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gtluu / timsconvert

https://gtluu.github.io/timsconvert/
Apache License 2.0
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OSError: /lib64/libm.so.6: version `GLIBC_2.29' not found #38

Closed She1111 closed 1 year ago

She1111 commented 1 year ago

Hi,

When I run test files on our own HPC, errors occurred like this. Are there any solutions to solve this problem?

She1111 commented 1 year ago

I also try the web version of timsconvert. By the way, I used dia-PASEF .d file. The errors occur as below:

Workflow execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'convert (1)'

Caused by: Process convert (1) terminated with an error exit status (1)

Command executed:

mkdir spectra python3 /data/beta-proteomics2/tools/timsconvert/release_31+server-refactor/client/bin/client.py --input T01862_EvoAurEl2_20SPDDIAPASEF-PSB-718_56_S1-E8_1_2074.d --outdir spectra --host "gnpsserver1.ucsd.edu:6521"

Command exit status: 1

Command output: (empty)

Command error: Traceback (most recent call last): File "/data/beta-proteomics2/tools/timsconvert/release_31+server-refactor/client/bin/client.py", line 68, in submit_timsconvert_job(args.input, args.outdir, "http://" + args.host) File "/data/beta-proteomics2/tools/timsconvert/release_31+server-refactor/client/bin/client.py", line 25, in submit_timsconvert_job req.raise_for_status() File "/data/beta-proteomics2/tools/miniconda3_gamma/envs/timsconvert/lib/python3.7/site-packages/requests/models.py", line 960, in raise_for_status raise HTTPError(http_error_msg, response=self) requests.exceptions.HTTPError: 404 Client Error: NOT FOUND for url: http://gnpsserver1.ucsd.edu:6521/convert

Work dir: /scratch/beta-proteomics2/aa46418826424250a7e58ebab92e95f5/timsconvert_nf_process/work/07/96b0ea2a7d884fd028054862b66598

Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option -resume

mwang87 commented 1 year ago

This nextflow workflow is not meant to run on your own HPC. I'd recommend folloiwng this guide:

https://github.com/gtluu/timsconvert#install-anaconda-on-linux

She1111 commented 1 year ago

This nextflow workflow is not meant to run on your own HPC. I'd recommend folloiwng this guide:

https://github.com/gtluu/timsconvert#install-anaconda-on-linux

I have download timsconvert on our own HPC and create an environment with Miniconda which we use usually. When I run test files on HPC, error occur like this: OSError: /lib64/libm.so.6: version `GLIBC_2.29' not found.

Thank you and I am looking forward to your reply!

mwang87 commented 1 year ago

I'd recommend chatting with your sys admins to get that version of GLIBC installed. Otherwise, i think you could put it into a singularity container.

She1111 commented 1 year ago

Hi,

Thank you very much for your kind reply!

Regards, Shel