[prinseq-news] prin-seq parser error

[Kristina G. <kga...@bc...>]

Hi,

I am running prin-seq on paired end reads

perl $prinseq -noniupac -ns_max_p 5 -lc_method dust -lc_threshold 50 
-trim_qual_right 20 -stats_all \
         -fastq  <(zcat $fq1 | paste - - - - | sort -k1,1 -t " " |tr 
"\t" "\n" ) \
         -fastq2 <(zcat $fq2 | paste - - - - | sort -k1,1 -t " " |tr 
"\t" "\n")

The error I receive is the following:
#-------------------------------------------------------------------------------------------------------------
ERROR: The number of bases and quality scores are not the same for 
sequence 
"CCFFFFFHHHHGJJJJJJJJIJJJJGIIIIJJJJHGIJJJJJJJJJJJIJJJGHIIJHHHHFFFFFFDEDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDCDACDDDDDDDDCDDDDDDDDDDDDDCDDDEEEDCA3<B>@A<@?BDDDB?BB@>328A@::<BB@BC@:>A(:>C@C###################################################################################################################".

Try 'perl prinseq-lite.pl -h' for more information.
Exit program.
#-----------------------------------------------------------------------------------------------------------

This is the read that contains the error, the length of the read string 
is the same as the length of the quality score:
@MISEQ1_8:1:10:10002:19889/2
TGTTGTTTGTCGAAATCCAAAATATAGAGCGAATGTAGGCCAATATTTTGGGGTTTCGAGATTCAGGGCTTTGCGAGTACGCGAGCCAGAAATCAACAAAAAATATTTCCCGAAATTGCAACAAGATGTCGAGTATTTCAGGGTTTCACGGTTTGGGTTTTCGTGAACACAAAAGTCAATCATCAAAACACTATAACTCCCGAAAATGCAAAAGAGAATTAGTACTTGCTGAATTCAGAGTGCGGGGTTTTAAAAGTGAAAGGGCACAACAAACACAATATACAAACCACCCAAAAGAGG
+
@CCFFFFFHHHHGJJJJJJJJIJJJJGIIIIJJJJHGIJJJJJJJJJJJIJJJGHIIJHHHHFFFFFFDEDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDCDACDDDDDDDDCDDDDDDDDDDDDDCDDDEEEDCA3<B>@A<@?BDDDB?BB@>328A@::<BB@BC@:>A(:>C@C################################################################################################################### 


The read quality starts however with "@" which is the start for the read 
name. I guess that there is an error in the parser.

Prin-seq version:
prinseq-lite-0.20.4

Thank you in advance for any help

-- 
Kristina Gagalova

Graduate Student
Canada's Michael Smith Genome Sciences Centre
Suite 100 - 570 West 7th Avenue
Vancouver, BC  V5Z 4S6