[fast-contrib] issue: sh:1 ./scripts/build-rmi.linear_spline.linear.sh was not found

[harisankarsadasivan]

hello, @SaurabhKalikar @lh3 after installing and adding rustc binary folder to path, getting the error "issue: sh:1 ./scripts/build-rmi.linear_spline.linear.sh was not found" when I try to run build_rmi.sh.

[SaurabhKalikar]

Hello @harisankarsadasivan

The script build-rmi.linear_spline.linear.sh should be present in ./ext/TAL/scripts/.

TAL is added as a submodule to fast-contrib. I suspect that the submodule might be missing in your git repo. Please check whether you have cloned fast-contrib using --recursive flag.

git clone --recursive https://github.com/lh3/minimap2.git -b fast-contrib mm2-fast

Another possibility of getting the above error is -- build_rmi.sh should be executed from mm2-fast directory. If the script is called from any other location, the relative paths would lead to such file not found errors.

Please check whether this helps solving your issue.

Thanks, Saurabh

[harisankarsadasivan]

@SaurabhKalikar Thanks for the response. This does not solve the issue for me. I am doing a recursive clone from the same command as you have captured. I just verified the existence of ./ext/TAL/scripts/build-rmi.linear_spline.linear.sh from my working directory. The only difference is my dataset path is hg38 from another directory. The error happens atleast after 5-10 minutes of running the script. Kindly, look into it.

My error log: Num_keys: 100167746, num_values = 552857382rmi file not found: /home/hsadasivan/datasets/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna_map-ont_minimizers_key_value_sorted_keys.rmi_PARAMETERS Number of rmi leaf nodes are not provided for 100167746 keys Using default number of leaf nodes: 3130242 sh: 1: ./scripts/build-rmi.linear_spline.linear.sh: not found n = 100167746 /home/hsadasivan/datasets/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna_map-ont_minimizers_key_value_sorted_keys.rmi_PARAMETERS file not found

[SaurabhKalikar]

Hi @harisankarsadasivan

From your error log, looks like there is some issue with the relative path to build-rmi.linear_spline.linear.sh at your end. I could not reproduce the issue at my end with CentOS and g++ 9.2.

Could you provide the details of your OS and compiler?

Thanks, Saurabh