Use of uninitialized value $qual in scalar chomp

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millipede...@gmail.com

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May 10, 2018, 8:03:09 PM5/10/18

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When I run prinseq-lite with my fastq files (generated from fastq-dump for NCBI SRA data), I get the following error:

Use of uninitialized value $qual in scalar chomp at /apps/prinseq/0.20.4/bin/prinseq-lite.pl line 2583, <FILE> line 26875674.

I do the following:

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

Research computing staff at my institution think the @ character in the quality string is causing the error (i.e., not considered a valid character). However, from what I've read, that character is a valid character. As such, I would think that prinseq-lite would also recognize that. If that is not the case, what format should the quality line be in and how can I can covert it to that?

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