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knights-lab / SHOGUN

SHallow shOtGUN profiler
GNU Affero General Public License v3.0
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Test failed after installing with conda #41

Closed ShixiangWang closed 2 years ago

ShixiangWang commented 2 years ago

Any suggestion?

$ python -m unittest discover shogun
/home/zhou/soft/SHOGUN/shogun/__main__.py:109: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if level is not 'off':
...E./home/zhou/soft/SHOGUN/shogun/aligners/burst_aligner.py:79: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  df = pd.DataFrame(samples_lca_map, dtype=np.int).fillna(0).astype(np.int)
.E.../home/zhou/soft/SHOGUN/shogun/function/_function.py:99: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  kegg_table = np.zeros((num_samples, num_kegg_ids), dtype=np.int)
12/14/2021 07:30:10 PM : WARNING : Overlap of taxa and function 0.38
/home/zhou/soft/SHOGUN/shogun/function/_function.py:118: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  columns=sorted(column_names, key=column_names.get), dtype=np.int).T
/home/zhou/soft/SHOGUN/shogun/function/_function.py:99: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  kegg_table = np.zeros((num_samples, num_kegg_ids), dtype=np.int)
/home/zhou/soft/SHOGUN/shogun/function/_function.py:118: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  columns=sorted(column_names, key=column_names.get), dtype=np.int).T
/home/zhou/soft/SHOGUN/shogun/function/_function.py:99: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  kegg_table = np.zeros((num_samples, num_kegg_ids), dtype=np.int)
/home/zhou/soft/SHOGUN/shogun/function/_function.py:118: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  columns=sorted(column_names, key=column_names.get), dtype=np.int).T
.....12/14/2021 07:30:20 PM : DEBUG : Initiate Logger bowtie2
12/14/2021 07:30:20 PM : DEBUG : bowtie2 --no-unal -x /home/zhou/soft/SHOGUN/shogun/tests/data/bowtie2/genomes.small -S /tmp/shogun-temp-dir-_v06qqbg/alignment.bowtie2.sam --np 1 --mp "1,1" --rdg "0,1" --rfg "0,1" --score-min "L,0,-0.02" -f /home/zhou/soft/SHOGUN/shogun/tests/data/combined_seqs.fna --very-sensitive -k 16 -p 96 --reorder --no-hd
12/14/2021 07:30:21 PM : DEBUG : 300 reads; of these:
12/14/2021 07:30:21 PM : DEBUG :   300 (100.00%) were unpaired; of these:
12/14/2021 07:30:21 PM : DEBUG :     112 (37.33%) aligned 0 times
12/14/2021 07:30:21 PM : DEBUG :     161 (53.67%) aligned exactly 1 time
12/14/2021 07:30:21 PM : DEBUG :     27 (9.00%) aligned >1 times
12/14/2021 07:30:21 PM : DEBUG : 62.67% overall alignment rate
12/14/2021 07:30:21 PM : DEBUG : 1.17 seconds
12/14/2021 07:30:21 PM : DEBUG : Subprocess finished.
12/14/2021 07:30:21 PM : DEBUG : Beginning post align with aligner bowtie2
12/14/2021 07:30:21 PM : DEBUG : strain
12/14/2021 07:30:21 PM : DEBUG : Beginning redistribution for file: /tmp/shogun-temp-dir-_v06qqbg/taxatable.bowtie2.txt
12/14/2021 07:30:21 PM : DEBUG : Attempting to load the database metadata file at /home/zhou/soft/SHOGUN/shogun/tests/data/metadata.yaml
.12/14/2021 07:30:22 PM : DEBUG : Initiate Logger burst
12/14/2021 07:30:22 PM : DEBUG : burst15 --queries /home/zhou/soft/SHOGUN/shogun/tests/data/combined_seqs.fna --references /home/zhou/soft/SHOGUN/shogun/tests/data/burst/genomes.small.edx --output /tmp/shogun-temp-dir-dcftb54i/alignment.burst.b6 --threads 96 --mode CAPITALIST --id 0.98 --npenalize --skipambig --forwardreverse --taxonomy /home/zhou/soft/SHOGUN/shogun/tests/data/genomes.small.tax --taxacut 5
F12/14/2021 07:30:22 PM : DEBUG : Initiate Logger utree
12/14/2021 07:30:22 PM : DEBUG : utree-search_gg /home/zhou/soft/SHOGUN/shogun/tests/data/utree/genomes.small.ctr /home/zhou/soft/SHOGUN/shogun/tests/data/combined_seqs.fna /tmp/shogun-temp-dir-9vcarvdg/alignment.utree.tsv 96 RC
F.........................12/14/2021 07:30:22 PM : DEBUG : bowtie2 --no-unal -x /home/zhou/soft/SHOGUN/shogun/tests/data/bowtie2/genomes.small -S /tmp/shogun-test-temp-qre7e33a/sims.sam --np 1 --mp "1,1" --rdg "0,1" --rfg "0,1" --score-min "L,0,-0.02" -f /home/zhou/soft/SHOGUN/shogun/tests/data/combined_seqs.fna --very-sensitive -k 16 -p 1 --reorder --no-hd
12/14/2021 07:30:22 PM : DEBUG : 300 reads; of these:
12/14/2021 07:30:22 PM : DEBUG :   300 (100.00%) were unpaired; of these:
12/14/2021 07:30:22 PM : DEBUG :     112 (37.33%) aligned 0 times
