Evaluate upgrading the project to use mtbseq-1.0.4 #59
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abhi18av
changed the title
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Na, still runs across the same problem 🤷 |
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Continuation of the saga #54 |
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Interestingly - if we use the But if we install via the |
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Hmm, now the transition to |
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Closing this issue since we've run across problems w.r.t Perl and GATK(3) , please refer #58 (comment) for context. |
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The problem still persists upon trying to install the latest version from Followed the instructions from https://github.com/ngs-fzb/MTBseq_source#conda
$ wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
$ gatk-register GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
ENV_PREFIX /mnt/lustre/users/econceicao/miniconda3/envs/mtbseq-env
Processing GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 as *.tar.bz2
Extracting GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
mkdir: cannot create directory '/tmp/gatk': File exists
tar: Ignoring unknown extended header keyword `LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword `SCHILY.dev'
tar: Ignoring unknown extended header keyword `SCHILY.ino'
tar: Ignoring unknown extended header keyword `SCHILY.nlink'
GenomeAnalysisTK-3.8-0-ge9d806836/
tar: Ignoring unknown extended header keyword `LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword `SCHILY.dev'
tar: Ignoring unknown extended header keyword `SCHILY.ino'
tar: Ignoring unknown extended header keyword `SCHILY.nlink'
GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar
Error: Unable to access jarfile ./GenomeAnalysisTK.jar
The version of the jar specified, , does not match the version expected by conda: 3.8==============
$ tar -xf GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 --wildcards '*.jar'
tar: Ignoring unknown extended header keyword `LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword `SCHILY.dev'
tar: Ignoring unknown extended header keyword `SCHILY.ino'
tar: Ignoring unknown extended header keyword `SCHILY.nlink'
tar: Ignoring unknown extended header keyword `LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword `SCHILY.dev'
tar: Ignoring unknown extended header keyword `SCHILY.ino'
tar: Ignoring unknown extended header keyword `SCHILY.nlink'
$ gatk-register GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar
ENV_PREFIX /mnt/lustre/users/econceicao/miniconda3/envs/mtbseq-env
Processing GenomeAnalysisTK.jar as *.jar
jar file specified matches expected version
Copying GenomeAnalysisTK.jar to /mnt/lustre/users/econceicao/miniconda3/envs/mtbseq-env/opt/gatk-3.8 |
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Interestingly, the version being installed via the default command is still $ MTBseq --version
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
MTBseq 1.0.3However, the bigger problem is the expectation of $ MTBseq --check (mtbseq-env)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
<INFO> [2023-02-06 16:23:19] Found perl module: MCE
<INFO> [2023-02-06 16:23:19] Found perl module: Statistics::Basic
<INFO> [2023-02-06 16:23:19] Found bwa in your PATH!
<INFO> [2023-02-06 16:23:19] Found samtools in your PATH!
<ERROR> [2023-02-06 16:23:19] gatk3 is not installed or not in your PATH!
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Even after explicitly installing + mtbseq 1.0.4 hdfd78af_2 bioconda/noarch Cached
The version mentioned by the |
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$ mamba activate mtbseq-103-env
$ gatk-register GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar
$ MTBseq --check (mtbseq-103-env)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
<INFO> [2023-02-06 16:41:36] Found perl module: MCE
<INFO> [2023-02-06 16:41:36] Found perl module: Statistics::Basic
<INFO> [2023-02-06 16:41:36] Found bwa in your PATH!
<INFO> [2023-02-06 16:41:36] Found samtools in your PATH!
<INFO> [2023-02-06 16:41:36] Found gatk in your PATH!
<INFO> [2023-02-06 16:41:36] Found picard in your PATH!
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The conda setup for mtbseq-1.0.3 always runs across the problem mentioned in the MTBseq Github repo (issue-29)
gatk-registernot foundThe text was updated successfully, but these errors were encountered: