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shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
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ERROR: Snakemake failed #112

Open baidefeng opened 3 weeks ago

baidefeng commented 3 weeks ago

When i run "hecatomb install", an snakemake error occurred. Do you have any ideas how to deal with it? Thanks a lot.

[2024:06:11 18:14:25] Copying system default config to hecatomb.out/hecatomb.config.yaml [2024:06:11 18:14:25] Updating config file with new values [2024:06:11 18:14:25] Writing config file to hecatomb.out/hecatomb.config.yaml [2024:06:11 18:14:25] ------------------ [2024:06:11 18:14:25] | Runtime config | [2024:06:11 18:14:25] ------------------

hecatomb: addHost: minViralAlnLen: 1000 args: assembly: merged conda_prefix: /data5/baidefeng/hecatomb/hecatomb/snakemake/conda configfile: hecatomb.out/hecatomb.config.yaml custom_aa: null custom_nt: null example_profile: false fastqc: false host: human log: hecatomb.out/hecatomb.log output: hecatomb.out profile: null search: sensitive simulate: false snake_args: [] system_config: /data5/baidefeng/hecatomb/hecatomb/snakemake/config/config.yaml system_workflow_profile: /data5/baidefeng/hecatomb/hecatomb/snakemake/profile/default/config.yaml threads: 32 trim: fastp use_conda: true workflow_profile: hecatomb.out/hecatomb.profile assembly: canu: correctedErrorRate=0.16 maxInputCoverage=10000 minInputCoverage=0 corOutCoverage=10000 corMhapSensitivity=high corMinCoverage=0 useGrid=False stopOnLowCoverage=False genomeSize=10M -nanopore flye: -g 1g megahit: --presets meta-large metaflye: --meta -g 1g --nano-raw mmseqs: fast: -s 4 filtAA: --min-length 30 -e 1e-5 filtNT: --min-length 90 -e 1e-20 linclustParams: --kmer-per-seq-scale 0.3 -c 0.8 --cov-mode 1 --min-seq-id 0.97 --alignment-mode 3 sensitive: --start-sens 2 --sens-steps 3 -s 7 taxIdIgnore: 0 1 2 10239 131567 12429 2759 resources: big: cpu: 32 mem: 64000 time: '24:00:00' lrg: cpu: 16 mem: 32000 time: 04:00:00 med: cpu: 8 mem: 16000 time: 04:00:00 ram: cpu: 2 mem: 16000 time: 04:00:00 sml: cpu: 1 mem: 2000 time: 01:00:00 trimnami: qc: compression: 1 cutadapt: -m 40 fastp: --qualified_quality_phred 15 --length_required 90 --cut_tail --cut_tail_window_size 25 --cut_tail_mean_quality 15 --dedup --dup_calc_accuracy 4 --trim_poly_x --detect_adapter_for_pe filtlong: --min_length 1000 --keep_percent 95 hostRemoveFlagstat: -f 4 -F 3584 minimapIndex: -I 8G prinseq: -min_len 60 -min_qual_mean 25 -ns_max_n 1 -derep 1 -out_format 0 -trim_tail_left 5 -trim_tail_right 5 -ns_max_n 5 -trim_qual_type min -trim_qual_left 30 -trim_qual_right 30 -trim_qual_window 10

[2024:06:11 18:14:25] Copying system default config to hecatomb.out/hecatomb.profile/config.yaml [2024:06:11 18:14:25] --------------------- [2024:06:11 18:14:25] | Snakemake command | [2024:06:11 18:14:25] ---------------------

snakemake -s /data5/baidefeng/hecatomb/hecatomb/snakemake/workflow/DownloadDB.smk --configfile hecatomb.out/hecatomb.config.yaml --cores 32 --use-conda --conda-prefix /data5/baidefeng/hecatomb/hecatomb/snakemake/conda --workflow-profile hecatomb.out/hecatomb.profile Using profile hecatomb.out/hecatomb.profile and workflow specific profile hecatomb.out/hecatomb.profile for setting default command line arguments. Config file /data5/baidefeng/hecatomb/hecatomb/snakemake/workflow/../config/config.yaml is extended by additional config specified via the command line. Config file /data5/baidefeng/hecatomb/hecatomb/snakemake/workflow/../config/dbFiles.yaml is extended by additional config specified via the command line. Config file /data5/baidefeng/hecatomb/hecatomb/snakemake/workflow/../config/immutable.yaml is extended by additional config specified via the command line. Building DAG of jobs... Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channelpriority strict'. Creating conda environment hecatomb/snakemake/workflow/envs/curl.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /data5/baidefeng/hecatomb/hecatomb/snakemake/workflow/envs/curl.yaml: Command: conda env create --quiet --file "/data5/baidefeng/hecatomb/hecatomb/snakemake/conda/6b0e909bfbff6795553256ec89c7507f.yaml" --prefix "/data5/baidefeng/hecatomb/hecatomb/snakemake/conda/6b0e909bfbff6795553256ec89c7507f_" Output: Collecting package metadata (repodata.json): ...working... failed