12/14/2021 07:30:22 PM : DEBUG :     161 (53.67%) aligned exactly 1 time
12/14/2021 07:30:22 PM : DEBUG :     27 (9.00%) aligned >1 times
12/14/2021 07:30:22 PM : DEBUG : 62.67% overall alignment rate
12/14/2021 07:30:22 PM : DEBUG : 0.23 seconds
12/14/2021 07:30:22 PM : DEBUG : Subprocess finished.
.12/14/2021 07:30:22 PM : DEBUG : bowtie2-build -f /home/zhou/soft/SHOGUN/shogun/tests/data/genomes.small.fna /tmp/shogun-test-temp-fr3jjj80/genomes.small
12/14/2021 07:30:22 PM : DEBUG : Settings:
12/14/2021 07:30:22 PM : DEBUG :   Output files: "/tmp/shogun-test-temp-fr3jjj80/genomes.small.*.bt2"
12/14/2021 07:30:22 PM : DEBUG :   Line rate: 6 (line is 64 bytes)
12/14/2021 07:30:22 PM : DEBUG :   Lines per side: 1 (side is 64 bytes)
12/14/2021 07:30:22 PM : DEBUG :   Offset rate: 4 (one in 16)
12/14/2021 07:30:22 PM : DEBUG :   FTable chars: 10
12/14/2021 07:30:22 PM : DEBUG :   Strings: unpacked
12/14/2021 07:30:22 PM : DEBUG :   Max bucket size: default
12/14/2021 07:30:22 PM : DEBUG :   Max bucket size, sqrt multiplier: default
12/14/2021 07:30:22 PM : DEBUG :   Max bucket size, len divisor: 4
12/14/2021 07:30:22 PM : DEBUG :   Difference-cover sample period: 1024
12/14/2021 07:30:22 PM : DEBUG :   Endianness: little
12/14/2021 07:30:22 PM : DEBUG :   Actual local endianness: little
12/14/2021 07:30:22 PM : DEBUG :   Sanity checking: disabled
12/14/2021 07:30:22 PM : DEBUG :   Assertions: disabled
12/14/2021 07:30:22 PM : DEBUG :   Random seed: 0
12/14/2021 07:30:22 PM : DEBUG :   Sizeofs: void*:8, int:4, long:8, size_t:8
12/14/2021 07:30:22 PM : DEBUG : Input files DNA, FASTA:
12/14/2021 07:30:22 PM : DEBUG :   /home/zhou/soft/SHOGUN/shogun/tests/data/genomes.small.fna
12/14/2021 07:30:22 PM : DEBUG : Building a SMALL index
12/14/2021 07:30:22 PM : DEBUG : Reading reference sizes
12/14/2021 07:30:22 PM : DEBUG :   Time reading reference sizes: 00:00:00
12/14/2021 07:30:22 PM : DEBUG : Calculating joined length
12/14/2021 07:30:22 PM : DEBUG : Writing header
12/14/2021 07:30:22 PM : DEBUG : Reserving space for joined string
12/14/2021 07:30:22 PM : DEBUG : Joining reference sequences
12/14/2021 07:30:22 PM : DEBUG :   Time to join reference sequences: 00:00:00
12/14/2021 07:30:22 PM : DEBUG : bmax according to bmaxDivN setting: 195017
12/14/2021 07:30:22 PM : DEBUG : Using parameters --bmax 146263 --dcv 1024
12/14/2021 07:30:22 PM : DEBUG :   Doing ahead-of-time memory usage test
12/14/2021 07:30:22 PM : DEBUG :   Passed!  Constructing with these parameters: --bmax 146263 --dcv 1024
12/14/2021 07:30:22 PM : DEBUG : Constructing suffix-array element generator
12/14/2021 07:30:22 PM : DEBUG : Building DifferenceCoverSample
12/14/2021 07:30:22 PM : DEBUG :   Building sPrime
12/14/2021 07:30:22 PM : DEBUG :   Building sPrimeOrder
12/14/2021 07:30:22 PM : DEBUG :   V-Sorting samples
12/14/2021 07:30:22 PM : DEBUG :   V-Sorting samples time: 00:00:00
12/14/2021 07:30:22 PM : DEBUG :   Allocating rank array
12/14/2021 07:30:22 PM : DEBUG :   Ranking v-sort output
12/14/2021 07:30:22 PM : DEBUG :   Ranking v-sort output time: 00:00:00
12/14/2021 07:30:22 PM : DEBUG :   Invoking Larsson-Sadakane on ranks
12/14/2021 07:30:22 PM : DEBUG :   Invoking Larsson-Sadakane on ranks time: 00:00:00
12/14/2021 07:30:22 PM : DEBUG :   Sanity-checking and returning
12/14/2021 07:30:22 PM : DEBUG : Building samples
12/14/2021 07:30:22 PM : DEBUG : Reserving space for 12 sample suffixes
12/14/2021 07:30:22 PM : DEBUG : Generating random suffixes
12/14/2021 07:30:22 PM : DEBUG : QSorting 12 sample offsets, eliminating duplicates
12/14/2021 07:30:22 PM : DEBUG : QSorting sample offsets, eliminating duplicates time: 00:00:00
12/14/2021 07:30:22 PM : DEBUG : Multikey QSorting 12 samples
12/14/2021 07:30:22 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:22 PM : DEBUG :   Multikey QSorting samples time: 00:00:00
12/14/2021 07:30:22 PM : DEBUG : Calculating bucket sizes
12/14/2021 07:30:22 PM : DEBUG : Splitting and merging
12/14/2021 07:30:22 PM : DEBUG :   Splitting and merging time: 00:00:00
12/14/2021 07:30:22 PM : DEBUG : Avg bucket size: 97507.8 (target: 146262)
12/14/2021 07:30:22 PM : DEBUG : Converting suffix-array elements to index image
12/14/2021 07:30:22 PM : DEBUG : Allocating ftab, absorbFtab
12/14/2021 07:30:22 PM : DEBUG : Entering Ebwt loop
12/14/2021 07:30:22 PM : DEBUG : Getting block 1 of 8
12/14/2021 07:30:22 PM : DEBUG :   Reserving size (146263) for bucket 1
