GabeAl
commented
6 years ago Hi, thanks for the report!
Could you tell me a bit more about the target computer(s) this fails on? What is the memory (RAM) and CPU?
I'll look into this! Gabe
On Thu, Apr 19, 2018, 8:45 PM Jon Sanders notifications@github.com wrote:
Hey guys,
We've been trying to track down a problem while adapting SHOGUN to Qiita, the symptom of which was finding this message when running integration tests in Travis:
- File "/home/travis/build/qiita-spots/qp-shotgun/miniconda3/envs/qp-shotgun/lib/python3.5/site-packages/pandas/core/groupby.py", line 2934, in _get_grouper
- raise KeyError(gpr)
- KeyError: 'summary'
@antgonza https://github.com/antgonza also was having the same error on his OS X install, but neither I (on Barnacle) nor @semarpetrus https://github.com/semarpetrus (on his Linux box) were encountering it.
Running SHOGUN directly using the following commands yielded a good alignment + downstream files on Barnacle:
aln_out=foo.align database=/home/jgsanders/git_sw/qp-shotgun/qp_shotgun/shogun/databases/shogun level=species aligner=burst threads=8 profile=profile.tsv aln_out_fp=foo.align/alignment.burst.b6 redistributed="profile.${level}.tsv" fun_output=functional
shogun align \ --aligner ${aligner} \ --threads ${threads} \ --database ${database} \ --input combined.fna \ --output ${aln_out}
shogun assign_taxonomy \ --aligner ${aligner} \ --database ${database} \ --input ${aln_out_fp} \ --output ${profile}
shogun redistribute \ --database ${database} \ --level ${level} \ --input ${profile} \ --output ${redistributed}
fun_level=$level shogun functional \ --database ${database} \ --input ${profile} \ --output ${fun_output} \ --level ${fun_level}
where the test database is here https://github.com/antgonza/qp-shotgun/blob/shogun/qp_shotgun/shogun/databases/shogun.tar.bz2 and the input data are here https://www.dropbox.com/s/ocu4c0ft8vhbjwx/combined.fna?dl=0
Running the same align command on an OS X box (using Gabe's supplied burst15 binary) ran for a bit and then produced an empty .b6 output file.
Running BURST directly on the OS X box produced the following output:
burst15 --references qp_shotgun/shogun/databases/shogun/burst/5min.edx --queries combined.fna --output test.b6 --accelerator qp_shotgun/shogun/databases/shogun/burst/5min.acx This is BURST [v0.99.7LL] --> Using accelerator file qp_shotgun/shogun/databases/shogun/burst/5min.acx Using up to AVX-128 with 8 threads. --> [Accel] Accelerator found. Parsing... --> [Accel] Total accelerants: 805949 [bytes = 2106932] --> [Accel] Reading 0 ambiguous entries
EDB database provided. Parsing... --> EDB: Fingerprints are DISABLED --> EDB: Parsing compressed headers --> EDB: Sheared database (shear size = 515) --> EDB: 970 refs [970 orig], 61 clumps, 1030 maxR Parsed 400000 queries (0.071752). Calculating minMax... Found min 150, max 150 (0.000109). Converting queries... Converted (0.007549) Copying queries... Copied (0.002561) Sorting queries... Sorted (0.088294) Copying indices... Copied (0.001531) Determining uniqueness... Done (0.007544). Number unique: 397338 Collecting unique sequences... Done (0.001721) Creating data structures... Done (0.004528) [maxED: 4] Determining query ambiguity... Determined (0.023589) Creating bins... Created (0.011927); Unambig: 391663, ambig: 5675, super-ambig: 0 [5675,397338,397338] Re-sorting... Re-sorted (0.194431) Calculating divergence... Calculated (0.009815) [10.120026 avg div; 150 max] Fingerprints not enabled Setting QBUNCH to 16 Using ACCELERATOR to align 397338 unique queries... Search Progress: [100.00%] Search complete. Consolidating results... Segmentation fault: 11
What do you think?
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antgonza
bhillmann
tanaes
H2CO3
Hey guys,
We've been trying to track down a problem while adapting SHOGUN to Qiita, the symptom of which was finding this message when running integration tests in Travis:
@antgonza also was having the same error on his OS X install, but neither I (on Barnacle) nor @semarpetrus (on his Linux box) were encountering it.
Running SHOGUN directly using the following commands yielded a good alignment + downstream files on Barnacle:
where the test database is here and the input data are here
Running the same align command on an OS X box (using Gabe's supplied burst15 binary) ran for a bit and then produced an empty
.b6output file.Running BURST directly on the OS X box produced the following output:
What do you think?