Processing whole dataset progress bar?

[majdabdul]

Hi,

I have what may be a dumb issue, but I just wanted to make sure everything is working correctly. I'm running pychopper on 12 samples.

Most of the samples show the standard processing verbiage, for lack of a better word:

Using kit: PCS111

Configurations to consider: "+:SSP,-VNP|-:VNP,-SSP"

Counting fastq records in input file: 10890_Control_noIR_rep2_combined_pass.fastq.gz

Total fastq records in input file: 20148852

Tuning the cutoff parameter (q) on 10041 sampled reads (0.0%) passing quality filters (Q >= 7.0).

Optimizing over 30 cutoff values.

100%|██████████| 30/30 [07:50<00:00, 15.36s/it]

Best cutoff (q) value is 0.1724 with 92% of the reads classified.

Processing the whole dataset using a batch size of 10000:

100%|██████████| 20148852/20148852 [3:12:30<00:00, 1744.43it/s]

Finished processing file

But a couple are missing the progress bar and some of the information for 'Processing the whole dataset':

Using kit: PCS111

Configurations to consider: "+:SSP,-VNP|-:VNP,-SSP"

Counting fastq records in input file: 10890_Control_noIR_rep3_combined_pass.fastq.gz

Total fastq records in input file: 25336564

Tuning the cutoff parameter (q) on 9983 sampled reads (0.0%) passing quality filters (Q >= 7.0).

Optimizing over 30 cutoff values.

100%|██████████| 30/30 [08:04<00:00, 16.02s/it]

Best cutoff (q) value is 0.1724 with 93% of the reads classified.

Processing the whole dataset using a batch size of 10000:

25336565it [3:50:55, 1828.58it/s]

Finished processing file

Is this okay? Can I still assume the file was processed correctly?

Thanks! Majd

[nrhorner]

Hi @majdabdul

As it's just the bar that is missing and none of the other logging text, I would assume this is an issue with the library used to create the progress bar (tqdm) and the results of the analysis should not be affected.

Thanks

[nrhorner]

Closing as likely not a problem