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build_failure.osx-64.yaml
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recipe_sha: b287ce58da1df7ae69fe34364641490bf5d3f3c1c7584dd49b2d9642ce30c278 # The hash of the recipe's meta.yaml at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
log: |-
|-OS: Darwin
|-threads: 2
**************************
15:29:48 - [1;37mINFO[0m - <<Parsnp started>>
15:29:48 - [1;37mINFO[0m - No genbank file provided for reference annotations, skipping..
15:29:48 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7149.fna seems to be aligned! Skip!
15:29:48 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7569.fna seems to be aligned! Skip!
15:29:48 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7770.fna seems to be aligned! Skip!
15:29:48 - [1;34mDEBUG[0m - Writing .ini file
15:29:48 - [1;37mINFO[0m - Filtering genomes...
15:29:48 - [1;33mWARNING[0m - You are using a randomly selected genome to filter genomes from your input with Mash. If input genomes vary greatly in size, results could be suboptimal. It is advised to select a reference genome for filter...
15:29:48 - [1;34mDEBUG[0m - time mash dist -t -d 0.1 -p 2 test-mash/Riyadh_14_2013.fna.ref -l test-mash/tmp/genomes.lst
15:29:48 - [1;34mDEBUG[0m - STDOUT was piped... please see output file: test-mash/log/mash.out
15:29:48 - [1;34mDEBUG[0m - STDERR was piped... please see output file: test-mash/log/mash.err
15:29:48 - [1;34mDEBUG[0m -
15:29:48 - [1;37mINFO[0m - Too few genomes to run partitions of size >50. Running all genomes at once.
15:29:48 - [1;37mINFO[0m - Running Parsnp multi-MUM search and libMUSCLE aligner...
15:29:48 - [1;34mDEBUG[0m - time /opt/mambaforge/envs/bioconda/conda-bld/parsnp_1734535473104/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/bin/parsnp_core test-mash/parsnpAligner.ini
15:29:48 - [1;34mDEBUG[0m - STDOUT was piped... please see output file: test-mash/log/parsnp-aligner.out
15:29:48 - [1;34mDEBUG[0m - STDERR was piped... please see output file: test-mash/log/parsnp-aligner.err
15:29:48 - [1;34mDEBUG[0m -
15:29:48 - [1;34mDEBUG[0m - Writing MAF file to test-mash/parsnp.maf
15:29:48 - [1;34mDEBUG[0m - harvesttools -q -o test-mash/parsnp.ggr -f test-mash/Riyadh_14_2013.fna.ref -x test-mash/parsnp.xmfa
15:29:48 - [1;34mDEBUG[0m -
15:29:48 - [1;34mDEBUG[0m -
15:29:48 - [1;34mDEBUG[0m -
15:29:48 - [1;34mDEBUG[0m - time harvesttools -i test-mash/parsnp.ggr -S test-mash/parsnp.snps.mblocks
15:29:48 - [1;34mDEBUG[0m - STDOUT was piped... please see output file: test-mash/log/harvest-mblocks.out
15:29:48 - [1;34mDEBUG[0m - STDERR was piped... please see output file: test-mash/log/harvest-mblocks.err
15:29:48 - [1;34mDEBUG[0m -
15:29:48 - [1;37mINFO[0m - Aligned 47 genomes in 0.82 seconds
15:29:48 - [1;37mINFO[0m - Parsnp finished! All output available in test-mash
15:29:48 - [1;34mDEBUG[0m - Validating output directory contents
15:29:49 - [1;37mINFO[0m - |--Parsnp 2.1.1--|
15:29:49 - [1;37mINFO[0m -
*****************************
SETTINGS:
|-refgenome: autopick
|-genomes:
mers_virus/genomes/Al-Hasa_12_2013.fna
mers_virus/genomes/Al-Hasa_15_2013.fna
...45 more file(s)...
mers_virus/genomes/Taif_1_2013.fna
mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna
|-aligner: muscle
|-outdir: test-fastani
|-OS: Darwin
|-threads: 2
*****************************
15:29:49 - [1;37mINFO[0m - <<Parsnp started>>
15:29:49 - [1;37mINFO[0m - No genbank file provided for reference annotations, skipping..
15:29:49 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7149.fna seems to be aligned! Skip!
15:29:49 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7569.fna seems to be aligned! Skip!
15:29:49 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7770.fna seems to be aligned! Skip!
15:29:49 - [1;34mDEBUG[0m - Writing .ini file
15:29:49 - [1;37mINFO[0m - Filtering genomes...
15:29:49 - [1;33mWARNING[0m - You have not selected a reference and are using ANI filter. All-to-all FastANI will be performed in order to obtain the best reference. As this is O(N^2), it is advised to select a reference genome if you have many query sequences.
15:29:49 - [1;34mDEBUG[0m - time fastANI --rl test-fastani/tmp/genomes.lst --ql test-fastani/tmp/genomes.lst --fragLen 500 -t 2 -o test-fastani/fastANI.tsv
15:29:49 - [1;31mCRITICAL[0m - The following command failed:
>>$ time fastANI --rl test-fastani/tmp/genomes.lst --ql test-fastani/tmp/genomes.lst --fragLen 500 -t 2 -o test-fastani/fastANI.tsv
Please veryify input data and restart Parsnp.
If the problem persists please contact the Parsnp development team.
STDOUT:
STDOUT was piped... please see output file: test-fastani/log/fastANI.out
STDERR:
STDERR was piped... please see output file: test-fastani/log/fastANI.err
WARNING: Tests failed for parsnp-2.1.1-he136a0b_1.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test
export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/parsnp_1734535473104/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl
export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/parsnp_1734535473104/test_tmp
parsnp 2.1.1
utils.check_call_env(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/parsnp_1734535473104/test_tmp/conda_test_runner.sh']' returned non-zero exit status 250.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute
api.build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build
return build_tree(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree
test(pkg, config=metadata.config.copy(), stats=stats)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test
tests_failed(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed
raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg))
conda_build.exceptions.CondaBuildUserError: TESTS FAILED: parsnp-2.1.1-he136a0b_1.tar.bz2
# Last 100 lines of the build log.
category: |-
test failure