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 17, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda_env/cli/main.py", line 56, in do_call
    exit_code = getattr(module, func_name)(arguments, parser)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/notices/core.py", line 124, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda_env/cli/main_create.py", line 162, in execute
    result[installer_type] = installer.install(
                             ^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda_env/installers/conda.py", line 51, in install
    unlink_link_transaction = solver.solve_for_transaction(
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/solve.py", line 154, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(
                               ^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/solve.py", line 215, in solve_for_diff
    final_precs = self.solve_final_state(
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/solve.py", line 358, in solve_final_state
    ssc = self._collect_all_metadata(ssc)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/common/io.py", line 84, in decorated
    return f(*args, **kwds)
           ^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/solve.py", line 572, in _collect_all_metadata
    index, r = self._prepare(prepared_specs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/solve.py", line 1286, in _prepare
    reduced_index = get_reduced_index(
                    ^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/index.py", line 287, in get_reduced_index
    new_records = SubdirData.query_all(
                  ^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/subdir_data.py", line 158, in query_all
    result = tuple(
             ^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/concurrent/futures/_base.py", line 619, in result_iterator
    yield _result_or_cancel(fs.pop())
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/concurrent/futures/_base.py", line 317, in _result_or_cancel
    return fut.result(timeout)
           ^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/data/meta/miniconda3/lib/python3.11/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/subdir_data.py", line 143, in subdir_query
    return tuple(
           ^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/subdir_data.py", line 165, in query
    self.load()
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/subdir_data.py", line 265, in load
    _internal_state = self._load()
                      ^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/core/subdir_data.py", line 322, in _load
    repodata, state = fetcher.fetch_latest_parsed()
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/gateways/repodata/__init__.py", line 758, in fetch_latest_parsed
    parsed, state = self.fetch_latest()
                    ^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/gateways/repodata/__init__.py", line 820, in fetch_latest
    cache.load_state()
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/gateways/repodata/__init__.py", line 626, in load_state
    self.load(state_only=True)
  File "/data/meta/miniconda3/lib/python3.11/site-packages/conda/gateways/repodata/__init__.py", line 573, in load
    with self.cache_path_state.open("r+") as state_file, lock(state_file):
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/meta/miniconda3/lib/python3.11/pathlib.py", line 1044, in open
    return io.open(self, mode, buffering, encoding, errors, newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
PermissionError: [Errno 13] Permission denied: '/data/meta/miniconda3/pkgs/cache/47929eba.info.json'

$ /data/meta/miniconda3/bin/conda-env create --quiet --file /data5/baidefeng/hecatomb/hecatomb/snakemake/conda/6b0e909bfbff6795553256ec89c7507f_.yaml --prefix /data5/baidefeng/hecatomb/hecatomb/snakemake/conda/6b0e909bfbff6795553256ec89c7507f_