12/14/2021 07:30:22 PM : DEBUG :   Calculating Z arrays for bucket 1
12/14/2021 07:30:22 PM : DEBUG :   Entering block accumulator loop for bucket 1:
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 10%
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 20%
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 30%
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 40%
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 50%
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 60%
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 70%
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 80%
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 90%
12/14/2021 07:30:22 PM : DEBUG :   bucket 1: 100%
12/14/2021 07:30:22 PM : DEBUG :   Sorting block of length 105140 for bucket 1
12/14/2021 07:30:22 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:22 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:22 PM : DEBUG : Returning block of 105141 for bucket 1
12/14/2021 07:30:22 PM : DEBUG : Getting block 2 of 8
12/14/2021 07:30:22 PM : DEBUG :   Reserving size (146263) for bucket 2
12/14/2021 07:30:22 PM : DEBUG :   Calculating Z arrays for bucket 2
12/14/2021 07:30:22 PM : DEBUG :   Entering block accumulator loop for bucket 2:
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 10%
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 20%
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 30%
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 40%
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 50%
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 60%
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 70%
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 80%
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 90%
12/14/2021 07:30:22 PM : DEBUG :   bucket 2: 100%
12/14/2021 07:30:22 PM : DEBUG :   Sorting block of length 117607 for bucket 2
12/14/2021 07:30:22 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:22 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:22 PM : DEBUG : Returning block of 117608 for bucket 2
12/14/2021 07:30:23 PM : DEBUG : Getting block 3 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 3
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 3
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 3:
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 56295 for bucket 3
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 56296 for bucket 3
12/14/2021 07:30:23 PM : DEBUG : Getting block 4 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 4
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 4
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 4:
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 101433 for bucket 4
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 101434 for bucket 4
12/14/2021 07:30:23 PM : DEBUG : Getting block 5 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 5
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 5
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 5:
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 125010 for bucket 5
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 125011 for bucket 5
12/14/2021 07:30:23 PM : DEBUG : Getting block 6 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 6
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 6
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 6:
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 119654 for bucket 6
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 119655 for bucket 6
12/14/2021 07:30:23 PM : DEBUG : Getting block 7 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 7
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 7
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 7:
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 122986 for bucket 7
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 122987 for bucket 7
12/14/2021 07:30:23 PM : DEBUG : Getting block 8 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 8
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 8
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 8:
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 31937 for bucket 8
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 31938 for bucket 8
12/14/2021 07:30:23 PM : DEBUG : Exited Ebwt loop
12/14/2021 07:30:23 PM : DEBUG : fchr[A]: 0
12/14/2021 07:30:23 PM : DEBUG : fchr[C]: 226540
12/14/2021 07:30:23 PM : DEBUG : fchr[G]: 388187
12/14/2021 07:30:23 PM : DEBUG : fchr[T]: 554183
12/14/2021 07:30:23 PM : DEBUG : fchr[$]: 780069
12/14/2021 07:30:23 PM : DEBUG : Exiting Ebwt::buildToDisk()
12/14/2021 07:30:23 PM : DEBUG : Returning from initFromVector
12/14/2021 07:30:23 PM : DEBUG : Wrote 4454705 bytes to primary EBWT file: /tmp/shogun-test-temp-fr3jjj80/genomes.small.1.bt2
12/14/2021 07:30:23 PM : DEBUG : Wrote 195024 bytes to secondary EBWT file: /tmp/shogun-test-temp-fr3jjj80/genomes.small.2.bt2
12/14/2021 07:30:23 PM : DEBUG : Re-opening _in1 and _in2 as input streams
12/14/2021 07:30:23 PM : DEBUG : Returning from Ebwt constructor
12/14/2021 07:30:23 PM : DEBUG : Headers:
12/14/2021 07:30:23 PM : DEBUG :     len: 780069
12/14/2021 07:30:23 PM : DEBUG :     bwtLen: 780070
12/14/2021 07:30:23 PM : DEBUG :     sz: 195018
12/14/2021 07:30:23 PM : DEBUG :     bwtSz: 195018
12/14/2021 07:30:23 PM : DEBUG :     lineRate: 6
12/14/2021 07:30:23 PM : DEBUG :     offRate: 4
12/14/2021 07:30:23 PM : DEBUG :     offMask: 0xfffffff0
12/14/2021 07:30:23 PM : DEBUG :     ftabChars: 10
12/14/2021 07:30:23 PM : DEBUG :     eftabLen: 20
12/14/2021 07:30:23 PM : DEBUG :     eftabSz: 80
12/14/2021 07:30:23 PM : DEBUG :     ftabLen: 1048577
12/14/2021 07:30:23 PM : DEBUG :     ftabSz: 4194308
12/14/2021 07:30:23 PM : DEBUG :     offsLen: 48755
12/14/2021 07:30:23 PM : DEBUG :     offsSz: 195020
12/14/2021 07:30:23 PM : DEBUG :     lineSz: 64
12/14/2021 07:30:23 PM : DEBUG :     sideSz: 64
12/14/2021 07:30:23 PM : DEBUG :     sideBwtSz: 48
12/14/2021 07:30:23 PM : DEBUG :     sideBwtLen: 192
12/14/2021 07:30:23 PM : DEBUG :     numSides: 4063
12/14/2021 07:30:23 PM : DEBUG :     numLines: 4063
12/14/2021 07:30:23 PM : DEBUG :     ebwtTotLen: 260032
12/14/2021 07:30:23 PM : DEBUG :     ebwtTotSz: 260032
12/14/2021 07:30:23 PM : DEBUG :     color: 0
12/14/2021 07:30:23 PM : DEBUG :     reverse: 0
12/14/2021 07:30:23 PM : DEBUG : Total time for call to driver() for forward index: 00:00:01
12/14/2021 07:30:23 PM : DEBUG : Reading reference sizes
12/14/2021 07:30:23 PM : DEBUG :   Time reading reference sizes: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Calculating joined length
12/14/2021 07:30:23 PM : DEBUG : Writing header
12/14/2021 07:30:23 PM : DEBUG : Reserving space for joined string
12/14/2021 07:30:23 PM : DEBUG : Joining reference sequences
12/14/2021 07:30:23 PM : DEBUG :   Time to join reference sequences: 00:00:00
12/14/2021 07:30:23 PM : DEBUG :   Time to reverse reference sequence: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : bmax according to bmaxDivN setting: 195017
12/14/2021 07:30:23 PM : DEBUG : Using parameters --bmax 146263 --dcv 1024
12/14/2021 07:30:23 PM : DEBUG :   Doing ahead-of-time memory usage test
12/14/2021 07:30:23 PM : DEBUG :   Passed!  Constructing with these parameters: --bmax 146263 --dcv 1024
12/14/2021 07:30:23 PM : DEBUG : Constructing suffix-array element generator
12/14/2021 07:30:23 PM : DEBUG : Building DifferenceCoverSample
12/14/2021 07:30:23 PM : DEBUG :   Building sPrime
12/14/2021 07:30:23 PM : DEBUG :   Building sPrimeOrder
12/14/2021 07:30:23 PM : DEBUG :   V-Sorting samples
12/14/2021 07:30:23 PM : DEBUG :   V-Sorting samples time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG :   Allocating rank array
12/14/2021 07:30:23 PM : DEBUG :   Ranking v-sort output
12/14/2021 07:30:23 PM : DEBUG :   Ranking v-sort output time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG :   Invoking Larsson-Sadakane on ranks
12/14/2021 07:30:23 PM : DEBUG :   Invoking Larsson-Sadakane on ranks time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG :   Sanity-checking and returning
12/14/2021 07:30:23 PM : DEBUG : Building samples
12/14/2021 07:30:23 PM : DEBUG : Reserving space for 12 sample suffixes
12/14/2021 07:30:23 PM : DEBUG : Generating random suffixes
12/14/2021 07:30:23 PM : DEBUG : QSorting 12 sample offsets, eliminating duplicates
12/14/2021 07:30:23 PM : DEBUG : QSorting sample offsets, eliminating duplicates time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Multikey QSorting 12 samples
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Multikey QSorting samples time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Calculating bucket sizes
12/14/2021 07:30:23 PM : DEBUG : Splitting and merging
