zsh & pipefail

[bennuru]

I am getting stuck at the tigmint step with the following error: tigmint-make tigmint-long draft=w16_x10_golden_path.goldrush-edit-polished reads=long_reads cut=250 t=32 G=94000000 span=2 dist=500 zsh: no such option: pipefail zsh: no such option: pipefail zsh: no such option: pipefail zsh: no such option: pipefail make[1]: Entering directory /.../.../.../.../goldrush' gzip -dc | /long-to-linked -l250 -m2000 -g94000000 | gzip > long_reads.cut250.fa.gz zsh: no such option: pipefail make[1]: *** [long_reads.cut250.fa.gz] Error 1 make[1]: Leaving directory/.../.../.../.../goldrush' make: *** [/.../.../.../.../conda/envs/goldrush/bin/goldrush.make:246: w16_x10_golden_path.goldrush-edit-polished.cut250.tigmint.fa] Error 2

[lcoombe]

Hi @bennuru,

How did you install GoldRush and Tigmint? Can you double check that you have zsh installed properly?

Thank you for your interest in GoldRush! Lauren

[bennuru]

Hi @lcoombe It is a Conda environment. And 'which zsh' does give me '/usr/bin/zsh'. So I do have zsh in my env. I just commented out Line 83 of tigmint-make, and it seems to be running fine. Will update if I can get it to completion without any further hiccups.

[lcoombe]

That's strange, because zsh is a listed dependency in the Tigmint conda recipe (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/tigmint/meta.yaml). I sometimes have seen that issue with older zsh versions which I have seen when using the /usr/bin/zsh.

What version of Tigmint is installed? I'm also not totally sure which line you are commenting out, because I'm guessing that you aren't referring to the current line 83 in the master branch? https://github.com/bcgsc/tigmint/blob/master/bin/tigmint-make#L83

I'd recommend running the test demo first to iron out any issues - it's fast and just helps to make you more confident in your installations. I can't guarantee that things will work as expected with commenting out lines of code :)

[bennuru]

@lcoombe

Here is the Conda env list:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge abyss 2.3.5 h41cdee2_1 bioconda arpack 3.7.0 hdefa2d7_2 conda-forge bcftools 1.3.1 h5bf99c6_7 bioconda bedtools 2.30.0 h468198e_3 bioconda btllib 1.5.1 py38h4a32c8e_0 bioconda bzip2 1.0.8 h7f98852_4 conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge curl 7.71.1 he644dc0_3 conda-forge gettext 0.21.1 h27087fc_0 conda-forge glpk 5.0 h445213a_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge goldrush 1.0.2 py38hfe0f59a_0 bioconda gperftools 2.10 h09c0d1c_0 conda-forge gzip 1.12 h166bdaf_0 conda-forge htslib 1.3.1 h18ffd7a_3 bioconda icu 72.1 hcb278e6_0 conda-forge intervaltree 3.0.2 py_0 conda-forge k8 0.2.5 hd03093a_2 bioconda krb5 1.17.2 h926e7f8_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcurl 7.71.1 hcdd3856_3 conda-forge libdivsufsort 2.0.2 hec16e2b_6 bioconda libedit 3.1.20191231 he28a2e2_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libhwloc 2.9.0 hd6dc26d_0 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libunwind 1.6.2 h9c3ff4c_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxml2 2.10.3 hfdac1af_6 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge lrzip 0.621 h159dde0_5 bioconda lzo 2.10 h516909a_1000 conda-forge make 4.3 hd18ef5c_1 conda-forge metis 5.1.0 h58526e2_1006 conda-forge minimap2 2.24 h7132678_1 bioconda mpfr 4.2.0 hb012696_0 conda-forge mpi 1.0 openmpi conda-forge ncurses 6.3 h27087fc_1 conda-forge ntlink 1.3.8 py38hf4f3596_1 bioconda numpy 1.24.2 py38h10c12cc_0 conda-forge openmpi 4.1.5 h414af15_101 conda-forge openssl 1.1.1t h0b41bf4_0 conda-forge pandas 2.0.0 py38hdc8b05c_0 conda-forge perl 5.32.1 2_h7f98852_perl5 conda-forge pigz 2.6 h27826a3_0 conda-forge pip 23.0.1 pyhd8ed1ab_0 conda-forge pybedtools 0.8.1 py38h1c8e9b9_2 bioconda pysam 0.9.1 py38hd1a2d5f_10 bioconda python 3.8.15 h257c98d_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-igraph 0.10.4 py38hd98a34f_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.8 3_cp38 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge readline 8.2 h8228510_1 conda-forge samtools 1.3.1 h80b0bb3_7 bioconda setuptools 67.6.1 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge suitesparse 5.10.1 h9e50725_1 conda-forge tar 1.34 hb2e2bae_1 conda-forge tbb 2021.8.0 hf52228f_0 conda-forge texttable 1.6.7 pyhd8ed1ab_0 conda-forge tigmint 1.2.1 py_0 bioconda tk 8.6.12 h27826a3_0 conda-forge util-linux 2.36 py38h7de7a29_1 conda-forge wget 1.20.3 ha56f1ee_1 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zip 3.0 h7f98852_1 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge

So I have tigmint 1.2.1 that got installed into the Conda env.

Also the line that I commented out from (/.../.../.../.../conda/envs/goldrush/bin/tigmint-make) is:

80. SHELL=bash -e -o pipefail
81. ifneq ($(shell command -v zsh),)

82. Set pipefail to ensure that all commands of a pipe succeed.

83. SHELL=zsh -e -o pipefail

84. Report run time and memory usage with zsh.

[lcoombe]

Hi @bennuru,

We're currently at Tigmint v1.2.9, so your installed version is a few releases old. You will likely have a smoother time if you update Tigmint to the newest version.

Otherwise, do try running the demo with your commented out version - it's the best way for you to make sure that your installation is working!

[bennuru]

@lcoombe I do not know why Conda installed the Tigmint 1.2.1. Manually installing 1.2.9 took care of the zsh problem. Thank you.

[lcoombe]

Great, I'm glad that solved the issue!