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Busco and antismash #112

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bharat1912 opened this issue Oct 19, 2024 · 0 comments
Open

Busco and antismash #112

bharat1912 opened this issue Oct 19, 2024 · 0 comments
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@bharat1912
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  1. I am reopening the error in busco. This is the error in busco, though checkm2 works so this is not an issue but I am reporting it. ---------------------------------------------------
    |Results from generic domain bacteria_odb10 |

    |C:99.2%[S:99.2%,D:0.0%],F:0.8%,M:0.0%,n:124 |
    |123 Complete BUSCOs (C) |
    |123 Complete and single-copy BUSCOs (S) |
    |0 Complete and duplicated BUSCOs (D) |
    |1 Fragmented BUSCOs (F) |
    |0 Missing BUSCOs (M) |
    |124 Total BUSCO groups searched |

    |Results from dataset mycoplasmatales_odb10 |

    |C:92.0%[S:91.4%,D:0.6%],F:1.7%,M:6.3%,n:174 |
    |160 Complete BUSCOs (C) |
    |159 Complete and single-copy BUSCOs (S) |
    |1 Complete and duplicated BUSCOs (D) |
    |3 Fragmented BUSCOs (F) |
    |11 Missing BUSCOs (M) |
    |174 Total BUSCO groups searched |

2024-10-19 11:54:52 INFO: BUSCO analysis done. Total running time: 76 seconds
2024-10-19 11:54:52 INFO: Results written in pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco
2024-10-19 11:54:52 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-19 11:54:52 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
2024-10-19 11:54:52 INFO: [hmmsearch] 100 of 124 task(s) completed
[11:54:52] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|NCKHFOEE_12:372289..372441 on - strand
2024-10-19 11:54:52 INFO: [hmmsearch] 112 of 124 task(s) completed
[11:54:53] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|NCKHFOEE_57:276..740 on - strand
2024-10-19 11:54:53 INFO: [hmmsearch] 112 of 124 task(s) completed
[11:54:53] Found 2741 CDS
[11:54:53] Connecting features back to sequences
[11:54:53] Not using genus-specific database. Try --usegenus to enable it.
[11:54:53] Annotating CDS, please be patient.
[11:54:53] Will use 4 CPUs for similarity searching.
cat: '/pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/auto_lineage/*/short_summary.json': No such file or directory
[Sat Oct 19 11:54:53 2024]
Error in rule busco:
jobid: 49
output: /pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/busco_done.flag, /pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/short_summary_extract.tsv
conda-env: /pvol/conda_envs/07df8e5f1335cbb72312ae9ac6e9feb1_
shell:

    # Collect version number.
    busco -v > "$(dirname /pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/short_summary_extract.tsv)/.software_version.txt"
    
    # Collect database version.
    echo -e "$(date -Iseconds)	/pvol/databases/comparem2_db/busco/comparem2_busco_database_representative.flag" > "$(dirname /pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/short_summary_extract.tsv)/.database_version.txt"

    # Busco fails because of a problem with the sepp package. This doesn't really matter as we just want the completeness results.
    # But, this means that we need a hacky workaround to let this job exit gracefully (exit code 0) on the basis of whether any completeness results have been written to disk.
    # Hence, the actual exit code of busco, we will ignore.        
    
    # https://busco.ezlab.org/busco_userguide.html#offline
    # Is the timeout bug fixed? Update: nope.
    timeout 1800             busco                 --cpu 1                 --in /pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/prokka/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641.faa                 --out /pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco                 --force                 --skip_bbtools                 --download_path /pvol/databases/comparem2_db/busco                 --mode protein                 --tar --auto-lineage-prok                 --offline || (>&2 echo "comparem2: Busco failed internally.")

    # Cat all auto lineage results together or create empty file
    # The following cat command will fail if the glob doesn't resolve any files: This is the wanted behaviour.
    cat /pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/auto_lineage/*/short_summary.json         > "/pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/short_summary_extract.tsv_temp"
    
    >&2 echo "comparem2: Intermediate results have been collected, as they are still useful."
    
    # Extract relevant features
    cat "/pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/short_summary_extract.tsv_temp"         | grep -oE "(\"in\"|\"name\"|\"one_line_summary\").+"         > /pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/short_summary_extract.tsv

    # Clean up
    rm "/pvol/Anoxy_comparem2/Anoxy_comparem2_results/samples/GCA_002243705_1_Anoxybacillus_flavithermus_DSM2641/busco/short_summary_extract.tsv_temp" || echo "no file"
    
