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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Log command output failed #1114

Closed liuyang2006 closed 2 weeks ago

liuyang2006 commented 3 weeks ago

Issue Report

Please describe the issue:

When I run command in command line, I can see the verbose command output. However, when I redirect the command output to a log file, there is nothing in the logfile.

Steps to reproduce the issue:

command I used:

dorado basecaller /project/sli68423_1316/users/yang/tools/dorado-0.8.2-linux-x64/models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0 /project/sli68423_1316/users/yang/aml_nanopore/results/2024_10_30_guppy_run_test/run_script_PT01/input_pod5/ --models-directory /project/sli68423_1316/users/yang/tools/dorado-0.8.2-linux-x64/models --modified-bases-models /project/sli68423_1316/users/yang/tools/dorado-0.8.2-linux-x64/models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v2 -x auto --verbose -r --reference /project/sli68423_1316/users/yang/reference/chm13v2.0/chm13v2.0.fa --output-dir . --batchsize 96    > aaa.log   2>&1

Logs

There is nothing output to aaa.log file

HalfPhoton commented 3 weeks ago

Hi @liuyang2006,

Can you try redirecting only the stderr instead? 

2> aaa.log
HalfPhoton commented 3 weeks ago

Also, you can use the model selection complex to clean up your Dorado call Removing the long paths to the model and modbase models.

dorado basecaller hac,5mCG_5hmCG ...