Error while running magicblast

[pablomics-star]

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

[boratyng]

Hello @pablomics-star,

I am sorry you ran into problems. This error indicates that Magic-BLAST cannot parse the FASTQ file. It expects a new sequence with a defline at line 981584, but it finds something else. It is difficult to say what exactly the problem is without seeing the FASTQ file. Can you post result of this command line:

cat YOUR-FASTQ-FILE | head -n 981585 | tail

where YOUR-FASTQ-FILE is the file for which Magic-BLAST gives the error.

Or if there is a way for you to share your FASTQ files, I can try to find the problematic region.