ERROR: CMD ended with status code 2 and no *contigs.fa output
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Emily Stander
Mar 8, 2018, 1:52:57 AM3/8/18
to Trans-ABySS
Hi,
I am running transabyss on my RNAseq data with transabyss 1.5.5 and abyss 1.5.2. I only get the following fasta files as output:
*-1.fa
*-3.fa
*.fa
*.r1.filtered.fa
Apparently the final assembly is in a contigs.fa file which was not generated in my case.
As part of the printed output I also get the error:
ERROR: CMD ended with status code 2
Could this have something to do with the missing contigs.fa file indicating an incomplete run?
Thanks in advance,
Emily
I am running transabyss on my RNAseq data with transabyss 1.5.5 and abyss 1.5.2. I only get the following fasta files as output:
*-1.fa
*-3.fa
*.fa
*.r1.filtered.fa
Apparently the final assembly is in a contigs.fa file which was not generated in my case.
As part of the printed output I also get the error:
ERROR: CMD ended with status code 2
Could this have something to do with the missing contigs.fa file indicating an incomplete run?
Thanks in advance,
Emily
Ka Ming Nip
Mar 8, 2018, 12:20:40 PM3/8/18
to trans...@googlegroups.com
Hi Emily,
An error in Trans-ABySS will always result in an incomplete run.
The final assembly is actually `*-final.fa` and you would also see an empty stamp file `*.FINAL.COMPLETE`.
Can you please send me the entire log of the run?
Were you able to assemble 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 Emily Stander [emily.amo...@gmail.com]
Sent: March 7, 2018 10:52 PM
To: Trans-ABySS
Subject: ERROR: CMD ended with status code 2 and no *contigs.fa output
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An error in Trans-ABySS will always result in an incomplete run.
The final assembly is actually `*-final.fa` and you would also see an empty stamp file `*.FINAL.COMPLETE`.
Can you please send me the entire log of the run?
Were you able to assemble 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 Emily Stander [emily.amo...@gmail.com]
Sent: March 7, 2018 10:52 PM
To: Trans-ABySS
Subject: ERROR: CMD ended with status code 2 and no *contigs.fa output
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Emily Stander
Mar 12, 2018, 6:30:06 AM3/12/18
to trans...@googlegroups.com
Hi Ka Ming,
I have run the software on the test data which completed and gave me the `*-final.fa` and `*.FINAL.COMPLETE` folder.Regards,
Ph.D. candidate
South African National Bioinformatics Institute
University of the Western Cape
South Africa
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Ka Ming Nip
Mar 12, 2018, 7:19:12 PM3/12/18
to trans...@googlegroups.com
Hi Emily,
There are several things to check for your read files:
1. Make sure the read names in `*_1.fq` have the `/1` suffix and the read names in `*_2.fq` have the `/2` suffix.
2. `*_1.fq` and `*_2.fq` must have the same number of lines and the number of lines in the files are divisible by 4 (for FASTQ format).
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 Emily Stander [emily.amo...@gmail.com]
Sent: March 12, 2018 3:30 AM
To: trans...@googlegroups.com
Subject: Re: ERROR: CMD ended with status code 2 and no *contigs.fa output
Hi Ka Ming,
I have run the software on the test data which completed and gave me the `*-final.fa` and `*.FINAL.COMPLETE` folder.
So I think its something to do with the format of my fastq file. I am running the assembly on the raw Illumina reads with the files from the service provider and with reads that have been trimmed which all give me a similar output (please find attached the complete output file). I am not too sure how to go further or whether I should convert to fasta file format. Your advice would be very much appreciated.
Kind regards,
Emily
Regards,
Emily Stander (M.Sc)
Ph.D. candidate
South African National Bioinformatics Institute
University of the Western Cape
South Africa
There are several things to check for your read files:
1. Make sure the read names in `*_1.fq` have the `/1` suffix and the read names in `*_2.fq` have the `/2` suffix.
2. `*_1.fq` and `*_2.fq` must have the same number of lines and the number of lines in the files are divisible by 4 (for FASTQ format).
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 Emily Stander [emily.amo...@gmail.com]
To: trans...@googlegroups.com
Subject: Re: ERROR: CMD ended with status code 2 and no *contigs.fa output
Hi Ka Ming,
I have run the software on the test data which completed and gave me the `*-final.fa` and `*.FINAL.COMPLETE` folder.