12/14/2021 07:30:23 PM : DEBUG :   Splitting and merging time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Split 1, merged 6; iterating...
12/14/2021 07:30:23 PM : DEBUG : Splitting and merging
12/14/2021 07:30:23 PM : DEBUG :   Splitting and merging time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Avg bucket size: 97507.8 (target: 146262)
12/14/2021 07:30:23 PM : DEBUG : Converting suffix-array elements to index image
12/14/2021 07:30:23 PM : DEBUG : Allocating ftab, absorbFtab
12/14/2021 07:30:23 PM : DEBUG : Entering Ebwt loop
12/14/2021 07:30:23 PM : DEBUG : Getting block 1 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 1
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 1
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 1:
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 1: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 54079 for bucket 1
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 54080 for bucket 1
12/14/2021 07:30:23 PM : DEBUG : Getting block 2 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 2
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 2
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 2:
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 2: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 139565 for bucket 2
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 139566 for bucket 2
12/14/2021 07:30:23 PM : DEBUG : Getting block 3 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 3
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 3
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 3:
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 3: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 36894 for bucket 3
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 36895 for bucket 3
12/14/2021 07:30:23 PM : DEBUG : Getting block 4 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 4
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 4
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 4:
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 4: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 134423 for bucket 4
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 134424 for bucket 4
12/14/2021 07:30:23 PM : DEBUG : Getting block 5 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 5
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 5
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 5:
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 5: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 119960 for bucket 5
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 119961 for bucket 5
12/14/2021 07:30:23 PM : DEBUG : Getting block 6 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 6
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 6
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 6:
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 6: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 131326 for bucket 6
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 131327 for bucket 6
12/14/2021 07:30:23 PM : DEBUG : Getting block 7 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 7
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 7
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 7:
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 7: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 111161 for bucket 7
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:23 PM : DEBUG :   Sorting block time: 00:00:00
12/14/2021 07:30:23 PM : DEBUG : Returning block of 111162 for bucket 7
12/14/2021 07:30:23 PM : DEBUG : Getting block 8 of 8
12/14/2021 07:30:23 PM : DEBUG :   Reserving size (146263) for bucket 8
12/14/2021 07:30:23 PM : DEBUG :   Calculating Z arrays for bucket 8
12/14/2021 07:30:23 PM : DEBUG :   Entering block accumulator loop for bucket 8:
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 10%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 20%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 30%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 40%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 50%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 60%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 70%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 80%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 90%
12/14/2021 07:30:23 PM : DEBUG :   bucket 8: 100%
12/14/2021 07:30:23 PM : DEBUG :   Sorting block of length 52654 for bucket 8
