Transabyss-error in running

[sri lakshmy]

Hello,

I am trying to run Transabyss with the command:

/usr/local/pkg/transabyss/1.5.2/transabyss --pe trim/s1_pe trim/s2_pe --threads 32 --pid 0.98 -k 61

It worked before with my smaller data set and got quite good results and looking forward more for downstream analysis.

But now I want to generate an assembly for my complete data set but it does not seem to work.

The error message is 

CMD: bash -euo pipefail -c 'MergeContigs --kmer=61 --out=/media/jumbonfs/salix/sri/complete_transcriptoms/transabyss_1.5.2_assembly/transabyss-unitigs.r1.filtered.fa /media/jumbonfs/salix/sri/complete_transcriptoms/transabyss_1.5.2_assembly/transabyss-1.fa /media/jumbonfs/salix/sri/complete_transcriptoms/transabyss_1.5.2_assembly/transabyss-1.adj /media/jumbonfs/salix/sri/complete_transcriptoms/transabyss_1.5.2_assembly/transabyss-unitigs.r1.path'

error: no edge 39430969+ -> 46791652+

MergeContigs: ../Common/ContigProperties.h:205: typename boost::edge_bundle_type<G>::type get(boost::edge_bundle_t, const Graph&, ContigNode, ContigNode) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >, typename boost::edge_bundle_type<G>::type = Distance]: Assertion `e.second' failed.

Aborted (core dumped)

Elapsed time: 0 h 13 m 23 s

Could someone please me how to fix this?

Your help will be greatly appreciated.

Thanks!

[Ka Ming Nip]

Hello,

Are you using ABySS 1.5.2?

Can you please try removing the files under this directory and try again?

/media/jumbonfs/salix/sri/complete_transcriptoms/transabyss_1.5.2_assembly/

If you are still getting an error after that (I hope not), would it be possible for you to send me these 2 files in private?

/media/jumbonfs/salix/sri/complete_transcriptoms/transabyss_1.5.2_assembly/transabyss-1.fa
/media/jumbonfs/salix/sri/complete_transcriptoms/transabyss_1.5.2_assembly/transabyss-1.adj

Thanks!

--
Ka Ming Nip
Graduate Student
Bioinformatics Technology Lab (Dr. Inanc Birol)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of sri lakshmy [laksha...@gmail.com]
Sent: January 29, 2015 3:13 AM
To: trans...@googlegroups.com
Subject: Transabyss-error in running

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[sri lakshmy]

Thanks for your reply.

I will do that and get back to you if the error occurs again!

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[sri lakshmy]

And yes I'm using ABySS 1.5.2

On Thursday, January 29, 2015 at 6:20:08 PM UTC+1, Ka Ming Nip wrote:

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[eyeziko]

Hello Ka Ming,

I am getting the same error message with ABySS 1.5.2. I have tried your suggestion to remove the files under transabyss_1.5.2_assembly and have done a re-run but I still came up with the same error. Here is my error

Elapsed time: 4 h 36 m 24 s
117941 potentially removable paths ...
Marked 322520 more vertices for removal.
CMD: bash -euo pipefail -c 'abyss-filtergraph --shim --assemble --kmer=31 --island=0 --remove=/.../transabyss-1.5.2/transabyss_1.5.2_assembly/davetrans-unitigs.r2.rm.cids --graph=/.../transabyss-1.5.2/transabyss_1.5.2_assembly/davetrans-unitigs.r2.filtered.adj /.../transabyss-1.5.2/transabyss_1.5.2_assembly/davetrans-unitigs.r1.filtered.adj > /.../transabyss-1.5.2/transabyss_1.5.2_assembly/davetrans-unitigs.r2.path'
Elapsed time: 0 h 1 m 30 s
CMD: bash -euo pipefail -c 'MergeContigs --kmer=31 --out=/.../transabyss-1.5.2/transabyss_1.5.2_assembly/davetrans-unitigs.r2.filtered.fa /.../transabyss-1.5.2/transabyss_1.5.2_assembly/davetrans-unitigs.r1.filtered.fa /.../transabyss-1.5.2/transabyss_1.5.2_assembly/davetrans-unitigs.r1.filtered.adj /.../transabyss-1.5.2/transabyss_1.5.2_assembly/davetrans-unitigs.r2.path'
error: no edge 7638498- -> 8066964-
MergeContigs: ../Common/ContigProperties.h:205: typename boost::edge_bundle_type<G>::type get(boost::edge_bundle_t, const Graph&, ContigNode, ContigNode) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; typename boost::edge_bundle_type<G>::type = Distance]: Assertion `e.second' failed.
Elapsed time: 0 h 1 m 27 s
ERROR: CMD ended with status code -6


