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R2C2_C3POa_10X_data analysis #22

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Usamahussein551980 opened this issue Nov 2, 2023 · 0 comments
Open

R2C2_C3POa_10X_data analysis #22

Usamahussein551980 opened this issue Nov 2, 2023 · 0 comments

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@Usamahussein551980
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Hello,
Thanks for the amazing tool.
I'm trying to analyze the long read data generated from the ONT sequencer according to your C3POa work flow, but the pre-processing doesn't continue and finished at Calling consensi.
Despite the tools were installed with their dependencies, and I prepared the UMI_Splint.fasta used in the experiment, but unfortunately the process stopped as showed below:

command:
(base) [ukhussein@ldragon3 C3POa-2.2.3]$ python3 C3POa.py -r ../../projects/nanopore_R2C2/10X_071_R2C2/test/dngqu0264_71_fastq_pass.tar.gz -s ./UMI_Splint.fasta/UMI_Splints.fasta -d 500 -l 100 -g 1000 -n 32 -o out2

abpoa

Output:
pr-processing

Log Contents:
$ cat/out/c3poa.log
C3POa version: v2.2.3
Total reads: 1687451
No splint reads: 1505291 (89.21%)
Under len cutoff: 15 (0.00%)
Total thrown away reads: 1505306 (89.21%)
Reads after preprocessing: 182145

Could you please help me to figure out what is the problem?

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