12/14/2021 07:30:23 PM : DEBUG :   (Using difference cover)
12/14/2021 07:30:24 PM : DEBUG :   Sorting block time: 00:00:01
12/14/2021 07:30:24 PM : DEBUG : Returning block of 52655 for bucket 8
12/14/2021 07:30:24 PM : DEBUG : Exited Ebwt loop
12/14/2021 07:30:24 PM : DEBUG : fchr[A]: 0
12/14/2021 07:30:24 PM : DEBUG : fchr[C]: 226540
12/14/2021 07:30:24 PM : DEBUG : fchr[G]: 388187
12/14/2021 07:30:24 PM : DEBUG : fchr[T]: 554183
12/14/2021 07:30:24 PM : DEBUG : fchr[$]: 780069
12/14/2021 07:30:24 PM : DEBUG : Exiting Ebwt::buildToDisk()
12/14/2021 07:30:24 PM : DEBUG : Returning from initFromVector
12/14/2021 07:30:24 PM : DEBUG : Wrote 4454705 bytes to primary EBWT file: /tmp/shogun-test-temp-fr3jjj80/genomes.small.rev.1.bt2
12/14/2021 07:30:24 PM : DEBUG : Wrote 195024 bytes to secondary EBWT file: /tmp/shogun-test-temp-fr3jjj80/genomes.small.rev.2.bt2
12/14/2021 07:30:24 PM : DEBUG : Re-opening _in1 and _in2 as input streams
12/14/2021 07:30:24 PM : DEBUG : Returning from Ebwt constructor
12/14/2021 07:30:24 PM : DEBUG : Headers:
12/14/2021 07:30:24 PM : DEBUG :     len: 780069
12/14/2021 07:30:24 PM : DEBUG :     bwtLen: 780070
12/14/2021 07:30:24 PM : DEBUG :     sz: 195018
12/14/2021 07:30:24 PM : DEBUG :     bwtSz: 195018
12/14/2021 07:30:24 PM : DEBUG :     lineRate: 6
12/14/2021 07:30:24 PM : DEBUG :     offRate: 4
12/14/2021 07:30:24 PM : DEBUG :     offMask: 0xfffffff0
12/14/2021 07:30:24 PM : DEBUG :     ftabChars: 10
12/14/2021 07:30:24 PM : DEBUG :     eftabLen: 20
12/14/2021 07:30:24 PM : DEBUG :     eftabSz: 80
12/14/2021 07:30:24 PM : DEBUG :     ftabLen: 1048577
12/14/2021 07:30:24 PM : DEBUG :     ftabSz: 4194308
12/14/2021 07:30:24 PM : DEBUG :     offsLen: 48755
12/14/2021 07:30:24 PM : DEBUG :     offsSz: 195020
12/14/2021 07:30:24 PM : DEBUG :     lineSz: 64
12/14/2021 07:30:24 PM : DEBUG :     sideSz: 64
12/14/2021 07:30:24 PM : DEBUG :     sideBwtSz: 48
12/14/2021 07:30:24 PM : DEBUG :     sideBwtLen: 192
12/14/2021 07:30:24 PM : DEBUG :     numSides: 4063
12/14/2021 07:30:24 PM : DEBUG :     numLines: 4063
12/14/2021 07:30:24 PM : DEBUG :     ebwtTotLen: 260032
12/14/2021 07:30:24 PM : DEBUG :     ebwtTotSz: 260032
12/14/2021 07:30:24 PM : DEBUG :     color: 0
12/14/2021 07:30:24 PM : DEBUG :     reverse: 1
12/14/2021 07:30:24 PM : DEBUG : Total time for backward call to driver() for mirror index: 00:00:01
12/14/2021 07:30:24 PM : DEBUG : 1.49 seconds
12/14/2021 07:30:24 PM : DEBUG : Subprocess finished.
..12/14/2021 07:30:24 PM : DEBUG : burst15 --queries /home/zhou/soft/SHOGUN/shogun/tests/data/combined_seqs.fna --references /home/zhou/soft/SHOGUN/shogun/tests/data/burst/genomes.small.edx --output /tmp/shogun-test-temp-7qad189c/sims.b6 --threads 1 --mode CAPITALIST --id 0.98 --npenalize --skipambig --forwardreverse --taxonomy /home/zhou/soft/SHOGUN/shogun/tests/data/genomes.small.tax --taxacut 5
E12/14/2021 07:30:24 PM : DEBUG : burst15 --references /home/zhou/soft/SHOGUN/shogun/tests/data/genomes.small.fna --output /tmp/shogun-test-temp-oqpdpg0u/genomes.small.edb --npenalize --makedb --fingerprint --shear 500 --clustradius 1050
EF12/14/2021 07:30:24 PM : DEBUG : utree-search_gg /home/zhou/soft/SHOGUN/shogun/tests/data/utree/genomes.small.gg.ctr /home/zhou/soft/SHOGUN/shogun/tests/data/combined_seqs.fna /tmp/shogun-test-temp-z5xw593k/utree_gg-test-sims.txt 1 RC
E12/14/2021 07:30:24 PM : DEBUG : utree-build_gg /home/zhou/soft/SHOGUN/shogun/tests/data/genomes.small.fna /home/zhou/soft/SHOGUN/shogun/tests/data/genomes.small.tax /tmp/shogun-test-temp-9yim61nd/genomes.small.gg.utr 1 2
EF
======================================================================
ERROR: test_burst_align (aligners.tests.test_aligner.TestAligner)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/aligners/tests/test_aligner.py", line 33, in test_burst_align
    self.assertTrue(aligner.align(infile, outdir)[0] == 0)
  File "/home/zhou/soft/SHOGUN/shogun/aligners/burst_aligner.py", line 55, in align
    proc, out, err = burst_align(infile, self.outfile,
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/burst_wrapper.py", line 86, in burst_align
    return run_command(cmd, shell=shell)
  File "/home/zhou/soft/SHOGUN/shogun/utils/_utils.py", line 54, in run_command
    with subprocess.Popen(
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 1821, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'burst15'

