UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

[Jyoti-Mridha]

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

[drmjc]

Hi, this repo is abandoned. Try github.com/kccg/mity. We have never tested it with ONT data, so YMMV.

…

On Fri, 13 Sept 2024, 6:26 pm Jyoti-Mridha, ***@***.***> wrote: 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 — Reply to this email directly, view it on GitHub <#9>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEQQM5XWTOVYUNULLSW2RDZWKORPAVCNFSM6AAAAABOE32MOWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZDIMRQHEZDINY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>