I am at a loss as to what to do next. I will appreciate your reply and suggestion if you can.
Thank you

[Ka Ming Nip]

Hi,

Would you mind sending me your read files off the mailing list?
Please also give me the exact command that you used. Let me see if this is a bug! :S

Thanks,
Ka Ming

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

From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of eyeziko [isaac....@eagles.usm.edu]
Sent: February 19, 2015 7:49 AM
To: trans...@googlegroups.com
Subject: Re: Transabyss-error in running

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[A.D DILIP]

Hello Ka Ming
I am getting the same error for my assembly. Here is the error message:

CMD: bash -euo pipefail -c 'MergeContigs --kmer=27 --out=/MMCI/MS/DeNovoAssembly/work/benchmark/analysis/human/Human/Transabyss/SRR332171/27/transabyss-unitigs.r1.filtered.fa /MMCI/MS/DeNovoAssembly/work/benchmark/analysis/human/Human/Transabyss/SRR332171/27/transabyss-1.fa /MMCI/MS/DeNovoAssembly/work/benchmark/analysis/human/Human/Transabyss/SRR332171/27/transabyss-1.adj /MMCI/MS/DeNovoAssembly/work/benchmark/analysis/human/Human/Transabyss/SRR332171/27/transabyss-unitigs.r1.path'
error: no edge 103438- -> 1363719-

could you please help me out

regards
Dilip

[A.D DILIP]

Here is the command I used:
./transabyss --pe /MMCI/MS/DeNovoAssembly/work/benchmark/analysis/human/Human/SOS/Different_K/Seperated_1.fa /MMCI/MS/DeNovoAssembly/work/benchmark/analysis/human/Human/SOS/Different_K/Seperated_2.fa --outdir /MMCI/MS/DeNovoAssembly/work/benchmark/analysis/human/Human/Transabyss/SRR332171/27/ --length 100 --threads 10 -k 27

[Ka Ming Nip]

Hi Dilip,

Did Trans-ABySS to work on our small sample dataset?
And, are you using ABySS 1.5.2?

If so, please send me these two files in a private email:
/MMCI/MS/DeNovoAssembly/work/benchmark/analysis/human/Human/Transabyss/SRR332171/27/transabyss-1.fa
/MMCI/MS/DeNovoAssembly/work/benchmark/analysis/human/Human/Transabyss/SRR332171/27/transabyss-1.adj
I will try to debug it.

Thanks!

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

From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of A.D DILIP [ddili...@gmail.com]
Sent: March 25, 2015 11:35 AM

To: trans...@googlegroups.com
Subject: Re: Transabyss-error in running

[Lakhansing Pardeshi]

Hi Ka Ming,

I am also getting same error when I try to run TransABySS for my single end data with kmer = 37. I am running TransABySS on my data with different kmer values. TransABySS is completing assembly for some kmer values like 29, 33, 41, 61 but failing for kmer values like 35, 37, 49, 43, 57.

CMD: bash -euo pipefail -c 'abyss-filtergraph --shim --assemble --kmer=37 --island=0 --remove=/mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-unitigs.r2.rm.cids --graph=/mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-unitigs.r2.filtered.adj /mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-unitigs.r1.filtered.adj > /mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-unitigs.r2.path'
Elapsed time: 0 h 0 m 15 s
CMD: bash -euo pipefail -c 'MergeContigs --kmer=37 --out=/mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-unitigs.r2.filtered.fa /mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-unitigs.r1.filtered.fa /mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-unitigs.r1.filtered.adj /mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-unitigs.r2.path'
error: no edge 1750712+ -> 1875131+

Please find the command below:
/root/programs/transabyss-1.5.2/transabyss --se /mnt/LABS2/IISER_data_analysis/8_invitro/adapterTrimming/adapterTrimmedSRR065639.fastq /mnt/LABS2/IISER_data_analysis/8_invitro/adapterTrimming/adapterTrimmedSRR065640.fastq /mnt/LABS2/IISER_data_analysis/8_invitro/adapterTrimming/adapterTrimmedSRR065641.fastq /mnt/LABS2/IISER_data_analysis/8_invitro/adapterTrimming/adapterTrimmedSRR065642.fastq /mnt/LABS2/IISER_data_analysis/8_invitro/adapterTrimming/adapterTrimmedSRR065643.fastq /mnt/LABS2/IISER_data_analysis/8_invitro/adapterTrimming/adapterTrimmedSRR065644.fastq /mnt/LABS2/IISER_data_analysis/8_invitro/adapterTrimming/adapterTrimmedSRR065645.fastq /mnt/LABS2/IISER_data_analysis/8_invitro/adapterTrimming/adapterTrimmedSRR065646.fastq --kmer 37 --threads 5 --name transabyss_37 --outdir transabyss_37 > logs/transabyss_37.log 2>&1

I have attached the command log for the above command in file transabyss_37.log.

