Closed npdungca closed 10 months ago
Sounds like your input fastq might have an invalid record. You can confirm this with seqkit
by running seqkit seq barcode05_duplex.fastq.gz > /dev/null
The error message from rasusa tells you the read id of the read that causes the error 5ad0b9e9-94a7-477c-b47f-0963e639d159
on line 1544857. You could also run wc -l
on the (decompressed) fastq and if the number of lines is 1544857 (or thereabouts) then it might be that the last read in the file got truncated?
Got it. It seems that the last line got trucated. Thank you so much for patiently answering my queries.
Hi. I'm trying to subsample by depth and I'm getting this error:
./rasusa -i barcode05_duplex.fastq.gz --coverage 400 --genome-size 243724 -s 100 -o BC05_400x.fq.gz [2023-10-02][13:20:16][rasusa][INFO] Target number of bases to subsample to is: 97489600 [2023-10-02][13:20:16][rasusa][INFO] Gathering read lengths... Error: unable to gather read lengths for the first input file
Caused by: 0: Failed to parse record 1: Sequence length is 373 but quality length is 120 (record '5ad0b9e9-94a7-477c-b47f-0963e639d159' at line 1544857)
Thank you for your help.