Open lxsteiner opened 10 months ago
Hi,
was running the tutorial example:
$ python3 go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -1 tutorial/thao2000.1.fq -2 tutorial/thao2000.2.fq -l 150 -o tutorial/example1_output -t 30 --notimestamps
but it failed:
REFERENCE genome file provided. Reference Selection step will be skipped. Building DAG of jobs... Using shell: /bin/bash Provided cores: 30 Rules claiming more threads will be scaled down. Job stats: job count -------------------- ------- all 1 assemble_unmapped 1 assembled_references 1 bowtie2_map 1 build_contigs 1 create_tsv 1 join_contigs 1 mapping_stats 1 polish_contigs 1 polish_map 1 stats_all 1 stats_genome 1 total 12 Select jobs to execute... [Mon Dec 18 15:14:24 2023] Job 5: ---Build index . Reason: Missing output files: tutorial/example1_output/logs/bowtie2map.log, tutorial/example1_output/assembly/mc.sam bowtie2-build -o 3 --threads 30 -q tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta tutorial/example1_output/assembly/mc.index 1>> tutorial/example1_output/assembly/mc.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 30 -x tutorial/example1_output/assembly/mc.index -q -U tutorial/thao2000.1.fq,tutorial/thao2000.2.fq -S tutorial/example1_output/assembly/mc.sam.all > tutorial/example1_output/logs/bowtie2map.log 2>&1; python3 /media/5c679734-9376-4617-815c-d4bd4177b8b2/leon/projects/01/soft/MetaCompass/bin/best_strata.py tutorial/example1_output/assembly/mc.sam.all tutorial/example1_output/assembly/mc.sam; rm tutorial/example1_output/assembly/mc.sam.all && touch tutorial/example1_output/assembly/.run1.ok [Mon Dec 18 15:14:30 2023] Finished job 5. 1 of 12 steps (8%) done Select jobs to execute... [Mon Dec 18 15:14:30 2023] Job 4: ---Build contigs . Reason: Missing output files: tutorial/example1_output/assembly/selected_maps.sam, tutorial/example1_output/assembly/contigs.fasta; Input files updated by another job: tutorial/example1_output/assembly/mc.sam /media/5c679734-9376-4617-815c-d4bd4177b8b2/leon/projects/01/soft/MetaCompass/bin/buildcontig -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -s tutorial/example1_output/assembly/mc.sam -o tutorial/example1_output/assembly -c 1 -l 1 -n F -b F -u F -k breadth 1>> tutorial/example1_output/logs/buildcontigs.log 2>&1 && touch tutorial/example1_output/assembly/.run2.ok [Mon Dec 18 15:14:31 2023] Finished job 4. 2 of 12 steps (17%) done Select jobs to execute... [Mon Dec 18 15:14:32 2023] Job 3: ---ntEDit polish contigs . Reason: Missing output files: tutorial/example1_output/error_correction/contigs_edited.fa; Input files updated by another job: tutorial/example1_output/assembly/contigs.fasta Building DAG of jobs... Using shell: /bin/bash Provided cores: 30 Rules claiming more threads will be scaled down. Select jobs to execute... touch tutorial/example1_output/error_correction/contigs_edited.fa /usr/bin/time -v -o tutorial/example1_output/error_correction/solidBF_c1.time nthits -c1 -b 36 -k 25 -t16 --outbloom tutorial/thao2000.1.fq tutorial/thao2000.2.fq -p tutorial/example1_output/error_correction/solidBF_c1> tutorial/example1_output/logs/polish.log 2>&1 [Mon Dec 18 15:14:33 2023] Error in rule polish_contigs: jobid: 0 input: tutorial/example1_output/assembly/contigs.fasta, tutorial/thao2000.1.fq, tutorial/thao2000.2.fq output: tutorial/example1_output/error_correction/contigs_edited.fa log: tutorial/example1_output/logs/polish.log (check log file(s) for error details) RuleException: CalledProcessError in file /media/5c679734-9376-4617-815c-d4bd4177b8b2/leon/projects/01/soft/MetaCompass/snakemake/metacompass.ref.paired.py, line 134: Command 'set -euo pipefail; /usr/bin/time -v -o tutorial/example1_output/error_correction/solidBF_c1.time nthits -c1 -b 36 -k 25 -t16 --outbloom tutorial/thao2000.1.fq tutorial/thao2000.2.fq -p tutorial/example1_output/error_correction/solidBF_c1> tutorial/example1_output/logs/polish.log 2>&1' returned non-zero exit status 1. File "/media/5c679734-9376-4617-815c-d4bd4177b8b2/leon/projects/01/soft/MetaCompass/snakemake/metacompass.ref.paired.py", line 134, in __rule_polish_contigs File "/home/leon/miniconda3/envs/metacompass_env/lib/python3.10/concurrent/futures/thread.py", line 58, in run Removing output files of failed job polish_contigs since they might be corrupted: tutorial/example1_output/error_correction/contigs_edited.fa Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2023-12-18T151423.726751.snakemake.log ERROR: snakemake command failed; exiting..