    mv busco_*.log .snakemake/log || echo "no logs to move"
    date -Iseconds >> /pvol/Anoxy_comparem2/Anoxy_comparem2_results/.comparem2_void_report.flag
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
  1. I am running: comparem2 v2.11.1 installed with mamba (miniforge2): mamba 1.5.10 and conda 24.9.1
  2. Conda list:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
amply 0.1.6 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
archspec 0.2.3 pyhd8ed1ab_0 conda-forge
attrs 24.2.0 pyh71513ae_0 conda-forge
boltons 24.0.0 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py310hf71b8c6_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.32.3 h4bc722e_0 conda-forge
ca-certificates 2024.8.30 hbcca054_0 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py310h8deb56e_0 conda-forge
charset-normalizer 3.4.0 pyhd8ed1ab_0 conda-forge
coin-or-cbc 2.10.12 h8b142ea_1 conda-forge
coin-or-cgl 0.60.9 h1d3f3f2_0 conda-forge
coin-or-clp 1.17.10 h07f2a63_0 conda-forge
coin-or-osi 0.108.11 h6514dde_1 conda-forge
coin-or-utils 2.11.12 h99da652_1 conda-forge
coincbc 2.10.12 1_metapackage conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comparem2 2.11.1 hdfd78af_0 bioconda
conda 24.9.1 py310hff52083_0 conda-forge
conda-libmamba-solver 24.9.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.3.0 pyh7900ff3_0 conda-forge
conda-package-streaming 0.10.0 pyhd8ed1ab_0 conda-forge
configargparse 1.7 pyhd8ed1ab_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
cpp-expected 1.1.0 hf52228f_0 conda-forge
datrie 0.8.2 py310ha75aee5_8 conda-forge
distro 1.9.0 pyhd8ed1ab_0 conda-forge
docutils 0.21.2 pyhd8ed1ab_0 conda-forge
dpath 2.2.0 pyha770c72_0 conda-forge
filelock 3.16.1 pyhd8ed1ab_0 conda-forge
fmt 11.0.2 h434a139_0 conda-forge
frozendict 2.4.5 py310ha75aee5_0 conda-forge
gitdb 4.0.11 pyhd8ed1ab_0 conda-forge
gitpython 3.1.43 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_0 conda-forge
importlib_resources 6.4.5 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
jsonpatch 1.33 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py310hff52083_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_1 conda-forge
libarchive 3.7.4 hfca40fe_0 conda-forge
libblas 3.9.0 24_linux64_openblas conda-forge
libcblas 3.9.0 24_linux64_openblas conda-forge
libcurl 8.10.1 hbbe4b11_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 14.1.0 h77fa898_1 conda-forge
libgcc-ng 14.1.0 h69a702a_1 conda-forge
libgfortran 14.1.0 h69a702a_1 conda-forge
libgfortran-ng 14.1.0 h69a702a_1 conda-forge
libgfortran5 14.1.0 hc5f4f2c_1 conda-forge
libgomp 14.1.0 h77fa898_1 conda-forge
libiconv 1.17 hd590300_2 conda-forge
liblapack 3.9.0 24_linux64_openblas conda-forge
liblapacke 3.9.0 24_linux64_openblas conda-forge
libmamba 1.5.10 hf72d635_1 conda-forge
libmambapy 1.5.10 py310h6639945_1 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge
libsolv 0.7.30 h3509ff9_0 conda-forge
libsqlite 3.46.1 hadc24fc_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 14.1.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.1.0 h4852527_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 he7c6b58_4 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 hd590300_1001 conda-forge
mamba 1.5.10 py310h51d5547_1 conda-forge
markupsafe 3.0.1 py310h89163eb_1 conda-forge
menuinst 2.1.2 py310hff52083_1 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
ncurses 6.5 he02047a_1 conda-forge
nlohmann_json 3.11.3 he02047a_1 conda-forge
numpy 2.1.2 py310hd6e36ab_0 conda-forge
openssl 3.3.2 hb9d3cd8_0 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.3 py310h5eaa309_1 conda-forge
pip 24.2 pyh8b19718_1 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
plac 1.4.3 pyhd8ed1ab_0 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_0 conda-forge
pluggy 1.5.0 pyhd8ed1ab_0 conda-forge
psutil 6.0.0 py310ha75aee5_1 conda-forge
pulp 2.7.0 py310hff52083_1 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.6 py310h2372a71_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.4 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.0 h543edf9_3_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 5_cp310 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py310ha75aee5_1 conda-forge
ratelimiter 1.2.0 pyhd8ed1ab_1003 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
reproc 14.2.4.post0 hd590300_1 conda-forge
reproc-cpp 14.2.4.post0 h59595ed_1 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
reretry 0.11.8 pyhd8ed1ab_0 conda-forge
rpds-py 0.20.0 py310h505e2c1_1 conda-forge
ruamel.yaml 0.18.6 py310h2372a71_0 conda-forge
ruamel.yaml.clib 0.2.8 py310h2372a71_0 conda-forge
scipy 1.14.1 py310ha3fb0e1_0 conda-forge
setuptools 75.1.0 pyhd8ed1ab_0 conda-forge
simdjson 3.10.1 h84d6215_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smart_open 7.0.5 pyhd8ed1ab_1 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
snakemake-minimal 7.15.2 pyhdfd78af_0 bioconda
spdlog 1.14.1 hed91bc2_1 conda-forge
sqlite 3.46.1 h9eae976_0 conda-forge
stopit 1.1.2 py_0 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toposort 1.10 pyhd8ed1ab_0 conda-forge
tqdm 4.66.5 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
truststore 0.9.2 pyhd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024b hc8b5060_0 conda-forge
urllib3 2.2.3 pyhd8ed1ab_0 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py310ha75aee5_1 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yaml-cpp 0.8.0 h59595ed_0 conda-forge
yte 1.5.4 pyha770c72_0 conda-forge
zipp 3.20.2 pyhd8ed1ab_0 conda-forge
zstandard 0.23.0 py310ha39cb0e_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge

  1. I have run metagenomes (bins from metawrap) and the following are reported from in the report section (anismash is missing):
    assembly_stats | 1 / 1 | 🟢 yes
    sequence_lengths | 88 / 88 | 🟢 yes
    busco | 0 / 88 | 🟠 no
    checkm2 | 1 / 1 | 🟢 yes
    gtdbtk | 1 / 1 | 🟢 yes
    mlst | 1 / 1 | 🟢 yes
    abricate | 4 / 4 | 🟢 yes
    prokka | 88 / 88 | 🟢 yes
    kegg_pathway | 0 / 1 | 🟠 no
    dbcan | 88 / 88 | 🟢 yes
    panaroo | 1 / 1 | 🟢 yes
    snp_dists | 0 / 1 | 🟠 no
    mashtree | 1 / 1 | 🟢 yes
    Thanks
@bharat1912 bharat1912 added the bug Something isn't working label Oct 19, 2024
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