environment variables: CIO_TEST= CONDA_AUTO_UPDATE_CONDA=false CONDA_BACKUP_ADDR2LINE=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu- addr2line CONDA_BACKUP_AR=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-ar CONDA_BACKUP_AS=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-as CONDA_BACKUP_BUILD=x86_64-conda-linux-gnu CONDA_BACKUP_CC=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-cc CONDA_BACKUP_CC_FOR_BUILD=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-cc CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector- strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno- plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_CMAKE_PREFIX_PATH=/data/meta/miniconda3/envs/kraken2:/data/meta/miniconda3/envs/kraken2/ x86_64-conda-linux-gnu/sysroot/usr CONDA_BACKUP_CONDA_BUILD_SYSROOT=/data/meta/miniconda3/envs/kraken2/x86_64-conda-linux-gnu/sysroot CONDA_BACKUP_CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu CONDA_BACKUP_CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu CONDA_BACKUP_CPP=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-cpp CONDA_BACKUP_CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/meta/miniconda3/envs/kraken2/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_CXX=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-c++ CONDA_BACKUP_CXXFILT=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-c++filt CONDA_BACKUP_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector- strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree- vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction- sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_CXX_FOR_BUILD=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-c++ CONDA_BACKUP_DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector- all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /data/meta/miniconda3/envs/kraken2/include -D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector- all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree- vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack- protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar- tracking-assignments -ffunction-sections -pipe -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno- plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack- protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar- tracking-assignments -ffunction-sections -pipe -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno- plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_ELFEDIT=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-elfedit CONDA_BACKUP_F77=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gfortran CONDA_BACKUP_F90=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gfortran CONDA_BACKUP_F95=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-f95 CONDA_BACKUP_FC=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gfortran CONDA_BACKUP_FC_FOR_BUILD=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gfortran CONDA_BACKUP_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack- protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno- plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack- protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno- plt -O2 -ffunction-sections -pipe -isystem /data/meta/miniconda3/envs/kraken2/include CONDA_BACKUP_GCC=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gcc CONDA_BACKUP_GCC_AR=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gcc-ar CONDA_BACKUP_GCC_NM=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gcc-nm CONDA_BACKUP_GCC_RANLIB=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gcc- ranlib CONDA_BACKUP_GFORTRAN=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gfortran CONDA_BACKUP_GPROF=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-gprof CONDA_BACKUP_GXX=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-g++ CONDA_BACKUP_HOST=x86_64-conda-linux-gnu CONDA_BACKUP_LD=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-ld CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl, --disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/data/meta/miniconda3/envs/kraken2/lib -Wl,-rpath- link,/data/meta/miniconda3/envs/kraken2/lib -L/data/meta/miniconda3/envs/kraken2/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-- gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/data/meta/miniconda3/envs/kraken2/lib -Wl,-rpath- link,/data/meta/miniconda3/envs/kraken2/lib -L/data/meta/miniconda3/envs/kraken2/lib CONDA_BACKUP_LD_GOLD=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-ld.gold CONDA_BACKUP_NM=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-nm CONDA_BACKUP_OBJCOPY=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-objcopy CONDA_BACKUP_OBJDUMP=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-objdump CONDA_BACKUP_RANLIB=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-ranlib CONDA_BACKUP_READELF=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-readelf CONDA_BACKUP_SIZE=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-size CONDA_BACKUP_STRINGS=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-strings CONDA_BACKUP_STRIP=/data/meta/miniconda3/envs/kraken2/bin/x86_64-conda-linux-gnu-strip CONDA_BACKUP_build_alias=x86_64-conda-linux-gnu CONDA_BACKUP_host_alias=x86_64-conda-linux-gnu CONDA_DEFAULT_ENV=hecatombDev CONDA_EXE=/data5/baidefeng/miniconda3/bin/conda CONDA_PREFIX=/data5/baidefeng/miniconda3/envs/hecatombDev CONDA_PREFIX_1=/data/meta/miniconda3 CONDA_PREFIX_10=/data/meta/miniconda3/envs/metawrap CONDA_PREFIX_11=/data/meta/miniconda3 CONDA_PREFIX_12=/data/meta/miniconda3/envs/metawrap CONDA_PREFIX_13=/data/meta/miniconda3 CONDA_PREFIX_14=/data/meta/miniconda3/envs/metawrap CONDA_PREFIX_15=/data/meta/miniconda3/envs/drep CONDA_PREFIX_16=/data/meta/miniconda3/envs/coverm CONDA_PREFIX_17=/data/meta/miniconda3/envs/humann3 CONDA_PREFIX_18=/data/meta/miniconda3/envs/gtdbtk2.3 CONDA_PREFIX_19=/data/meta/miniconda3 CONDA_PREFIX_2=/data/meta/miniconda3/envs/kneaddata CONDA_PREFIX_20=/data/meta/miniconda3/envs/eggnog CONDA_PREFIX_21=/data/meta/miniconda3 CONDA_PREFIX_22=/data/meta/miniconda3/envs/kneaddata CONDA_PREFIX_23=/data/meta/miniconda3 CONDA_PREFIX_24=/data/meta/miniconda3/envs/kneaddata CONDA_PREFIX_25=/data/meta/miniconda3 CONDA_PREFIX_26=/data/meta/miniconda3/envs/kneaddata CONDA_PREFIX_27=/data/meta/miniconda3 CONDA_PREFIX_28=/data/meta/miniconda3/envs/kneaddata CONDA_PREFIX_29=/data/meta/miniconda3 CONDA_PREFIX_3=/data/meta/miniconda3/envs/humann3 CONDA_PREFIX_30=/data/meta/miniconda3/envs/kneaddata CONDA_PREFIX_31=/data/meta/miniconda3/envs/humann3 CONDA_PREFIX_32=/data/meta/miniconda3/envs/humann2 CONDA_PREFIX_33=/data/meta/miniconda3/envs/lefse CONDA_PREFIX_34=/data/meta/miniconda3/envs/kraken2 CONDA_PREFIX_35=/data/meta/miniconda3 CONDA_PREFIX_36=/data/meta/miniconda3/envs/humann2 CONDA_PREFIX_37=/data/meta/miniconda3 CONDA_PREFIX_38=/data/meta/miniconda3/envs/kneaddata CONDA_PREFIX_39=/data/meta/miniconda3 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CONDA_PREFIX_76=/data5/baidefeng/miniconda3 CONDA_PREFIX_77=/data5/baidefeng/miniconda3/envs/hecatomb CONDA_PREFIX_78=/data5/baidefeng/miniconda3 CONDA_PREFIX_79=/data5/baidefeng/miniconda3/envs/hecatomb CONDA_PREFIX_8=/data/meta/miniconda3/envs/eggnog CONDA_PREFIX_80=/data5/baidefeng/miniconda3/envs/snakemake CONDA_PREFIX_81=/data5/baidefeng/miniconda3 CONDA_PREFIX_82=/data5/baidefeng/miniconda3/envs/snakemake_env CONDA_PREFIX_83=/data5/baidefeng/miniconda3 CONDA_PREFIX_84=/data5/baidefeng/miniconda3/envs/hecatomb CONDA_PREFIX_85=/data5/baidefeng/miniconda3 CONDA_PREFIX_86=/data5/baidefeng/miniconda3/envs/hecatomb CONDA_PREFIX_87=/data5/baidefeng/miniconda3 CONDA_PREFIX_88=/data5/baidefeng/miniconda3/envs/snakemake_env CONDA_PREFIX_89=/data5/baidefeng/miniconda3/envs/hecatomb CONDA_PREFIX_9=/data/meta/miniconda3/envs/kraken2 CONDA_PREFIX_90=/data5/baidefeng/miniconda3/envs/snakemake CONDA_PREFIX_91=/data5/baidefeng/miniconda3 CONDA_PREFIX_92=/data5/baidefeng/miniconda3/envs/hecatomb 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a/meta/db/EasyMicrobiome/linux:/data/meta/db/EasyMicrobiome/script:/da ta/meta/db/EasyMicrobiome/linux:/data/meta/db/EasyMicrobiome/script:/d ata/meta/db/EasyMicrobiome/linux:/data/meta/db/EasyMicrobiome/script:/ usr/bin:/usr/local/go/bin:/data/meta/db/EasyMicrobiome/linux:/data/met a/db/EasyMicrobiome/script:/data/meta/db/EasyMicrobiome/linux:/data/me ta/db/EasyMicrobiome/script:/data/meta/db/EasyMicrobiome/linux:/data/m eta/db/EasyMicrobiome/script:/data/meta/db/EasyMicrobiome/linux:/data/ meta/db/EasyMicrobiome/script REQUESTS_CA_BUNDLE= RMARKDOWN_MATHJAX_PATH=/usr/lib/rstudio-server/resources/mathjax-27 RS_RPOSTBACK_PATH=/usr/lib/rstudio-server/bin/rpostback RS_SERVER_RPC_SOCKET_PATH=/var/run/rstudio-server/rstudio-rserver/session-server-rpc.socket SSL_CERT_FILE=

