resume option and memory usage

[xhuashen]

Hi,
I am very confused, why resume didn't work.
I encounter failure with out of memory(400GB) when first run，then I added --resume over pervious command, but it didn't work and report 'You cannot specify options other than --output/--threads/--debug/--high_memory with --resume option', but I indeed hadn't change any other option.

first run
/qitinglab/software/IsoQuant-3.10.0/isoquant.py --reference $ref_fa --yaml blood_yaml.yaml
--genedb "$REF_ANNOTATION"
--data_type ${platform}
--threads 10
-o "$output_Isoquant" --polya_trimmed all --sqanti_output --check_canonical --count_exons

resume run(didn't work)
/qitinglab/software/IsoQuant-3.10.0/isoquant.py --reference $ref_fa --yaml blood_yaml.yaml
--genedb "$REF_ANNOTATION"
--data_type ${platform}
--threads 10
-o "$output_Isoquant" --polya_trimmed all --sqanti_output --check_canonical --count_exons --resume

The other thing also confused me a lot, I observed that isoquant always use large memory in the end time of the tasks with very low memory usage in most of moment, so it always failed after 10 hours running for the sake of insufficient memory. I think it is very unfriendly for HPC computer, do you have any recommendation for us to deal with this?

[andrewprzh]

Dear @xhuashen

When using --resume no other options should be specified (https://ablab.github.io/IsoQuant/cmd.html).
I fact, it tried a similar command and it does not allow me to specify --resume with other options. Could you send me the log with the failed resume run?

Could you also send the log so I could check which stage caused the memory peak?
Overall, reducing the number of threads might help, but I need to check the log first.

Best
Andrey