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Error while running magicblast

Open pablomics-star opened this issue 1 year ago • 1 comments

Hi everyone, I find my individual samples paired-reads against an 18S database using the following function by following the tutorial at https://astrobiomike.github.io/amplicon/16S_and_18S_mixed#evaluating-the-outcome:

for sample in $(cat samples.txt) do

printf "\n  Doing sample: ${sample}\n"

magicblast -db pr2-magicblast-db -query "${sample}"_1_trimmed.fastq.gz \
         -query_mate "${sample}"_2_trimmed.fastq.gz -infmt fastq \
         -out "${sample}"_mblast_out.txt -outfmt tabular \
         -num_threads 2 -splice F -no_unaligned
         

done

With the test data I don't have any errors when running the command, but when I run my own data I get this in the prompt:

Doing sample: 19S7 Error: (CInputException::eInvalidInput) FASTQ parse error: defline expected at line: 981584 Error: (117.2) CThread::Wrapper: CThread::Main() failed (CInputException::eInvalidInput) FASTQ parse error: defline expected at line: 981584

I would like to know if you have any idea what this error is due to

I am looking forward to your response Regards

pablomics-star avatar Jan 22 '23 19:01 pablomics-star