======================================================================
ERROR: test_utree_align (aligners.tests.test_aligner.TestAligner)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/aligners/tests/test_aligner.py", line 55, in test_utree_align
    self.assertTrue(aligner.align(infile, outdir)[0] == 0)
  File "/home/zhou/soft/SHOGUN/shogun/aligners/utree_aligner.py", line 36, in align
    proc, out, err = utree_search_gg(self.compressed_tree, infile, outfile, threads=self.threads, shell=self.shell)
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/utree_wrapper.py", line 66, in utree_search_gg
    return run_command(cmd, shell=shell)
  File "/home/zhou/soft/SHOGUN/shogun/utils/_utils.py", line 54, in run_command
    with subprocess.Popen(
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 1821, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'utree-search_gg'

======================================================================
ERROR: test_burst_align (wrappers.tests.test_burst.TestBurst)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/tests/test_burst.py", line 33, in test_burst_align
    self.assertTrue(burst_align(infile, outfile, database, tax=tax)[0] == 0)
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/burst_wrapper.py", line 86, in burst_align
    return run_command(cmd, shell=shell)
  File "/home/zhou/soft/SHOGUN/shogun/utils/_utils.py", line 54, in run_command
    with subprocess.Popen(
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 1821, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'burst15'

======================================================================
ERROR: test_burst_build (wrappers.tests.test_burst.TestBurst)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/tests/test_burst.py", line 39, in test_burst_build
    print(burst_build(fasta, outfile, shell=False, clustradius=1050, shear=500))
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/burst_wrapper.py", line 108, in burst_build
    return run_command(cmd, shell=shell)
  File "/home/zhou/soft/SHOGUN/shogun/utils/_utils.py", line 54, in run_command
    with subprocess.Popen(
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 1821, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'burst15'