tutorial/example1_output/logs/polish.log
Unknown argument: -c1 Usage: ntHits --frequencies VAR --out-file VAR [--min-count VAR] [--max-count VAR] [--kmer-length VAR] [--seeds VAR] [-h] [--error-rate VAR] [--threads VAR] [--solid] [--long-mode] out_type files Filters k-mers based on counts (cmin <= count <= cmax) in input files Positional arguments: out_type Output format: Bloom filter 'bf', counting Bloom filter ('cbf'), or table ('table') [required] files Input files [nargs: 0 or more] [required] Optional arguments: -f, --frequencies Frequency histogram file (e.g. from ntCard) [required] -o, --out-file Output file's name [required] -cmin, --min-count Minimum k-mer count (>=1), ignored if using --solid [default: 1] -cmax, --max-count Maximum k-mer count (<=254) [default: 254] -k, --kmer-length k-mer length, ignored if using spaced seeds (-s) [default: 64] -s, --seeds If specified, use spaced seeds (separate with commas, e.g. 10101,11011) -h, --num-hashes Number of hashes to generate per k-mer/spaced seed [default: 3] -p, --error-rate Target Bloom filter error rate [default: 0.0001] -t, --threads Number of parallel threads [default: 4] --solid Automatically tune 'cmin' to filter out erroneous k-mers --long-mode Optimize data reader for long sequences (>5kbp) -v Level of details printed to stdout (-v: normal, -vv detailed) Copyright 2023 Canada's Michael Smith Genome Science Centre
Installed the dependencies in a conda environment:
mamba create -n metacompass_env -c conda-forge -c bioconda "python=>3.1" biopython "snakemake>=3.7.1" "blast>=2.4.0" "bowtie2>=2.2.9" "mash>=2.1" "samtools>=1.2.13" "megahit>=1.0.6" nthits ntedit meryl
here are the versions:
# Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge aioeasywebdav 2.4.0 pyha770c72_0 conda-forge aiohttp 3.9.1 py310h2372a71_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge amply 0.1.6 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge attmap 0.13.2 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge bcrypt 4.1.2 py310hcb5633a_0 conda-forge **biopython 1.81 py310h2372a71_1 conda-forge** **blast 2.15.0 pl5321h6f7f691_1 bioconda** boto3 1.34.2 pyhd8ed1ab_0 conda-forge botocore 1.34.2 pyhd8ed1ab_0 conda-forge **bowtie2 2.5.2 py310ha0a81b8_0 bioconda** brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge btllib 1.7.0 py310h0dbaff4_0 bioconda bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.24.0 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge cachetools 5.3.2 pyhd8ed1ab_0 conda-forge capnproto 0.9.1 ha19adfc_4 conda-forge certifi 2023.11.17 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py310h2fee648_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge coin-or-cbc 2.10.10 h9002f0b_0 conda-forge coin-or-cgl 0.60.7 h516709c_0 conda-forge coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge coin-or-osi 0.108.8 ha2443b9_0 conda-forge coin-or-utils 2.11.9 hee58242_0 conda-forge coincbc 2.10.10 0_metapackage conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge configargparse 1.7 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge cryptography 41.0.7 py310hb8475ec_1 conda-forge curl 8.5.0 hca28451_0 conda-forge datrie 0.8.2 py310h2372a71_7 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge docutils 0.20.1 py310hff52083_3 conda-forge dpath 2.1.6 pyha770c72_0 conda-forge dropbox 11.36.2 pyhd8ed1ab_0 conda-forge eido 0.2.2 pyhd8ed1ab_0 conda-forge entrez-direct 16.2 he881be0_1 bioconda exceptiongroup 1.2.0 pyhd8ed1ab_0 