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mazzalab / fastqwiper

An ensemble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and settle reads interleaving.
GNU General Public License v3.0
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Empty output expected? #3

Closed bcantarel closed 1 year ago

bcantarel commented 1 year ago

I tried running on a small file with some formatting issues, ie duplicate sequences, not having the proper number of lines per record, etc. The resulting file is empty. Is that expected?

fastqwiper --fastq_in smallONT.fastq --fastq_out smallONT.fix.fastq Start wiping smallONT.fastq Successfully terminated

Wiped lines: 0/19580 (0.0%) Len(SEQ) neq Len(QUAL): 0/19580 BAD QUAL lines: 0/19580 BAD + lines: 0/19580 BAD SEQ lines: 206/19580 Not printable header lines: 0/19580 Not printable qual lines: 0/19580 Fixed header lines: 4702/19580 Fixed + lines: 90/19580 Blank lines: 0/19580 Missplaced lines: 0/19580

ls -lh smallONT.fix.fastq -rw-r--r-- 1 root root 0 Feb 5 15:15 smallONT.fix.fastq

mazzalab commented 1 year ago

Hi, can you share a test file with us? (bioinformatics@css-mendel.it)

mazzalab commented 1 year ago

Due to inactivity, I'm closing this issue