======================================================================
ERROR: test_utree_align_gg (wrappers.tests.test_utree.TestUtree)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/tests/test_utree.py", line 49, in test_utree_align_gg
    self.assertTrue(utree_search_gg(database, infile, outfile)[0] == 0)
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/utree_wrapper.py", line 66, in utree_search_gg
    return run_command(cmd, shell=shell)
  File "/home/zhou/soft/SHOGUN/shogun/utils/_utils.py", line 54, in run_command
    with subprocess.Popen(
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 1821, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'utree-search_gg'

======================================================================
ERROR: test_utree_build_gg (wrappers.tests.test_utree.TestUtree)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/tests/test_utree.py", line 40, in test_utree_build_gg
    utree_build_gg(fasta, tax, outfile_uncompressed, shell=False)
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/utree_wrapper.py", line 32, in utree_build_gg
    return run_command(cmd, shell=shell)
  File "/home/zhou/soft/SHOGUN/shogun/utils/_utils.py", line 54, in run_command
    with subprocess.Popen(
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/zhou/miniconda2/envs/shogun/lib/python3.9/subprocess.py", line 1821, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'utree-build_gg'

======================================================================
FAIL: test_burst_pipeline (tests.test_pipeline.TestAligner)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/tests/test_pipeline.py", line 86, in test_burst_pipeline
    self.assertTrue(len(outfile_ra) == 1)
AssertionError: False is not true

======================================================================
FAIL: test_utree_pipeline (tests.test_pipeline.TestAligner)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/tests/test_pipeline.py", line 38, in test_utree_pipeline
    self.assertTrue(len(outfile_ra) == 1)
AssertionError: False is not true

======================================================================
FAIL: test_burst_path (wrappers.tests.test_burst.TestBurst)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/tests/test_burst.py", line 26, in test_burst_path
    self.assertTrue(shutil.which("burst15") is not None)
AssertionError: False is not true

======================================================================
FAIL: test_utree_path (wrappers.tests.test_utree.TestUtree)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zhou/soft/SHOGUN/shogun/wrappers/tests/test_utree.py", line 31, in test_utree_path
    self.assertTrue(shutil.which("utree-build_gg") is not None)
AssertionError: False is not true

----------------------------------------------------------------------
Ran 52 tests in 33.336s

FAILED (failures=4, errors=6)

The conda environment:

$ conda list
# packages in environment at /home/zhou/miniconda2/envs/shogun:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
bowtie2                   2.4.4            py39hbb4e92a_0    bioconda
ca-certificates           2021.10.26           h06a4308_2    defaults
click                     8.0.3            py39hf3d152e_1    conda-forge
cytoolz                   0.11.2           py39h3811e60_1    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
libblas                   3.9.0           12_linux64_openblas    conda-forge
libcblas                  3.9.0           12_linux64_openblas    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 11.2.0              h1d223b6_11    conda-forge
libgfortran-ng            11.2.0              h69a702a_11    conda-forge
libgfortran5              11.2.0              h5c6108e_11    conda-forge
libgomp                   11.2.0              h1d223b6_11    conda-forge
liblapack                 3.9.0           12_linux64_openblas    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_11    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
numpy                     1.21.4           py39hdbf815f_0    conda-forge
openssl                   3.0.0                h7f98852_2    conda-forge
pandas                    1.3.4            py39hde0f152_1    conda-forge
perl                      5.32.1          1_h7f98852_perl5    conda-forge
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
python                    3.9.7           hf930737_3_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py39h3811e60_3    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
scipy                     1.7.3            py39hee8e79c_0    conda-forge
setuptools                59.4.0           py39hf3d152e_0    conda-forge
shogun                    1.0.8                    pypi_0    pypi
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.37.0               h9cd32fc_0    conda-forge
tbb                       2020.3               hfd86e86_0    defaults
tk                        8.6.11               h27826a3_1    conda-forge
toolz                     0.11.2             pyhd8ed1ab_0    conda-forge
tzdata                    2021e                he74cb21_0    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.4.9                ha95c52a_0    conda-forge
ShixiangWang commented 2 years ago

It works after I created a Python3.7 environment and run conda install -c knights-lab -c bioconda -conda-forge shogun from https://github.com/knights-lab/SHOGUN/issues/19.