 active environment : /data5/baidefeng/miniconda3/envs/hecatombDev
active env location : /data5/baidefeng/miniconda3/envs/hecatombDev
        shell level : 98
   user config file : /data5/baidefeng/.condarc

populated config files : conda version : 23.7.4 conda-build version : not installed python version : 3.11.4.final.0 virtual packages : __archspec=1=x86_64 glibc=2.35=0 linux=6.5.0=0 __unix=0=0 base environment : /data/meta/miniconda3 (read only) conda av data dir : /data/meta/miniconda3/etc/conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /data/meta/miniconda3/pkgs /data5/baidefeng/.conda/pkgs envs directories : /data5/baidefeng/.conda/envs /data/meta/miniconda3/envs platform : linux-64 user-agent : conda/23.7.4 requests/2.29.0 CPython/3.11.4 Linux/6.5.0-28-generic ubuntu/22.04.2 glibc/2.35 UID:GID : 1009:1001 netrc file : None offline mode : False

An unexpected error has occurred. Conda has prepared the above report. If you suspect this error is being caused by a malfunctioning plugin, consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install

beardymcjohnface commented 2 weeks ago

Hi, it looks like an error building the conda env. I think this is the key line here: PermissionError: [Errno 13] Permission denied: '/data/meta/miniconda3/pkgs/cache/47929eba.info.json'

do you have read permissions for that conda package cache directory? are you using a module for miniconda or did you install your own version?

baidefeng commented 2 weeks ago

Thanks for your response. When i solve the permission problem and run "hecatomb install ", another ERROR occurred as below. Do you know how to fix it?

Error in rule downloadtaxdump: jobid: 63 output: /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy/citations.dmp, /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy/delnodes.dmp, /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy/division.dmp, /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy/gc.prt, /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy/gencode.dmp, /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy/merged.dmp, /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy/names.dmp, /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy/nodes.dmp, taxdump.tar.gz conda-env: /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/conda/af2fc30e385f331538790795233e05db shell:

    curl https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz -o taxdump.tar.gz
    curl https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz.md5 | md5sum -c
    mkdir -p /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy
    tar xvf taxdump.tar.gz -C /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/tax/taxonomy

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
beardymcjohnface commented 2 weeks ago

I'm not sure why it's failed but you should try running those commands manually one by one. Was there any other error message?

baidefeng commented 2 weeks ago

When i rerun "hecatomb install", no error occurred again. Then i run "hecatomb test --threads 2" and there is an error.

Error in rule index_host_genome: jobid: 4 input: /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/host/human/masked_ref.fa.gz output: hecatomb.out/trimnami/temp/masked_ref.fa.idx log: hecatomb.out/trimnami/logs/index_hostgenome.log (check log file(s) for error details) conda-env: /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/conda/d0948b388800f98818a19a437160e856/lib/python3.12/site-packages/trimnami/workflow/conda/94ed3c58c658bd219e7cdedfab82ff53_ shell: minimap2 -t 2 -I 8G -d hecatomb.out/trimnami/temp/masked_ref.fa.idx /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/host/human/masked_ref.fa.gz &> hecatomb.out/trimnami/logs/index_host_genome.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Logfile hecatomb.out/trimnami/logs/index_host_genome.log: empty file

Removing output files of failed job index_host_genome since they might be corrupted: hecatomb.out/trimnami/temp/masked_ref.fa.idx Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message cat .snakemake/log/2024-06-18T101546.068754.snakemake.log >> hecatomb.out/trimnami/trimnami.log Complete log: .snakemake/log/2024-06-18T101546.068754.snakemake.log [2024:06:18 10:16:20] ERROR: Snakemake failed [Tue Jun 18 10:16:20 2024] Error in rule run_trimnami: jobid: 1 input: hecatomb.out/results/hecatomb.samples.tsv, hecatomb.out/processing/temp/trimnami.config.yaml output: hecatomb.out/trimnami/results/fastp/A13-04-182-06_TAGCTT_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-04-182-06_TAGCTT_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-04-182-06_TAGCTT_RS.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-12-250-06_GGCTAC_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-12-250-06_GGCTAC_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-12-250-06_GGCTAC_RS.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-135-177-06_AGTTCC_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-135-177-06_AGTTCC_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-135-177-06_AGTTCC_RS.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-151-169-06_ATGTCA_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-151-169-06_ATGTCA_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-151-169-06_ATGTCA_RS.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-252-114-06_CCGTCC_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-252-114-06_CCGTCC_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-252-114-06_CCGTCC_RS.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-253-140-06_GTCCGC_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-253-140-06_GTCCGC_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-253-140-06_GTCCGC_RS.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-255-183-06_GTGGCC_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-255-183-06_GTGGCC_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-255-183-06_GTGGCC_RS.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-256-115-06_GTTTCG_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-256-115-06_GTTTCG_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-256-115-06_GTTTCG_RS.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-256-117-06_ACTGAT_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-256-117-06_ACTGAT_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-256-117-06_ACTGAT_RS.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-258-124-06_CGTACG_R1.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-258-124-06_CGTACG_R2.host_rm.fastq.gz, hecatomb.out/trimnami/results/fastp/A13-258-124-06_CGTACG_RS.hostrm.fastq.gz conda-env: /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/conda/d0948b388800f98818a19a437160e856 shell: trimnami run fastp --reads hecatomb.out/results/hecatomb.samples.tsv --configfile hecatomb.out/processing/temp/trimnami.config.yaml --host /home/baidefeng/miniconda3/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../databases/host/human/masked_ref.fa.gz --output hecatomb.out/trimnami --threads 2 --minimap sr --workflow-profile hecatomb.out/hecatomb.profile ; (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message cat .snakemake/log/2024-06-18T101542.755942.snakemake.log >> hecatomb.out/hecatomb.log