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error: overlap is not transmuted! #237

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ArtyomVodnev opened this issue May 27, 2023 · 0 comments
Open

error: overlap is not transmuted! #237

ArtyomVodnev opened this issue May 27, 2023 · 0 comments

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@ArtyomVodnev
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Hello,
I'm trying to run Racon and get this error, I checked another issues with the similar error, but not sure if some of them relates to my issue.
The code I used:

bwa index /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/contigs.fasta &&
awk '{{print (NR%4 == 1) ? "@1_" ++i : $0}}' /home/arvodnev/test_project/rawdata/SR/trimmed_1.fastq > /home/arvodnev/test_project/rawdata/SR/merged_1_2.fastq &&
awk '{{print (NR%4 == 1) ? "@2_" ++i : $0}}' /home/arvodnev/test_project/rawdata/SR/trimmed_2.fastq >> /home/arvodnev/test_project/rawdata/SR/merged_1_2.fastq &&
bwa mem /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/contigs.fasta /home/arvodnev/test_project/rawdata/SR/trimmed_1.fastq /home/arvodnev/test_project/rawdata/SR/trimmed_2.fastq > /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/Polishing_Racon/output.sam &&
samtools view -b /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/Polishing_Racon/output.sam > /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/Polishing_Racon/output.bam &&
samtools sort -o /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/Polishing_Racon/output.sorted.bam /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/Polishing_Racon/output.bam &&
samtools view -h -o /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/Polishing_Racon/output.sorted.sam /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/Polishing_Racon/output.sorted.bam &&
racon --include-unpolished /home/arvodnev/test_project/rawdata/SR/merged_1_2.fastq /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/Polishing_Racon/output.sorted.sam /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/contigs.fasta > /home/arvodnev/test_project/AssemblyHY/SPAdesHY/AssemblyHY/Polishing_Racon/HY.polish.SPAdes.fasta

The error is

[racon::Polisher::initialize] loaded target sequences 2.332907 s
[racon::Polisher::initialize] loaded sequences 491.529525 s
 [racon::Polisher::initialize] loaded overlaps 319.481349 s
[racon::Overlap::find_breaking_points] error: overlap is not transmuted!

Hope you can help to fix it,
Thank you

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