Can you please look into this issue?

Regards,
Lakhansing Pardeshi.

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[Ka Ming Nip]

Hi Lakhansing,

Can you please send me these 2 files in a private email?
/mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-1.fa
/mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-1.adj

I am a bit busy this week, will definitely look into it next week.

Thanks!

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

From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Lakhansing Pardeshi [lakh...@gmail.com]
Sent: March 30, 2015 10:42 PM

To: trans...@googlegroups.com
Subject: Re: Transabyss-error in running

From: trans...@googlegroups.com<javascript:> [trans...@googlegroups.com<javascript:>] On Behalf Of A.D DILIP [ddili...@gmail.com<javascript:>]

Sent: March 25, 2015 11:35 AM

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

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[Lakhansing Pardeshi]

Hi Ka Ming,

I had sent you the files which you asked. Did you get chance to look into the issue?

Regards,
Lakhan.

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[Ka Ming Nip]

Hi Lakhan,

Sorry, I have had a really tough week.
I am trying to reproduce the results now!

Thanks for your patience.

Ka Ming

--
Ka Ming Nip
Graduate Student
Bioinformatics Technology Lab (Dr. Inanc Birol)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Lakhansing Pardeshi [lakh...@gmail.com]

Sent: April 12, 2015 9:23 PM

To: trans...@googlegroups.com
Subject: Re: Transabyss-error in running

Hi Ka Ming,

I had sent you the files which you asked. Did you get chance to look into the issue?

Regards,
Lakhan.

On Tuesday, March 31, 2015 at 11:25:34 PM UTC+5:30, Ka Ming Nip wrote:
Hi Lakhansing,

Can you please send me these 2 files in a private email?
/mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-1.fa
/mnt/LABS2/IISER_data_analysis/8_invitro/transAbyss/transabyss_37/transabyss_37-1.adj

I am a bit busy this week, will definitely look into it next week.

Thanks!

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

From: trans...@googlegroups.com<javascript:> [trans...@googlegroups.com<javascript:>] On Behalf Of Lakhansing Pardeshi [lakh...@gmail.com<javascript:>]

Sent: March 30, 2015 10:42 PM

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[Ka Ming Nip]

Just an update on this issue...
I was able to reproduce the bug for both Lakhan and Dilip and I traced it back to a module from ABySS called `abyss-filtergraph'.
I would need to file a bug report for the ABySS developers. However, I figured a trick to bypass the bug without a fix in a clunky way... 8-) I will see if I can create a patch later this week or early next week.

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

From: Ka Ming Nip
Sent: April 13, 2015 3:44 PM
To: trans...@googlegroups.com
Subject: RE: Transabyss-error in running

[Lakhansing Pardeshi]

Thats great news...!!! Thanks a lot Ka Ming for working on this bug. :)
I will wait for the patch..

Regards,
Lakhan.

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[Lakhansing Pardeshi]

Hi Ka Ming,

If possible, can you please share the patch for the issue which you traced in `abyss-filtergraph'. I will apply that patch and start reprocessing my data.

Regards,
Lakhan.

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[Ka Ming Nip]

Yes, but I need to make sure that the patch works first!
I'm currently testing on your dataset and Dilip's dataset now.

Ka Ming

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Ka Ming Nip
Graduate Student
Bioinformatics Technology Lab (Dr. Inanc Birol)
Canada's Michael Smith Genome Sciences Centre
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From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Lakhansing Pardeshi [lakh...@gmail.com]

Sent: April 24, 2015 6:20 AM

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[Ka Ming Nip]

Hi,

Thanks for your patience. The bugfix is now on GitHub.
Otherwise, you may apply the patch attached manually, ie.

patch -p1 < 0001-bypass-a-bug-in-abyss-filtergraph.patch

--
Ka Ming Nip
Graduate Student
Bioinformatics Technology Lab (Dr. Inanc Birol)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: Ka Ming Nip

Sent: April 24, 2015 12:23 PM
To: trans...@googlegroups.com
Subject: RE: Transabyss-error in running

[Lakhansing Pardeshi]

Hi Ka Ming,

Thanks a lot for your efforts in fixing the bug. Appreciate the good work you are doing.

