Running fastq-generated SRA files from NCBI through prinseq-lite. The program generates an error:
Use of uninitialized value $qual in scalar chomp at /apps/prinseq/0.20.4/bin/prinseq-lite.pl line 2583, <FILE> line 26875674.
It still continues on until it has finished, but clearly there is something wrong going on. Here's what comes up when I look around that line:
sed -n 26875668,26875680p ../../test_1_renamed.fastq CCCFFFFFHGHHHJJJJFHIJJJJJIGII@GIIIJJJJJJJJJJJIJJJJJJJJHHHHAEHFFFFFFEEEECCEDDDDCD>CDEDDDDADC @SRR5040251.6718918/1 FCC4LTMACXX:1:1215:20679:14461 length=91 CTCCTTCCCAAAGTAGCACTTCCTTCCCTTCTCGCTACGATCAAGAGATTTAGCCATCCCTGACCGAGATCGTTGTGAACTCTGGCTTTTT +SRR5040251.6718918/1 FCC4LTMACXX:1:1215:20679:14461 length=91 @@CFFDFFFHHGDDHIIJJJJGHGHDFHIJGIHHIIIIIEEGHIJ@HIIJHGJJJCEGHGEEHGAEHED?@BCBC?;@>CCC:AC5<BDC@ @SRR5040251.6718919/1 FCC4LTMACXX:1:1215:20521:14498 length=91 CGAAGGAAACATCATAAGAAGCATCACAAAG
One person told me that the @ character in the quality line is an invalid character. I've read elsewhere that it is a valid character, plus it occurs in lines before this and they don't thrown this error. However, I wonder if the @ character at the beginning of the quality line might be throwing the program off.