Comments (6)
When I do this it seems to progress as expected up until alignment of the 16th sequence, at which point it aborts with the following error message:
I'm assuming you meant 16th file. The loop you posted should not affect SINA in any way at all. Does that file fail if run directly? Or really only in the loop?
Time for alignment phase: 41.081814s
Terminating PT server…
ARB_PT_SERVER: received shutdown message
That's not an error, but should always be the last bit. You can in theory start an ARB PT server on your own, and point SINA to the server using "--pt-port" (and "--search-db-port"), to save on startup time with small files. If you don't, SINA will start one itself and terminate it once SINA is finished. That's the output you are seeing, SINA saying Terminating PT server
and the PT server than saying received shutdown message
.
If the file is empty, that may just mean that nothing in there was sufficiently similar to 16S to even have an alignment. Try without the classifier, that should get you more results.
I tried using --search-all within the loop and that worked fine, but was too slow. I’d like to run the loop with the PT server, so any suggestions would be much appreciated!
Yes, that's more of a debug feature. SINA will use a k-mer heuristic to find the most similar sequences (top 1000 by default) and then uses the alignment to compute a score on those. With --search-all
it will check each input sequence against each reference sequence, which with a big database just takes forever indeed. It doesn't gain you much either. You can test by increasing the output from the heuristic and watching the results (not) change (--search-kmer-candidates 10000
shouldn't get you much else than the default, and --search-kmer-candidates 100
should only see a minor benefit on performance).
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No, I was meaning the 16th sequence in the first file (which is why it seemed very strange). I tried running the file directly and it worked fine, it only aborts early when in the loop.
I'll try a few other things and see if I can resolve what it going on - thanks
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Ok. Please close this if you figure out what went wrong. It does sound to me like SINA terminated normally after 16 sequences. Perhaps the command line wasn't exactly the same (forgotten \
at the end of a line in your script or something similar).
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Yes, I see now, you are correct - the loop ran file 10 (containing 16 sequences) before file 1 (containing 600 sequences) . However, the PT Server terminated at the end of running the first file, so the loop failed. Is there any way to run multiple files without the Server terminating?
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However, the PT Server terminated at the end of running the first file, so the loop failed.
No. The PT server terminated, as did SINA, because they were finished. That was not an error. Put echo SINA exited with code $?;
into your loop to have bash print the exit code, it should be 0.
Is there any way to run multiple files without the Server terminating?
Quoting myself from above:
That's not an error, but should always be the last bit. You can in theory start an ARB PT server on your own, and point SINA to the server using "--pt-port" (and "--search-db-port"), to save on startup time with small files. If you don't, SINA will start one itself and terminate it once SINA is finished. That's the output you are seeing, SINA saying Terminating PT server and the PT server than saying received shutdown message.
However, it's not really necessary.
Here's a script for running many instances of SINA in parallel on a single large file: https://github.com/epruesse/SINA/blob/master/src/psina
Works just fine for me (if you use that, watch out for memory, no more than one thread per 16GB if you use e.g. the SILVA DB - PT server is quite memory hungry).
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Thanks!
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Related Issues (20)
- Problems installing sina on macOS Big Sur HOT 1
- Failing to load db index HOT 4
- error while loading shared libraries: libtbb.so.2 HOT 6
- Support arb 7.0
- Compile issue on Debian 10 (linker command line)
- Problem building / installing documentation on Debian 10
- libboost library conflict with qiime2 HOT 3
- sina not working within a docker container HOT 2
- Replace LCA classifier HOT 2
- SINA not processing fasta files that have been filtered using vsearch HOT 2
- sina keeps rebuilding pt-server from scratch HOT 2
- Sina does not actually output LCA classification anymore? HOT 3
- Implement banded alignment
- Problems with LCA quorum HOT 7
- Base shift in copied alignment HOT 3
- How could I calculate identity between two 16S rDNA sequence? HOT 1
- necessary fields for "-f" not stated correctly in documentation, and also not given by "--arb-list-fields"? HOT 1
- Custom ARB database has no taxonomy fields HOT 1
- build failure ‘tbb_allocator’ is not a member of ‘tbb’ HOT 8
- --add-relatives outputs unexpected sequence ID HOT 3
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