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lilit-nersisyan / computel

Compute mean telomere length from Whole Genome Sequencing data.
http://big.sci.am/software/computel/
14 stars 11 forks source link

readlink: missing operand Issue #4

Open irobii opened 2 years ago

irobii commented 2 years ago

I found below error message when I executed with example files. Please let me know what is the problem and the solution of the error.

$./computel.sh -1 src/examples/tel_reads1.fq.gz -2 src/examples/tel_reads2.fq.gz -o mytest readlink: missing operand Try 'readlink --help' for more information. readlink: missing operand Try 'readlink --help' for more information. Computel: testing setup:

Error: There are problems with executable. Please, check if works properly in your system.

lilit-nersisyan commented 2 years ago

hi, thanks for reporting it: could you, please, clone the latest version and confirm whether you still see the error?

thanks, lilit

lilit-nersisyan commented 2 years ago

Dear Ka-Kyung Kim,

Thank you for your interest in Computel.

There seems to be a problem finding and setting the path to either bowtie2 or samtools executables. I have commited a new version of Computel with more descriptive error messages.

Could you, please:

  1. Clone the recent version from github: git clone https://github.com/lilit-nersisyan/computel.git
  2. Make sure you have bowtie2 and samtools installed
  3. If you are getting errors, please also try specifying the paths to your installation directories with the options -sam for samtools, -bowal for bowtie2, and -bowb for bowtie2-build.

Would be glad to follow up with the results.

With kind regards, Lilit

On Mon, Dec 6, 2021 at 11:39 AM Ka-Kyung Kim @.***> wrote:

I found below error message when I executed with example files. Please let me know what is the problem and the solution of the error.

$./computel.sh -1 src/examples/tel_reads1.fq.gz -2 src/examples/tel_reads2.fq.gz -o mytest readlink: missing operand Try 'readlink --help' for more information. readlink: missing operand Try 'readlink --help' for more information. Computel: testing setup:

Error: There are problems with executable. Please, check if works properly in your system.

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-- Lilit Nersisyan, PhD Founding Director, Armenian Bioinformatics Institute Researcher, Karolinska Institutet, SciLifeLab