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oschwengers / asap

A scalable bacterial genome assembly, annotation and analysis pipeline
https://doi.org/10.1371/journal.pcbi.1007134
GNU General Public License v3.0
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Tutorial error #18

Open gtsiamis opened 3 years ago

gtsiamis commented 3 years ago

I am working in bacterial strains isolated from insect-guts and we have several strains sequenced. Asap looks like the kind of program that will very much fit the needs of the analysis that we are looking for.

I am working on a Mac with 128GB of RAM with Mac OS X 10.13.6.

Installation of asap was smooth without any issues. So in order to see that everything is working properly, I run the tutorial/example with the ecoli data.

At the end of the run, the assembly step has failed together with the mlst analysis. I am attaching the asap.log and also the assembly log. Any suggestions?

Regards George

asap.log std.log

oschwengers commented 3 years ago

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).

gtsiamis commented 3 years ago

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 notifications@github.com 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).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/oschwengers/asap/issues/18#issuecomment-723825884, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAUCELEGNW7NEHSDWLAQN3LSO6L33ANCNFSM4TO46H5A .

--

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: gtsiamis@upatras.gr; gtsiamis1@gmail.com 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

oschwengers commented 3 years ago

Could you provide the log files of the example-lmonocytogenes run?

gtsiamis commented 3 years ago

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 notifications@github.com wrote:

Could you provide the log files of the example-lmonocytogenes run?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/oschwengers/asap/issues/18#issuecomment-724712992, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAUCELGZAXAMPL34FT2N2X3SPFAFHANCNFSM4TO46H5A .

--

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: gtsiamis@upatras.gr; gtsiamis1@gmail.com 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

oschwengers commented 3 years ago

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?