Regards,
Lakhan.

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[jean-philippe buffet]

Dear transabyss users and Ka Ming,

I used transabyss 1.5.3 with abyss 1.5.2. It works perfectly with my dataset using low kmers (27 to 61). But I get the same error with high kmers value such as 67, 75, 83 or 91.
Here is the failure I get:

CMD: /usr/local/genome2/transabyss-1.5.3/transabyss --name transabyss-SAB-67 -k 67 --pe /projet/externe/mnhn/jpbuffet/AssemblagesVF/Sabellaria_Trinity/insilico_read_normalization_altogether//left.norm.fq /projet/externe/mnhn/jpbuffet/AssemblagesVF/Sabellaria_Trinity/insilico_read_normalization_altogether//right.norm.fq --outdir /projet/externe/mnhn/jpbuffet/AssemblagesVF/TransABySS/transabyss-SAB-67 --length 200 --threads 24
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Found Trans-ABySS directory at: /usr/local/genome2/transabyss-1.5.3
Found Trans-ABySS `bin` directory at: /usr/local/genome2/transabyss-1.5.3/bin
Found script at: /usr/local/genome2/transabyss-1.5.3/bin/skip_psl_self.awk
Found script at: /usr/local/genome2/transabyss-1.5.3/bin/skip_psl_self_ss.awk
Found `blat' at /usr/local/genome2/bin/blat
Found `MergeContigs' at /usr/local/genome2/abyss/bin/MergeContigs
Found `abyss-filtergraph' at /usr/local/genome2/abyss/bin/abyss-filtergraph
Found `abyss-map' at /usr/local/genome2/abyss/bin/abyss-map
Found `abyss-pe' at /usr/local/genome2/abyss/bin/abyss-pe
Found `abyss-junction' at /usr/local/genome2/abyss/bin/abyss-junction
CMD: bash -euo pipefail -c 'abyss-pe --directory=/projet/externe/mnhn/jpbuffet/AssemblagesVF/TransABySS/transabyss-SAB-67 k=67 name=transabyss-SAB-67 E=0 e=2 c=2 j=24 transabyss-SAB-67-1.fa transabyss-SAB-67-1.adj q=3 se="/projet/externe/mnhn/jpbuffet/AssemblagesVF/Sabellaria_Trinity/insilico_read_normalization_altogether/left.norm.fq /projet/externe/mnhn/jpbuffet/AssemblagesVF/Sabellaria_Trinity/insilico_read_normalization_altogether/right.norm.fq"'
make: Entering directory `/projet/externe/mnhn/jpbuffet/AssemblagesVF/TransABySS/transabyss-SAB-67'
ABYSS -k67 -q3 -e2 -E0 -c2   --coverage-hist=coverage.hist -s transabyss-SAB-67-bubbles.fa  -o transabyss-SAB-67-1.fa  /projet/externe/mnhn/jpbuffet/AssemblagesVF/Sabellaria_Trinity/insilico_read_normalization_altogether/left.norm.fq /projet/externe/mnhn/jpbuffet/AssemblagesVF/Sabellaria_Trinity/insilico_read_normalization_altogether/right.norm.fq
make: Leaving directory `/projet/externe/mnhn/jpbuffet/AssemblagesVF/TransABySS/transabyss-SAB-67'
ERROR: CMD ended with status code 2

How can I do to solve this issue ?

Thanks in advance for your response.
Best regards

Jean-Philippe

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[Ka Ming Nip]

Hi Jean-Philippe,

The error that you got here is not the same as the one reported previously in this thread.

The default max kmer for ABySS is 64, that's why you cannot assemble with longer kmer lengths such as 67, 75, 83 or 91.
To solve this issue, please reconfigure and then recompile ABySS to use a larger max kmer length, ie.

./configure --enable-maxk=96

Hope that helps!

Ka Ming


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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 jean-philippe buffet [jeanphili...@gmail.com]
Sent: May 12, 2016 5:35 AM
To: Trans-ABySS

Subject: Re: Transabyss-error in running

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

Subject: RE: Transabyss-error in running

Yes, but I need to make sure that the patch works first!
I'm currently testing on your dataset and Dilip's dataset now.

Ka Ming

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

From: trans...@googlegroups.com<javascript:> [trans...@googlegroups.com<javascript:>] On Behalf Of Lakhansing Pardeshi [lakh...@gmail.com<javascript:>]

Sent: April 24, 2015 6:20 AM

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[jean-philippe buffet]

Thanks a lot Ka Ming for your fast and clear answer !

I am trying to reconfigure abyss with this command.

All the best,
Jean-Philippe

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