So I think its something to do with the format of my fastq file. I am running the assembly on the raw Illumina reads with the files from the service provider and with reads that have been trimmed which all give me a similar output (please find attached the complete output file). I am not too sure how to go further or whether I should convert to fasta file format. Your advice would be very much appreciated.
Kind regards,
Emily
Regards,
Emily Stander (M.Sc)
Ph.D. candidate
South African National Bioinformatics Institute
University of the Western Cape
South Africa
On 8 March 2018 at 19:15, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca>> wrote:
Hi Emily,
An error in Trans-ABySS will always result in an incomplete run.
The final assembly is actually `*-final.fa` and you would also see an empty stamp file `*.FINAL.COMPLETE`.
Can you please send me the entire log of the run?
Were you able to assemble 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<mailto:trans...@googlegroups.com> [trans...@googlegroups.com<mailto:trans...@googlegroups.com>] On Behalf Of Emily Stander [emily.amo...@gmail.com<mailto:emily.amo...@gmail.com>]
Hi Emily,
An error in Trans-ABySS will always result in an incomplete run.
The final assembly is actually `*-final.fa` and you would also see an empty stamp file `*.FINAL.COMPLETE`.
Can you please send me the entire log of the run?
Were you able to assemble our sample dataset?
Ka Ming
--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
Sent: March 7, 2018 10:52 PM
To: Trans-ABySS
Subject: ERROR: CMD ended with status code 2 and no *contigs.fa output
Hi,
I am running transabyss on my RNAseq data with transabyss 1.5.5 and abyss 1.5.2. I only get the following fasta files as output:
*-1.fa
*-3.fa
*.fa
*.r1.filtered.fa
Apparently the final assembly is in a contigs.fa file which was not generated in my case.
As part of the printed output I also get the error:
ERROR: CMD ended with status code 2
Could this have something to do with the missing contigs.fa file indicating an incomplete run?
Thanks in advance,
Emily
--
You received this message because you are subscribed to the Google Groups "Trans-ABySS" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trans-abyss...@googlegroups.com<mailto:trans-abyss%2Bunsu...@googlegroups.com><mailto:trans-abyss...@googlegroups.com<mailto:trans-abyss%2Bunsu...@googlegroups.com>>.
To: Trans-ABySS
Subject: ERROR: CMD ended with status code 2 and no *contigs.fa output
Hi,
I am running transabyss on my RNAseq data with transabyss 1.5.5 and abyss 1.5.2. I only get the following fasta files as output:
*-1.fa
*-3.fa
*.fa
*.r1.filtered.fa
Apparently the final assembly is in a contigs.fa file which was not generated in my case.
As part of the printed output I also get the error:
ERROR: CMD ended with status code 2
Could this have something to do with the missing contigs.fa file indicating an incomplete run?
Thanks in advance,
Emily
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Emily Stander
Mar 14, 2018, 3:13:35 AM3/14/18
to trans...@googlegroups.com
I will check this. Thank you so much for your help :)
Kind regards,Regards,
Ph.D. candidate
South African National Bioinformatics Institute
University of the Western Cape
South Africa
On 8 March 2018 at 19:15, Ka Ming Nip <km...@bcgsc.ca<mailto:kmnip@bcgsc.ca>> wrote:
Hi Emily,
An error in Trans-ABySS will always result in an incomplete run.
The final assembly is actually `*-final.fa` and you would also see an empty stamp file `*.FINAL.COMPLETE`.
Can you please send me the entire log of the run?
Were you able to assemble 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<mailto:trans-abyss@googlegroups.com> [trans...@googlegroups.com<mailto:trans-abyss@googlegroups.com>] On Behalf Of Emily Stander [emily.amo...@gmail.com<mailto:emily.amor.stander@gmail.com>]
Sent: March 7, 2018 10:52 PM
To: Trans-ABySS
Subject: ERROR: CMD ended with status code 2 and no *contigs.fa output
Hi,
I am running transabyss on my RNAseq data with transabyss 1.5.5 and abyss 1.5.2. I only get the following fasta files as output:
*-1.fa
*-3.fa
*.fa
*.r1.filtered.fa
Apparently the final assembly is in a contigs.fa file which was not generated in my case.
As part of the printed output I also get the error:
ERROR: CMD ended with status code 2
Could this have something to do with the missing contigs.fa file indicating an incomplete run?
Thanks in advance,
Emily
--
You received this message because you are subscribed to the Google Groups "Trans-ABySS" group.
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