Invalid option `--vcf'

[npsonis]

I installed sequencetools 1.6.0.0 with conda (fresh env). However, when I am using pileupcaller and the --vcf option, I get an "invalid option --vcf" error and then it reports below that " This tool is part of sequenceTools version 1.5.2". Can you provide in conda the latest version of pileupcaller?

conda list packages in environment:

Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bzip2 1.0.8 h4bc722e_7 conda-forge c-ares 1.34.4 hb9d3cd8_0 conda-forge ca-certificates 2025.1.31 hbcca054_0 conda-forge gmp 6.3.0 hac33072_2 conda-forge htslib 1.21 h566b1c6_1 bioconda keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.21.3 h659f571_0 conda-forge libcurl 8.13.0 h332b0f4_0 conda-forge libdeflate 1.23 h4ddbbb0_0 conda-forge libedit 3.1.20250104 pl5321h7949ede_0 conda-forge libev 4.33 hd590300_2 conda-forge libgcc 14.2.0 h767d61c_2 conda-forge libgcc-ng 14.2.0 h69a702a_2 conda-forge libgomp 14.2.0 h767d61c_2 conda-forge liblzma 5.8.1 hb9d3cd8_0 conda-forge libnghttp2 1.64.0 h161d5f1_0 conda-forge libssh2 1.11.1 hf672d98_0 conda-forge libstdcxx 14.2.0 h8f9b012_2 conda-forge libstdcxx-ng 14.2.0 h4852527_2 conda-forge libzlib 1.3.1 hb9d3cd8_2 conda-forge ncurses 6.5 h2d0b736_3 conda-forge openssl 3.4.1 h7b32b05_0 conda-forge samtools 1.21 h96c455f_1 bioconda sequencetools 1.6.0.0 hebebf5b_0 bioconda zlib 1.3.1 hb9d3cd8_2 conda-forge zstd 1.5.7 hb8e6e7a_2 conda-forge

It is also weird that the --vcf option is provided when executing --help.

[stschiff]

Goodness, sorry, and thanks for letting me know. I'll take a look ASAP.

[stschiff]

I cannot reproduce this. When I run conda install sequenctools I get the right version with This tool is part of sequenceTools version 1.6.0.0 at the bottom of the help screen.

[npsonis]

I will try to took a second look, but might take some time as I am currently on a leave. I might have installed it with an experimental solver of conda (libmamba), so I will try to replicate it in a fresh environment.

Στις Τετ, 9 Απρ 2025, 13:55 ο χρήστης Stephan Schiffels < @.***> έγραψε:

I cannot reproduce this. When I run conda install sequenctools I get the right version with This tool is part of sequenceTools version 1.6.0.0 at the bottom of the help screen.

— Reply to this email directly, view it on GitHub https://github.com/stschiff/sequenceTools/issues/39#issuecomment-2789262321, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFJD7MCEEOG5DSZPZ5MKJRT2YT34HAVCNFSM6AAAAAB2O27LTGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOOBZGI3DEMZSGE . You are receiving this because you authored the thread.Message ID: @.***> stschiff left a comment (stschiff/sequenceTools#39) https://github.com/stschiff/sequenceTools/issues/39#issuecomment-2789262321

I cannot reproduce this. When I run conda install sequenctools I get the right version with This tool is part of sequenceTools version 1.6.0.0 at the bottom of the help screen.

— Reply to this email directly, view it on GitHub https://github.com/stschiff/sequenceTools/issues/39#issuecomment-2789262321, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFJD7MCEEOG5DSZPZ5MKJRT2YT34HAVCNFSM6AAAAAB2O27LTGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOOBZGI3DEMZSGE . You are receiving this because you authored the thread.Message ID: @.***>

[npsonis]

Hello again,

I tried to replicate the issue and I have half-succeeded.

So I made a new env and installed only sequencetools from bioconda) (conda install bioconda::sequencetools) Now it properly states the version (1.6.0.0) but the --vcf issue is still there (Invalid option `--vcf')

The command I used was the following mpileup -B -q30 -Q30 -l 1240K.bed -R -f hs37d5.fa 112.hs37d5.bam | pileupCaller --randomHaploid --sampleNames 112 -f 1240K.snp -e test_out --vcf

It works when removing the --vcf option

[stschiff]

This is a user error (I admit the error message isn't helpful): you choose eigenstrat output with -e which clashes with VCF output (--vcf). Remove the -e, then it will work and output VCF to stdout, which you can pipe into a file via > myfile.vcf

See pileupCaller --help

[npsonis]

Oh I see. I thought that the vcf output is additionally generated to that of eigenstrat/bed. Thanks

[stschiff]

Yeah, my command-line interfaces are sometimes a bit intricate, but it's all described in the help-output, even if it may be somewhat subtle (for example looking at the specific bracketing of the optional parameters).

I will close this then.