conda-forge filechunkio 1.8 py_2 conda-forge frozenlist 1.4.1 py310h2372a71_0 conda-forge ftputil 5.0.4 pyhd8ed1ab_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gitdb 4.0.11 pyhd8ed1ab_0 conda-forge gitpython 3.1.40 pyhd8ed1ab_0 conda-forge google-api-core 2.15.0 pyhd8ed1ab_0 conda-forge google-api-python-client 2.111.0 pyhd8ed1ab_0 conda-forge google-auth 2.25.2 pyhca7485f_0 conda-forge google-auth-httplib2 0.2.0 pyhd8ed1ab_0 conda-forge google-cloud-core 2.4.1 pyhd8ed1ab_0 conda-forge google-cloud-storage 2.14.0 pyhca7485f_0 conda-forge google-crc32c 1.1.2 py310hc5c09a0_5 conda-forge google-resumable-media 2.7.0 pyhd8ed1ab_0 conda-forge googleapis-common-protos 1.62.0 pyhd8ed1ab_0 conda-forge grpcio 1.60.0 py310h1b8f574_0 conda-forge gsl 2.7 he838d99_0 conda-forge gzip 1.13 hd590300_0 conda-forge htslib 1.19 h81da01d_0 bioconda httplib2 0.22.0 pyhd8ed1ab_0 conda-forge humanfriendly 10.0 pyhd8ed1ab_6 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.6 pyhd8ed1ab_0 conda-forge importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge jsonschema 4.20.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.11.2 pyhd8ed1ab_0 conda-forge jupyter_core 5.5.0 py310hff52083_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.21.2 h659d440_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libabseil 20230802.1 cxx17_h59595ed_0 conda-forge libblas 3.9.0 20_linux64_openblas conda-forge libcblas 3.9.0 20_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcurl 8.5.0 hca28451_0 conda-forge libdeflate 1.19 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgfortran-ng 13.2.0 h69a702a_3 conda-forge libgfortran5 13.2.0 ha4646dd_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libgrpc 1.60.0 hd6c4280_0 conda-forge libhwloc 2.9.3 default_h554bfaf_1009 conda-forge libiconv 1.17 hd590300_2 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge liblapack 3.9.0 20_linux64_openblas conda-forge liblapacke 3.9.0 20_linux64_openblas conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge libprotobuf 4.24.4 hf27288f_0 conda-forge libre2-11 2023.06.02 h7a70373_0 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxml2 2.11.6 h232c23b_0 conda-forge libzlib 1.2.13 hd590300_5 conda-forge logmuse 0.2.6 pyh8c360ce_0 conda-forge lrzip 0.621 hedc9cd1_7 bioconda lzo 2.10 h516909a_1000 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.3 py310h2372a71_1 conda-forge **mash 2.3 ha9a2dd8_3 bioconda** mdurl 0.1.0 pyhd8ed1ab_0 conda-forge **megahit 1.2.9 h43eeafb_4 bioconda** meryl 2013 0 bioconda multidict 6.0.4 py310h2372a71_1 conda-forge nbformat 5.9.2 pyhd8ed1ab_0 conda-forge ncbi-vdb 3.0.9 hdbdd923_0 bioconda ncurses 6.4 h59595ed_2 conda-forge **ntedit 1.3.5 hd03093a_1 bioconda** **nthits 1.0.2 h4ac6f70_0 bioconda** numpy 1.26.2 py310hb13e2d6_0 conda-forge oauth2client 4.1.3 py_0 conda-forge openssl 3.2.0 hd590300_1 conda-forge ossuuid 1.6.2 hf484d3e_1000 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge pandas 2.1.4 py310hcc13569_0 conda-forge paramiko 3.3.1 pyhd8ed1ab_0 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge peppy 0.35.7 pyhd8ed1ab_0 conda-forge perl 5.22.2.1 0 conda-forge perl-archive-tar 2.18 1 bioconda perl-common-sense 3.74 0 bioconda perl-exporter-tiny 0.042 1 bioconda perl-json 2.90 1 bioconda perl-json-xs 2.34 0 bioconda perl-list-moreutils 0.413 1 bioconda perl-threaded 5.32.1 hdfd78af_1 bioconda perl-uri 1.71 0 bioconda perl-xml-libxml 2.0124 0 bioconda perl-xml-namespacesupport 