Question: Abyss error: duplicate ID
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gravatar for xzhouaw
7 months ago by
xzhouaw0
xzhouaw0 wrote:

I am fresh in genome assembly. Now I have 200bp paired end sequence data of a mouse cell line in hand and want to assemble it with Abyss 2.0 since it can run in multiple cluster nodes parallelly. the command line I used is attached below :

> $PATH/mpiexec --mca opal_cuda_support 1 abyss-pe name=test-1 k=50 in='V300032821_8A_L03_13.R1.fastq V300032821_8A_L03_13.R2.fastq'  B=100G H=32 kc=3 v=-v np=4

I submitted it to the cluster and used 4 nodes to run it. It can load reads into Bloom filter and process normally. But after that it gave an error as the following:

Assembly complete
AdjList -v -k50 -m0 --dot test-1-1.fa > test-1-1.dot Reading `test-1-1.fa'...

error: duplicate ID: `4079879'

bash: line 1: 4493 Aborted

(core dumped)

AdjList -v -k50 -m0 --dot test-1-1.fa > test-1-1.dot

make: * [/home4/xzhouaw/miniconda2/bin/abyss-pe.Makefile:560: test-1-1.dot] Error 134

make: * Deleting file 'test-1-1.dot'

-------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- make: * Deleting file 'test-1-1.fa' make: wait: No child processes. Stop. make: Waiting for unfinished jobs.... make: wait: No child processes. Stop. make: wait: No child processes. Stop. make: Waiting for unfinished jobs.... make: wait: Nochild processes. Stop. make: wait: No child processes. Stop. make: Waiting for unfinished jobs.... make: * wait: No child processes. Stop. -------------------------------------------------------------------------- mpiexec detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:

Process name: [[4772,1],2] Exit code: 2

I cannot check whether the duplicate ID is present in test-1-1.fa because the pipeline directly deleted the fa file. I am wondering why Abyss gave this error and what is the solution?

Thanks !!

abyss tool assembly • 188 views
ADD COMMENTlink written 7 months ago by xzhouaw0

Sounds like abyss did assemble two regions giving them the same ID. (which should not happen).

Can you also check if your cmdline syntax is OK (have a look in the manual for ABySS to see how to start it with mpi support)

Is 2.0 the latest version you have installed. I think there already at 2.2.4 or something? (perhaps updating to a newer version might help?)

otherwise you can always post a bug report on their github : https://github.com/bcgsc/abyss/issues

ADD REPLYlink modified 7 months ago • written 7 months ago by lieven.sterck8.7k

Thanks for your reply! Yes, I checked the manual and followed it to use "np" to identify processing nodes. Since my cluster needs to open mpi support by adding "$PATH/mpiexec --mca opal_cuda_support 1" before the command, so I think the command is correct. My AByss is the lastest version: 2.2.4.

ADD REPLYlink written 7 months ago by xzhouaw0

not 100% sure but the np parameter points to the number of threads it's gonna use, not necessarily to the number of nodes you want to use. (but that should not have any influence on the current issue I assume)

ADD REPLYlink written 7 months ago by lieven.sterck8.7k
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