Open nick-youngblut opened 4 years ago
I'm getting a cryptic assertion error lacking an informative trackback:
============================== check_reads ============================== 1 chunks to run. Starting... 2020-07-24 20:12:18 - INFO - index fastq /ebio/abt3_scratch/haptag-mg_49025743982/athena/0.5/3/2000000/sim_reads/1/R1-2.fq 2020-07-24 20:13:04 - INFO - get seed contigs from input assembly 2020-07-24 20:13:04 - INFO - computing seed coverages (required pass thru *bam) 2020-07-24 20:13:36 - INFO - 79298 total inputs seeds covering 94388578 bases 2020-07-24 20:13:36 - INFO - 491 input seed contigs >= 400bp and >= 10.0x coverage covering 10925225 bases 2020-07-24 20:13:36 - INFO - created 492 bins from seeds 2020-07-24 20:13:36 - INFO - done 2020-07-24 20:13:36 - ERROR - ========== Exception ========== 2020-07-24 20:13:36 - ERROR - Traceback (most recent call last): 2020-07-24 20:13:36 - ERROR - File "/ebio/abt3_projects/software/dev/haptag-mg/data_sim/.snakemake/conda/a7933a08/lib/python2.7/site-packages/athena/pipeline.py", line 52, in _run_chunk 2020-07-24 20:13:36 - ERROR - chunk.finalize() 2020-07-24 20:13:36 - ERROR - File "/ebio/abt3_projects/software/dev/haptag-mg/data_sim/.snakemake/conda/a7933a08/lib/python2.7/site-packages/athena/stages/step.py", line 109, in finalize 2020-07-24 20:13:36 - ERROR - assert not self.needs_to_run() 2020-07-24 20:13:36 - ERROR - AssertionError 2020-07-24 20:13:36 - ERROR - 2020-07-24 20:13:36 - ERROR - Traceback (most recent call last): File "/ebio/abt3_projects/software/dev/haptag-mg/data_sim/.snakemake/conda/a7933a08/bin/athena-meta", line 10, in <module> sys.exit(main()) File "/ebio/abt3_projects/software/dev/haptag-mg/data_sim/.snakemake/conda/a7933a08/lib/python2.7/site-packages/main.py", line 211, in main run(options) File "/ebio/abt3_projects/software/dev/haptag-mg/data_sim/.snakemake/conda/a7933a08/lib/python2.7/site-packages/main.py", line 42, in run runner.run_stage(stage, stage_name) File "/ebio/abt3_projects/software/dev/haptag-mg/data_sim/.snakemake/conda/a7933a08/lib/python2.7/site-packages/athena/pipeline.py", line 33, in run_stage cluster.map(_run_chunk, to_run) File "/ebio/abt3_projects/software/dev/haptag-mg/data_sim/.snakemake/conda/a7933a08/lib/python2.7/site-packages/athena/cluster.py", line 43, in map return pool.map_async(fn, args).get(9999999) File "/ebio/abt3_projects/software/dev/haptag-mg/data_sim/.snakemake/conda/a7933a08/lib/python2.7/multiprocessing/pool.py", line 572, in get raise self._value AssertionError
It appears that assert not self.needs_to_run() may be the cause, but that isn't very informative in itself.
