this?

Cheers, Dario


Am Montag, 14. November 2016 18:26:42 UTC+1 schrieb Ka Ming Nip:
Hi,

As outlined on GitHub, Trans-ABySS 1.5.5 only works with ABySS 1.5.2:
https://github.com/bcgsc/transabyss

Hope that help!

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 bilal....@cemb.edu.pk [bilal....@cemb.edu.pk]
Sent: November 14, 2016 2:13 AM
To: Trans-ABySS
Subject: denovo assembly collapsed with error " "ERROR: CMD ended with status code 2"

Hello all

i am trying to assemble my RNA-seq data by using trans-Abyss 1.5.5 version while abyss version is 2.0.2. I used the following command

transabyss --pe all.left.reads.1.fq all.right.reads.2.fr<http://all.right.reads.2.fr> -k 25 --name 25-merassembely --outdir ..../...

I setup 4 different commands on the server with different K mer size (25-31), but all collapsed after ~12h of running with following error. "ERROR: CMD ended with status code 2"
for further information please find the snap of terminal here with also.

[https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s320/Capture.PNG]<https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s1600/Capture.PNG>

please help me in this regard. how to fix this problem



Popping bubbles
Removed 229509 bubbles.
Removed 229509 bubbles
Marked 14705656 edges of 6117867 ambiguous vertices.
Left 168831 unassembled k-mer in circular contigs.
Assembled 208633800 k-mer in 6458730 contigs.
Removed 621735446 k-mer.
The signal-to-noise ratio (SNR) is -4.53654 dB.
make: *** No rule to make target `37mer_assembly-1.adj'. Stop.
make: Leaving directory `/data/storage_green/mbil/compressed_file/trnas-abyss37'
Elapsed time: 12 h 12 m 28 s
"ERROR: CMD ended with status code 2"



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With best Regards

Muhammad Bilal Sarwar
Ph.D. Research Fellow
Plant Genomic Lab
National Center of Excellence in Molecular Biology
University of The Punjab, Lahore
bilal....@cemb.edu.pk
bilal_...@yahoo.com
Ph # +92 (323) 6409666

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[dario.ka...@googlemail.com]

I just tried to assemble the dataset under 'sample_dataset' and got similar error messages.

I'm attaching a screenshot of both the STDOUT and STDERR.

Cheers,

Dario

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--
With best Regards

Muhammad Bilal Sarwar
Ph.D. Research Fellow
Plant Genomic Lab
National Center of Excellence in Molecular Biology
University of The Punjab, Lahore
bilal....@cemb.edu.pk
bilal_...@yahoo.com
Ph # +92 (323) 6409666

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[Ka Ming Nip]

You are still running a new version of ABySS, that's why it cannot generate the *.adj file.

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com]

Sent: February 16, 2017 3:24 AM

To: Trans-ABySS
Subject: Re: denovo assembly collapsed with error " "ERROR: CMD ended with status code 2"

I just tried to assemble the dataset under 'sample_dataset' and got similar error messages.
I'm attaching a screenshot of both the STDOUT and STDERR.

Cheers,
Dario


Am Dienstag, 14. Februar 2017 18:19:47 UTC+1 schrieb Ka Ming Nip:
Trans-ABySS has a very tiny sample dataset under the `sample_dataset` directory. Were you able to process that?

ABySS itself also has a test dataset as well.
https://github.com/bcgsc/abyss#assemble-a-small-synthetic-data-set
Were you able to process that, too?

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

From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com<javascript:>]

transabyss --pe all.left.reads.1.fq all.right.reads.2.fr<http://all.right.reads.2.fr><http://all.right.reads.2.fr> -k 25 --name 25-merassembely --outdir ..../...

I setup 4 different commands on the server with different K mer size (25-31), but all collapsed after ~12h of running with following error. "ERROR: CMD ended with status code 2"
for further information please find the snap of terminal here with also.

[https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s320/Capture.PNG]<https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s1600/Capture.PNG>

please help me in this regard. how to fix this problem



Popping bubbles
Removed 229509 bubbles.
Removed 229509 bubbles
Marked 14705656 edges of 6117867 ambiguous vertices.
Left 168831 unassembled k-mer in circular contigs.
Assembled 208633800 k-mer in 6458730 contigs.
Removed 621735446 k-mer.
The signal-to-noise ratio (SNR) is -4.53654 dB.
make: *** No rule to make target `37mer_assembly-1.adj'. Stop.
make: Leaving directory `/data/storage_green/mbil/compressed_file/trnas-abyss37'
Elapsed time: 12 h 12 m 28 s
"ERROR: CMD ended with status code 2"



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--
With best Regards

Muhammad Bilal Sarwar
Ph.D. Research Fellow
Plant Genomic Lab
National Center of Excellence in Molecular Biology
University of The Punjab, Lahore

bilal....@cemb.edu.pk<javascript:>
bilal_...@yahoo.com<javascript:>

Ph # +92 (323) 6409666

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[dario.ka...@googlemail.com]

Dear Ka,

thank you very much for your help!

We were indeed using the wrong version of ABySS due to an error during installation...

One more question:

Is it "normal" to get error messages like the following? (This occurred while using the sample dataset.)

contigs-0.fa:0: warning: file is empty

snp-0.fa:0: warning: file is empty

snp-3.fa:0: warning: file is empty

Building the suffix array...

Building the Burrows-Wheeler transform...

Building the character occurrence table...

Cheers, Dario

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--
With best Regards

Muhammad Bilal Sarwar
Ph.D. Research Fellow
Plant Genomic Lab
National Center of Excellence in Molecular Biology
University of The Punjab, Lahore
bilal....@cemb.edu.pk<javascript:>
bilal_...@yahoo.com<javascript:>
Ph # +92 (323) 6409666

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[Ka Ming Nip]

Hi Dario,

Probably not... Do you see the *-1.fa, *-3.fa, etc.?

Ka Ming

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

From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com]
Sent: February 22, 2017 6:18 AM

To: Trans-ABySS
Subject: Re: denovo assembly collapsed with error " "ERROR: CMD ended with status code 2"

Dear Ka,

thank you very much for your help!
We were indeed using the wrong version of ABySS due to an error during installation...

One more question:
Is it "normal" to get error messages like the following? (This occurred while using the sample dataset.)
contigs-0.fa:0: warning: file is empty

snp-0.fa:0: warning: file is empty

snp-3.fa:0: warning: file is empty

Building the suffix array...

Building the Burrows-Wheeler transform...

Building the character occurrence table...

Cheers, Dario

Am Donnerstag, 16. Februar 2017 18:08:09 UTC+1 schrieb Ka Ming Nip:
You are still running a new version of ABySS, that's why it cannot generate the *.adj file.

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

From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com<javascript:>]

transabyss --pe all.left.reads.1.fq all.right.reads.2.fr<http://all.right.reads.2.fr><http://all.right.reads.2.fr><http://all.right.reads.2.fr> -k 25 --name 25-merassembely --outdir ..../...

I setup 4 different commands on the server with different K mer size (25-31), but all collapsed after ~12h of running with following error. "ERROR: CMD ended with status code 2"
for further information please find the snap of terminal here with also.

[https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s320/Capture.PNG]<https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s1600/Capture.PNG>

please help me in this regard. how to fix this problem



Popping bubbles
Removed 229509 bubbles.
Removed 229509 bubbles
Marked 14705656 edges of 6117867 ambiguous vertices.
Left 168831 unassembled k-mer in circular contigs.
Assembled 208633800 k-mer in 6458730 contigs.
Removed 621735446 k-mer.
The signal-to-noise ratio (SNR) is -4.53654 dB.
make: *** No rule to make target `37mer_assembly-1.adj'. Stop.
make: Leaving directory `/data/storage_green/mbil/compressed_file/trnas-abyss37'
Elapsed time: 12 h 12 m 28 s
"ERROR: CMD ended with status code 2"



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--
With best Regards

Muhammad Bilal Sarwar
Ph.D. Research Fellow
Plant Genomic Lab
National Center of Excellence in Molecular Biology
University of The Punjab, Lahore
bilal....@cemb.edu.pk<javascript:>
bilal_...@yahoo.com<javascript:>
Ph # +92 (323) 6409666

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[dario.ka...@googlemail.com]

Hi Ka Ming,

yes, the *-1.fa and *-3.fa are present in the output directory and they contain sequences.

However, the files contigs-0.fa, snp-0.fa and snp-3.fa are not present in the output directory.

Cheers,

Dario

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--
With best Regards

Muhammad Bilal Sarwar
Ph.D. Research Fellow
Plant Genomic Lab
National Center of Excellence in Molecular Biology
University of The Punjab, Lahore
bilal....@cemb.edu.pk<javascript:>
bilal_...@yahoo.com<javascript:>
Ph # +92 (323) 6409666

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[Ka Ming Nip]

Ok, then that is fine. Those are temporary files from ABySS, which is why you don't see them in the directory.

Ka Ming
--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com]

Sent: March 2, 2017 3:03 AM

To: Trans-ABySS
Subject: Re: denovo assembly collapsed with error " "ERROR: CMD ended with status code 2"

Hi Ka Ming,

yes, the *-1.fa and *-3.fa are present in the output directory and they contain sequences.
However, the files contigs-0.fa, snp-0.fa and snp-3.fa are not present in the output directory.

Cheers,
Dario


Am Donnerstag, 23. Februar 2017 04:45:06 UTC+1 schrieb Ka Ming Nip:
Hi Dario,

Probably not... Do you see the *-1.fa, *-3.fa, etc.?

Ka Ming

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

From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com<javascript:>]

transabyss --pe all.left.reads.1.fq all.right.reads.2.fr<http://all.right.reads.2.fr><http://all.right.reads.2.fr><http://all.right.reads.2.fr><http://all.right.reads.2.fr> -k 25 --name 25-merassembely --outdir ..../...

I setup 4 different commands on the server with different K mer size (25-31), but all collapsed after ~12h of running with following error. "ERROR: CMD ended with status code 2"
for further information please find the snap of terminal here with also.

[https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s320/Capture.PNG]<https://lh3.googleusercontent.com/-RG8SDgM9ocI/WCmOKfzan2I/AAAAAAAAAHA/faxSC6B70eUiEucbx1jWyENn8EysY7H8gCLcB/s1600/Capture.PNG>

please help me in this regard. how to fix this problem



Popping bubbles
Removed 229509 bubbles.
Removed 229509 bubbles
Marked 14705656 edges of 6117867 ambiguous vertices.
Left 168831 unassembled k-mer in circular contigs.
Assembled 208633800 k-mer in 6458730 contigs.
Removed 621735446 k-mer.
The signal-to-noise ratio (SNR) is -4.53654 dB.
make: *** No rule to make target `37mer_assembly-1.adj'. Stop.
make: Leaving directory `/data/storage_green/mbil/compressed_file/trnas-abyss37'
Elapsed time: 12 h 12 m 28 s
"ERROR: CMD ended with status code 2"



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With best Regards

Muhammad Bilal Sarwar
Ph.D. Research Fellow
Plant Genomic Lab
National Center of Excellence in Molecular Biology
University of The Punjab, Lahore
bilal....@cemb.edu.pk<javascript:>
bilal_...@yahoo.com<javascript:>
Ph # +92 (323) 6409666

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