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Keywords {🔍}

condaforge, cutadapt, stderr, marcelm, errors, johanneskoester, stdout, issue, commented, report, sign, logging, pyhdedab, send, change, writes, bioconda, owner, author, wrapper, navigation, pull, requests, actions, security, closed, output, docs, information, pyhbfae, hed, hba, pyha, agree, file, make, release, rhpvorderman, github, labels, projects, milestone, footer, skip, content, menu, product, solutions, resources, open,

Topics {✒️}

johanneskoester edits author recognize cutadapt logs marcelm closed bioconda recipe update comment metadata assignees fasta/fastq data expected report information send error messages snakemake wrapper docs 6724bb1 sign cutadapt 4 cutadapt cutadapt fastq nonexistentfile qc stats mamba env historic reasons multiqc parses quick release release today rhpvorderman mentioned rhpvorderman added assigned labels labels projects projects milestone milestone relationships qc report output file github issue logging output wrapper change send errors send report wrapper file stderr sign logging change errors skip jump stdout misunderstand 6 insallation agree fixing

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Questions {❓}

• Already have an account?
• Did I misunderstand that?
• Errors to stdout or to stderr?
• Since I will have to fix the snakemake wrapper for cutadapt: chances for a quick release with that change (then no wrapper change is needed)?
• Would that resolve the issue for you?

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DiscussionForumPosting:
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      headline:Cutadapt writes some errors to STDOUT instead of STDERR
      articleBody:Cutadapt writes its logging output and errors to STDOUT. According to the docs, I expected report information (qc stats) on STDOUT, but logging and errors on STDERR. Did I misunderstand that? cutadapt 4.6 insallation via mamba env: ``` _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bzip2 1.0.8 hd590300_5 conda-forge ca-certificates 2024.2.2 hbcca054_0 conda-forge cffi 1.16.0 py310h2fee648_0 conda-forge cutadapt 4.6 py310h4b81fae_1 bioconda dnaio 1.2.0 py310h4b81fae_0 bioconda isa-l 2.31.0 hd590300_1 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_5 conda-forge libgomp 13.2.0 h807b86a_5 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libsqlite 3.45.1 h2797004_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge ncurses 6.4 h59595ed_2 conda-forge openssl 3.2.1 hd590300_0 conda-forge pbzip2 1.1.13 h1fcc475_2 conda-forge pigz 2.8 h2797004_0 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge python 3.10.13 hd12c33a_1_cpython conda-forge python-isal 1.6.0 py310h2372a71_0 conda-forge python_abi 3.10 4_cp310 conda-forge readline 8.2 h8228510_1 conda-forge setuptools 69.1.1 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tzdata 2024a h0c530f3_0 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge xopen 1.9.0 py310hff52083_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zstandard 0.22.0 py310h1275a96_0 conda-forge zstd 1.5.5 hfc55251_0 conda-forge ```
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         url:https://github.com/johanneskoester
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      headline:Cutadapt writes some errors to STDOUT instead of STDERR
      articleBody:Cutadapt writes its logging output and errors to STDOUT. According to the docs, I expected report information (qc stats) on STDOUT, but logging and errors on STDERR. Did I misunderstand that? cutadapt 4.6 insallation via mamba env: ``` _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bzip2 1.0.8 hd590300_5 conda-forge ca-certificates 2024.2.2 hbcca054_0 conda-forge cffi 1.16.0 py310h2fee648_0 conda-forge cutadapt 4.6 py310h4b81fae_1 bioconda dnaio 1.2.0 py310h4b81fae_0 bioconda isa-l 2.31.0 hd590300_1 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_5 conda-forge libgomp 13.2.0 h807b86a_5 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libsqlite 3.45.1 h2797004_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge ncurses 6.4 h59595ed_2 conda-forge openssl 3.2.1 hd590300_0 conda-forge pbzip2 1.1.13 h1fcc475_2 conda-forge pigz 2.8 h2797004_0 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge python 3.10.13 hd12c33a_1_cpython conda-forge python-isal 1.6.0 py310h2372a71_0 conda-forge python_abi 3.10 4_cp310 conda-forge readline 8.2 h8228510_1 conda-forge setuptools 69.1.1 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tzdata 2024a h0c530f3_0 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge xopen 1.9.0 py310hff52083_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zstandard 0.22.0 py310h1275a96_0 conda-forge zstd 1.5.5 hfc55251_0 conda-forge ```
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