Fastqwiper generates problematic names for paired reads

[search42]

I encountered an issue with a paired-end fastq data. I attempted to fix my data using the image mazzalab/fastqwiper:2023.2.82 and the fix_wipe_pairs_reads_parallel.smk within it. The software fastp can handle the output data properly, but when aligning the resulting files of the software fastp to a genome using BWA, an error message appeared: :

[mem_sam_pe] paired reads have different names: "=/>;780?3=:GD<IH+985I23H5D>II521+<54HA8=G", "="

I examined the fastq data produced by the fix_wipe_pairs_reads_parallel.smk workflow and indeed found such problems:

==> test_fastp_1.out.fq.gz <== 112468777-@XXXX_R08108324978/1 112468778-ATTGAAGAGATATTGAAGAGATAATTGAAGAGATAATTGAAGAGATAATTGAAGAGATAATTGAAGA 112468779-+ 112468780-FB@GDDEEEDBFFGDGGEFFGGEEFFEFEDEEFFFFCADEEEDBDEFD:GDDDAE@FHDEFG@ECDD 112468781:@=/>;780?3=:GD<IH+985I23H5D>II521+<54HA8=G 112468782-ATGGAAGGACATGACCCTGAAAGCAGACATCCCATCTTCCTTTCTCCCTCACCCACACACTGGGCGT 112468783-+ 112468784-HFGFGIFFFGIHHGGHHIIGHEIGIIGGHHGHHGGIIHHIHHGHHGGHIGGGHHIHIIIHHIEFIIG

==> test_fastp_2.out.fq.gz <== 112468777-@XXXX_R08108324978/2 112468778-ATTGTCTAGGTCTAGGTCTAGGTCTAGGTCTAGGTCTAGGTCTAGGTCTAGGTCTAGGTCTAGGTAA 112468779-+ 112468780-GEEFDFFEEFEHFFGEFBGFFHFDEFDCEFG6FCEFFEEFDDFHEEGGFEBEFEFCDDFDGDDFFGE 112468781:@= 112468782-GGTACTGGTTTTCTATTCCAAGGCTGTTTTCTATACAAACATGCTTGAAAACAATCATTTGGAACAA 112468783-+ 112468784-GIFHIIHGDGFFIHGGFHHGEIGGGIFHHHGGGIGGFGEGFGHGGHIFFGGHHEHHGFHHHGFGIFF

The same issue also appears in the output paired-end reads of fix_wipe_pairs_reads_parallel.smk

[mazzalab]

Can you report the command line used to fix your files?

[search42]

Can you report the command line used to fix your files?

Thank you for such a quick reply. After the data is mounted, run the following command in the image:

set -eu -o pipefail cd ${out-dir} ln -s /fastqwiper/bbmap /fastqwiper/pipeline /fastqwiper/run_wiping.sh ${out-dir} mkdir -p ${out-dir}/data ln -s ${read1-input} ${out-dir}/data/${sample-id}_R1.fastq.gz ln -s ${read2-input} ${out-dir}/data/${sample-id}_R2.fastq.gz perl -i -pwe 's#cd /fastqwiper##' run_wiping.sh bash run_wiping.sh paired 8 ${sample-id} 50000000

[mazzalab]

OK, I'm afraid I need to use your fastq files to debug fastqwiper. Can you send them to me?

[mazzalab]

To debug the software we really need to use your files. Can you share them?

[search42]

To debug the software we really need to use your files. Can you share them?

I'm sorry, but I can't share it with you because of the data privacy policy. If I'm having the same problem with public data, I'd be happy to share it with you

[mazzalab]

Please share them or link

[mazzalab]

If you can share any file that causes this error, please reopen the task