1.11 0 bioconda perl-xml-sax 0.99 0 bioconda perl-xml-sax-base 1.08 0 bioconda pigz 2.8 h2797004_0 conda-forge pip 23.3.2 pyhd8ed1ab_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge plac 1.4.2 pyhd8ed1ab_0 conda-forge platformdirs 4.1.0 pyhd8ed1ab_0 conda-forge pluggy 1.3.0 pyhd8ed1ab_0 conda-forge ply 3.11 py_1 conda-forge prettytable 3.9.0 pyhd8ed1ab_0 conda-forge protobuf 4.24.4 py310h620c231_0 conda-forge psutil 5.9.7 py310h2372a71_0 conda-forge pulp 2.7.0 py310hff52083_1 conda-forge pyasn1 0.5.1 pyhd8ed1ab_0 conda-forge pyasn1-modules 0.3.0 pyhd8ed1ab_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.17.2 pyhd8ed1ab_0 conda-forge pynacl 1.5.0 py310h2372a71_3 conda-forge pyopenssl 23.3.0 pyhd8ed1ab_0 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pysftp 0.2.9 py_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 7.4.3 pyhd8ed1ab_0 conda-forge **python 3.10.13 hd12c33a_0_cpython conda-forge** python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.19.0 pyhd8ed1ab_0 conda-forge python-irodsclient 1.1.9 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 4_cp310 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py310h2372a71_1 conda-forge re2 2023.06.02 h2873b5e_0 conda-forge readline 8.2 h8228510_1 conda-forge referencing 0.32.0 pyhd8ed1ab_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge reretry 0.11.8 pyhd8ed1ab_0 conda-forge rich 13.7.0 pyhd8ed1ab_0 conda-forge rpds-py 0.13.2 py310hcb5633a_0 conda-forge rsa 4.9 pyhd8ed1ab_0 conda-forge s3transfer 0.9.0 pyhd8ed1ab_0 conda-forge **samtools 1.19 h50ea8bc_0 bioconda** setuptools 68.2.2 pyhd8ed1ab_0 conda-forge setuptools-scm 8.0.4 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge slacker 0.14.0 py_0 conda-forge smart_open 6.4.0 pyhd8ed1ab_0 conda-forge smmap 5.0.0 pyhd8ed1ab_0 conda-forge **snakemake 7.32.4 hdfd78af_1 bioconda** snakemake-minimal 7.32.4 pyhdfd78af_1 bioconda stone 3.3.1 pyhd8ed1ab_0 conda-forge stopit 1.1.2 py_0 conda-forge tabulate 0.9.0 pyhd8ed1ab_1 conda-forge tar 1.34 hb2e2bae_1 conda-forge tbb 2021.11.0 h00ab1b0_0 conda-forge throttler 1.2.2 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toposort 1.10 pyhd8ed1ab_0 conda-forge traitlets 5.14.0 pyhd8ed1ab_0 conda-forge typing-extensions 4.9.0 hd8ed1ab_0 conda-forge typing_extensions 4.9.0 pyha770c72_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge ubiquerg 0.6.3 pyhd8ed1ab_0 conda-forge uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge urllib3 1.26.18 pyhd8ed1ab_0 conda-forge veracitools 0.1.3 py_0 conda-forge wcwidth 0.2.12 pyhd8ed1ab_0 conda-forge wget 1.20.3 ha35d2d1_1 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge wrapt 1.16.0 py310h2372a71_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yarl 1.9.3 py310h2372a71_0 conda-forge yte 1.5.4 pyha770c72_0 conda-forge zip 3.0 hd590300_3 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge
Is there a version requirement for nthits (because it's not specified) or where does the error come from?
nthits
Also, what is go_metacompass2.py and how does it differ from go_metacompass.py ?
go_metacompass2.py
go_metacompass.py
Thanks!
Hi,
was running the tutorial example:
but it failed:
tutorial/example1_output/logs/polish.log
Installed the dependencies in a conda environment:
here are the versions:
Is there a version requirement for
nthits(because it's not specified) or where does the error come from?Also, what is
go_metacompass2.pyand how does it differ fromgo_metacompass.py?Thanks!