assert not self.needs_to_run()
My conda env:
# Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 0_gnu conda-forge athena_meta 1.3 py_1 bioconda backports 1.0 py_2 conda-forge backports.shutil_get_terminal_size 1.0.0 py_3 conda-forge backports_abc 0.5 py_1 conda-forge bwa 0.7.17 hed695b0_7 bioconda bx-python 0.8.9 py27h213ead4_1 bioconda bzip2 1.0.8 h516909a_2 conda-forge ca-certificates 2020.6.20 hecda079_0 conda-forge certifi 2019.11.28 py27h8c360ce_1 conda-forge configparser 3.7.3 py27h8c360ce_2 conda-forge curl 7.71.1 he644dc0_3 conda-forge decorator 4.4.2 py_0 conda-forge entrypoints 0.3 py27h8c360ce_1001 conda-forge enum34 1.1.10 py27h8c360ce_1 conda-forge flye 2.3.1 py27_0 bioconda futures 3.3.0 py27h8c360ce_1 conda-forge htslib 1.9 ha228f0b_7 bioconda idba_subasm 1.1.3a1 py27pl526hf484d3e_0 bioconda ipykernel 4.10.0 py27_1 conda-forge ipyparallel 6.2.4 py27h8c360ce_0 conda-forge ipython 5.8.0 py27_1 conda-forge ipython-cluster-helper 0.6.4 py_0 bioconda ipython_genutils 0.2.0 py_1 conda-forge jupyter_client 5.3.4 py27_1 conda-forge jupyter_core 4.6.3 py27h8c360ce_1 conda-forge krb5 1.17.1 hfafb76e_1 conda-forge ld_impl_linux-64 2.34 h53a641e_7 conda-forge libblas 3.8.0 17_openblas conda-forge libcblas 3.8.0 17_openblas conda-forge libcurl 7.71.1 hcdd3856_3 conda-forge libdeflate 1.0 h14c3975_1 bioconda libedit 3.1.20191231 h46ee950_1 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.2.0 h24d8f2e_2 conda-forge libgfortran-ng 7.5.0 hdf63c60_6 conda-forge libgomp 9.2.0 h24d8f2e_2 conda-forge liblapack 3.8.0 17_openblas conda-forge libopenblas 0.3.10 pthreads_hb3c22a3_3 conda-forge libsodium 1.0.17 h516909a_0 conda-forge libssh2 1.9.0 hab1572f_4 conda-forge libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge lzo 2.10 h14c3975_1000 conda-forge ncurses 6.1 hf484d3e_1002 conda-forge netifaces 0.10.4 py27_1 bioconda numpy 1.11.3 py27he5ce36f_1207 conda-forge openssl 1.1.1g h516909a_0 conda-forge pathlib2 2.3.5 py27h8c360ce_1 conda-forge perl 5.26.2 h516909a_1006 conda-forge pexpect 4.8.0 py27h8c360ce_1 conda-forge pickleshare 0.7.5 py27h8c360ce_1001 conda-forge pigz 2.3.4 hed695b0_1 conda-forge pip 20.1.1 pyh9f0ad1d_0 conda-forge prompt_toolkit 1.0.15 py_1 conda-forge ptyprocess 0.6.0 py_1001 conda-forge pygments 2.5.2 py_0 conda-forge pysam 0.15.3 py27hda2845c_1 bioconda python 2.7.15 h5a48372_1011_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python-lzo 1.12 py27h42e1302_1001 conda-forge python_abi 2.7 1_cp27mu conda-forge pyzmq 19.0.0 py27h76efe43_1 conda-forge readline 8.0 h46ee950_1 conda-forge samtools 1.9 h10a08f8_12 bioconda scandir 1.10.0 py27hdf8410d_1 conda-forge setuptools 44.0.0 py27_0 conda-forge simplegeneric 0.8.1 py_1 conda-forge singledispatch 3.4.0.3 py27_1000 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sqlite 3.32.3 hcee41ef_1 conda-forge tk 8.6.10 hed695b0_0 conda-forge tornado 5.1.1 py27h14c3975_1000 conda-forge traitlets 4.3.3 py27h8c360ce_1 conda-forge wcwidth 0.2.5 pyh9f0ad1d_0 conda-forge wheel 0.34.2 py_1 conda-forge xz 5.2.5 h516909a_1 conda-forge zeromq 4.3.2 he1b5a44_2 conda-forge zlib 1.2.11 h516909a_1006 conda-forge
I'm getting a cryptic assertion error lacking an informative trackback:
It appears that
assert not self.needs_to_run()may be the cause, but that isn't very informative in itself.My conda env: