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cytham / nanovar

Structural variant caller for low-depth long-read sequencing data
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Bam input - UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb8 in position 4: invalid start byte #88

Closed Jyoti-Mridha closed 1 month ago

Jyoti-Mridha commented 5 months ago

Hi, While using the nanovar with fastq files, it is running well. (nanovar /pfs/home/jyotimridha/Mito_ONT/Structural_variants/Batch1/fq_zip/barcode06.fastq.gz /pfs/home/jyotimridha/Mito_ONT/Database_Mito_Genome_hg38/nanovar/hg38_chrM.fa /pfs/home/jyotimridha/Mito_ONT/Structural_variants/Batch1/nanovar/barcode06/)

The same command when i am using for bam input i am encountering the following error. Mapping reads and calling SVs - /    (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb8 in position 4: invalid start byte

Here i am copying the command which i have used nanovar /pfs/home/jyotimridha/Mito_ONT/Batch1_3runs/previous_bam/barcode06_sorted.bam /pfs/home/jyotimridha/Mito_ONT/Database_Mito_Genome_hg38/nanovar/hg38_chrM.fa /pfs/home/jyotimridha/Mito_ONT/Structural_variants/Batch1/nanovar/barcode06_bam/

My bam is mapped with minimap2, then samtools view, sort and indexed. Same bam file I am using for other "SV"  tools is working fine, but with nanovar i am not sure whether i am making a mistake in which part while running nanovar using the bam file.

Any help will be really appreciate, I value the insights and guidance.

cytham commented 5 months ago

Hi @Jyoti-Mridha, thanks for reporting this. Can you attach the log file please. Also, I think you might be using an old version. Please try the latest version v1.7.0

git clone https://github.com/cytham/nanovar.git 
cd nanovar 
pip install .
Jyoti-Mridha commented 5 months ago

Hellow, Please find here is attached log file.

On Wed, Jun 12, 2024 at 6:55 PM Cheng Yong Tham @.***> wrote:

Hi, thanks for report this. Can you attach the log file please, thanks

— Reply to this email directly, view it on GitHub https://github.com/cytham/nanovar/issues/88#issuecomment-2163005708, or unsubscribe https://github.com/notifications/unsubscribe-auth/BDQL2ZHKVHCMZKCDZ442FFLZHBD4NAVCNFSM6AAAAABJGLI7PSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRTGAYDKNZQHA . You are receiving this because you authored the thread.Message ID: @.***>

cytham commented 5 months ago

@Jyoti-Mridha Can't view the log, nevermind, please try the latest version v1.7.0

cytham commented 1 month ago

Closed due to inactivity