samblaster not found

[CeciliaDeng]

Description of the bug

Hi @GallVp , AssemblyQC successfully completed assessing an assembly with HiC data. When I check the HiC QC report, it mentioned [forward/reverse] Hi-C reads not found, as well as 'samblaster command not found'.

Is somehow samblaster not loaded?
Thank you.

Command used and terminal output

sbatch pfr_assemblyqc
Submitted batch job 7756409

Relevant files

No response

System information

No response

[GallVp]

Thank you for submitting an issue on this. I have looked at the report for the pipeline test data and it also has the same items missing.

I think this information is missing because we don't provide the path to the raw reads to the HICQC module. I'll investigate and see if this can be fixed.

Nonetheless, if Subjective Hi-C library judgment is given along with other statistics that means that HICQC had enough information to reach a judgement on the quality of the library. See the following link for interpreting the judgement: https://phasegenomics.github.io/2019/09/19/hic-alignment-and-qc.html