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YalamanchiliLab / PolyA-miner

MIT License
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"Error in data process module" in fastq mode #8

Open 694588 opened 2 years ago

694588 commented 2 years ago

When I process the raw fastq file from the test files, it always print "Error in data process module". I don't know what's wrong with my code.

Is the -index parameter wrong?

Here is my code. There are 6 bowtie2 index files(named GRCh38.1.bt2,GRCh38.2.bt2,GRCh38.3.bt2,GRCh38.4.bt2,GRCh38.rev.1.bt2,GRCh38.rev.2.bt2 in thefolder bowtie2_index/index ) I have tried hundreds of times and I need help.

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python3 PolyA-miner.py -mode fastq -d TestFastq_Data -o LHDoutput3 -pa Human_hg38.PolyA_DB.bed -index bowtie2_index/index/GRCh38 -fasta GRCH38.fa -bed GRCh38v33.Genes.bed -p 20 -pa_p 0.6 -pa_a 3 -pa_m 1 -ip 30 -outPrefix FastqBBAno -c1 C1.fastq.gz,C2.fastq.gz,C3.fastq.gz -c2 T1.fastq.gz,T2.fastq.gz,T3.fastq.gz -expNovel 0 -umi 0 -t BB

Error in data processing module ...

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Thanks and looking forward to your help!

chenghui03 commented 11 months ago

Hello, Before running this script, please ensure that you have installed the following dependencies: umi_tools, fastp, and pigz.

I have the same problem , after install pigz by sudo apt install pigz, it could run properly. Hope that could fix your problem!