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relipmoc / skewer

MIT License
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Progress bar is > 100% #22

Open tseemann opened 8 years ago

tseemann commented 8 years ago

I ran it on a 20GB FASTQ file and the progress bar has one over 100% ?

skewer -t 32 -n -q 10 -z -o clipped MVE_S1_L001_R1_001.fastq.gz MVE_S1_L001_R2_001.fastq.gz -x CGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG -y GACGCTGCCGACGANNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT -m any
Parameters used:
-- 3' end adapter sequence (-x):        CGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG
-- paired 3' end adapter sequence (-y): GACGCTGCCGACGANNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT
-- maximum error ratio allowed (-r):    0.100
-- maximum indel error ratio allowed (-d):      0.030
-- end quality threshold (-q):          10
-- minimum read length allowed after trimming (-l):     18
-- file format (-f):            Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):   3
-- number of concurrent threads (-t):   32
Thu Nov  5 15:00:16 2015 >> started
|=================================================>| (114.02%)
relipmoc commented 8 years ago

In most cases, the original file size can be estimated by the tail record of a .GZ file. However, there is no guarantee. The reason is that only 4 bytes are used to store the size of original file.