RNA_Make_Index and SCATAC_Merged_Make_KNN Errors

[phoebe460]

Hello Taiji Developers,

Happy new year! First off, thank you for making this awesome tool. So this is my first time trying out your tool, and I've run into some unusual errors. See below:

For what I used to run my program, I've made my input file with only quantification expression profiles, since I aligned my RNA-seq reads a different way and .bed files since I also aligned my ATAC-seq reads differently as well. For my configuration file, I provided my own index since I aligned my RNA-seq reads to a human GRCh38 transcriptome under "index" and also provided the actual transcriptome file I used in FASTA format (.fa) under "genome". Everything else in the configuration file, I kept commented and left the minimal settings section similar to what was given in the example config file.

Do you know any reason why I am getting the RNA_Make_Index and SCATAC_Merged_Make_KNN errors? If you can help me out, then that I would greatly appreciate it!

Thank you! Phoebe

P.S. If you need to see my configuration and input files, I have attached them as well.

config_PV.txt input_PV.txt

[kaizhang]

@phoebe460 Since you are using distributed computing, you need to set the parameters for workload manager properly, for example:

submit_params: "-p glean"
submit_command: "sbatch"
submit_cpu_format: "--ntasks-per-node=%d"
submit_memory_format: "--mem=%d000"

%d is a placeholder, and will be substituted by values defined in Resource section. For example, if you set memory to 50 in Resource, then it will request 50000 memory for the particular job. Please modify this accordingly.

[phoebe460]

Ok, thank you for your suggestion. After your comments, I have configured my file as follows:

It looks like it is running smoothly (so far) now and I will go ahead and close this issue. Thanks again for the help!