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KCCG / mity

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
MIT License
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UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte #55

Open Jyoti-Mridha opened 1 month ago

Jyoti-Mridha commented 1 month ago

Hi i am running mity via docker but encountered with some bam error, could not able to rectify it, actually i was trying to find out INDELS for long read ONT generated data, using minimap2 aligned bam. If any suggestion from your side will be great help.

error i am facing is: UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

Command i am using is: sudo docker run -w /media/manish/Data/Jyoti_Mridha_AIC/Program -v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3 -v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Structural_Variants/mity:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Structural_Variants/mity drmjc/mity call --prefix MITO60 --output-dir /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Structural_Variants/mity/ --normalise --bam-file-list /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3/MITO60_sorted.bam

trentzz commented 1 month ago

Hi @Jyoti-Mridha,

Is your file gzipped? A byte of 0x8b at position 1 usually indicates that the file is compressed (e.g. with gzip/bgzip).

And would you be able to post the full error message?

Thanks! Trent Zeng