Comments (5)
oschwengers
commented on June 1, 2024
Hi George,
due to the assembly log file there is an internal bug within the Daligner tool of the SMRT package (HGAP). Unfortunately, I cannot further deep dive into it right now. We tested the Docker image on Mac OS. But it could be, that it has only been tested with Illumina data, only. I will check this, but it might take a while.
Just in case you have Illumina/ONT data only, you might try the other example (example-lmonocytogenes-4.tar.gz).
from asap.
gtsiamis
commented on June 1, 2024
Hi Oliver,
I tried the lmonocytogenes-4 example and I get similar errors. Please see
attached log file.
Regards
George
…On Mon, 9 Nov 2020 at 09:37, Oliver Schwengers ***@***.***> wrote:
Hi George,
due to the assembly log file there is an internal bug within the Daligner
tool of the SMRT package (HGAP). Unfortunately, I cannot further deep dive
into it right now. We tested the Docker image on Mac OS. But it could be,
that it has only been tested with Illumina data, only. I will check this,
but it might take a while.
Just in case you have Illumina/ONT data only, you might try the other
example (example-lmonocytogenes-4.tar.gz).
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Department of Environmental Engineering
p: +30 26410 74149 m: +30 697 6685 012 a: 2 Seferi St., 30100, Agrinio,
Greece
e: [email protected]; [email protected] s: gtsiamis
*Specialty Chief Editor Systems Microbiology*
*https://www.frontiersin.org/journals/microbiology/sections/systems-microbiology
<https://www.frontiersin.org/journals/microbiology/sections/systems-microbiology>*
*www.biodetect.co <http://www.biodetect.co>*
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oschwengers
commented on June 1, 2024
Could you provide the log files of the example-lmonocytogenes run?
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gtsiamis
commented on June 1, 2024
Dear Oliver,
I set up a Linux virtual machine and I was able to work around most of the
issues. I notice that in the lmonocytogenes-4 and in the lmonocytogenes-32
examples that although all genome analyses and comparative analyses have
been completed the abr has failed in both .
I am attaching the asap log file and the abr.log files.
Regards
George
…On Tue, 10 Nov 2020 at 15:49, Oliver Schwengers ***@***.***> wrote:
Could you provide the log files of the example-lmonocytogenes run?
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.
--
George Tsiamis, PhD
Associate Professor - University of Patras
Department of Environmental Engineering
p: +30 26410 74149 m: +30 697 6685 012 a: 2 Seferi St., 30100, Agrinio,
Greece
e: [email protected]; [email protected] s: gtsiamis
*Specialty Chief Editor Systems Microbiology*
*https://www.frontiersin.org/journals/microbiology/sections/systems-microbiology
<https://www.frontiersin.org/journals/microbiology/sections/systems-microbiology>*
*www.biodetect.co <http://www.biodetect.co>*
from asap.
oschwengers
commented on June 1, 2024
Hello @gtsiamis , sorry for the late reply, but I still need the log files. It looks like you maybe responded via email? If this is the case, it doesn't work. If this bug is still relevant, could you please provide the files via the GitHub webpage?
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Related Issues (20)
- characterization steps failed HOT 12
- Download of "main" tarball fails HOT 2
- [help] pipeline stuck HOT 9
- Rewrite Readme by usage of an popular template and adding a Makefile ✍️ HOT 1
- add input support HOT 2
- Doesn't work under conda HOT 2
- User facing issue during QC step HOT 8
- Add resume option
- abr fails with example data HOT 4
- Random Genome Failings HOT 4
- helper tool [suggestion] HOT 1
- max waiting period (86400000 s) exceeded! HOT 2
- Issues downloading asap.tar.gz HOT 4
- M1 Macbook compatibility HOT 1
- Groovy error at startup HOT 3
- Java.lang.IllegalStateException: abnormal ABR exit code! exitCode=1
- how to avoid sudo privileges while using the docker container? HOT 1
- asap/asap-docker.sh script can not be found in its container HOT 2
- Question: how to specify threads in asap-docker.sh? HOT 3
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