Question: (Closed) ABySS fails to write out coverage.hist file and stops
0
gravatar for lieven.sterck
3.6 years ago by
lieven.sterck6.0k
VIB, Ghent, Belgium
lieven.sterck6.0k wrote:

Dear,

I'm running on assembly on our universities HPC cluster but unfortunately it is not working very well. The process successfully reads in the data files but then it fails in one of the next steps with the following error:

ABYSS-P: ../Assembly/CoverageAlgorithm.h:80: void AssemblyAlgorithms::setCoverageParameters(const Histogram &): Assertion `histFile.good()' failed.
make: *** [Test1-1.fa] Error 134

As far as I can see, there is a coverage.hist file created but it remains empty.

Here is the cmdline I use to start the assembly:

abyss-pe name=Test1 k=64 np=3 in='C1J25ACXX_1_0_1.clean.fq.gz C1J25ACXX_1_0_2.clean.fq.gz' se='C1J25ACXX_1_0.singl.fq.gz'

/apps/software/impi/5.0.2.044-iccifort-2015.1.133-GCC-4.9.2/bin64/mpirun -np 3 \
        ABYSS-P -k64 -q3 -v \
        --coverage-hist=coverage.hist \
        -s Test1-bubbles.fa  \
        -o Test1-1.fa \
        C1J25ACXX_1_0_1.clean.fq.gz \
        C1J25ACXX_1_0_2.clean.fq.gz \
        C1J25ACXX_1_0.singl.fq.gz

After reading in the data I get the following message in my STDOUT file:

1: Read 123000000 reads. 1: Hash load: 2181361997 / 4294967296 = 0.508 using 75.7 GB
1: Read 123100000 reads. 1: Hash load: 2181932089 / 4294967296 = 0.508 using 75.7 GB
1: Read 123129475 reads. 1: Hash load: 2182094879 / 4294967296 = 0.508 using 75.8 GB
0: Loaded 12: Loaded 2182154414 k-mer.
2: 2182061765 k-mer.
0: Hash load: 2182061765 / 4294967296 = 0.508 using : Loaded 2182094879Hash load: 2182154414 / 4294967296 = 75.8 GB
 k-mer.
10.508 using : Hash load: 2182094879 / 4294967296 = 0.508 using 75.7 G75.8 GB
B
Loaded 6546311058 k-mer. At least 209 GB of RAM is required.

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 144429 RUNNING AT smp1
=   EXIT CODE: 134
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
Sun Feb 21 03:22:41 CET 2016
========================================================================

Grateful for any help/advise.

wkr,

lieven

abyss assembly • 1.9k views
ADD COMMENTlink modified 13 months ago by RamRS24k • written 3.6 years ago by lieven.sterck6.0k

That's odd. I've never seen any ABySS job fail while attempting to write that file. Btw, coverage.hist is the first file that the assembly pipeline tries to create.

The only thing I can guess is that you are running the assembly in a directory where you don't have write permissions or where you have exceeded your disk quota. To clarify the problem, you could perhaps try running a simple test job where you attempt to write "hello world" to a file, or something like that.

ADD REPLYlink modified 13 months ago by RamRS24k • written 3.6 years ago by benv710

Hello lieven.sterck!

We believe that this post does not fit the main topic of this site.

Issue resolved. It was due to a conflicting share access configuration on our HPC system.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 13 months ago by RamRS24k • written 3.6 years ago by lieven.sterck6.0k
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