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Simple error and simple quality score models #2

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rpelicae opened this issue Mar 9, 2015 · 0 comments
Open

Simple error and simple quality score models #2

rpelicae opened this issue Mar 9, 2015 · 0 comments

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@rpelicae
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rpelicae commented Mar 9, 2015

Hello,
I tried using BEAR to simulate reads for metagenomic analysis, temporarily without DRISEE.
I ran subsequently the parametric_abundance.pl, generate_reads.py and trim_reads.pl.
For the latter I tried using the simple error and quality score models:
perl trim_reads.pl -f /BEAR_release/uniformreads.txt -o /BEAR_release/realreads.txt -r 0 -q 0 -m 0

I obtain the following error:
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 181.
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 181.
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 188.
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 188.
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 197.
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 197.
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 206.
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 206.
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 216.
Use of uninitialized value $length in numeric le (<=) at trim_reads.pl line 216.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 2.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 2.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 2.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 4.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 4.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 4.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 6.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 6.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 6.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 8.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 8.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 8.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 10.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 10.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 10.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 12.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 12.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 12.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 14.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 14.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 14.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 16.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 16.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 16.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 18.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 18.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 18.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 20.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 20.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 20.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 22.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 22.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 22.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 24.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 24.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 24.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 26.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 26.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 26.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 28.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 28.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 28.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 30.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 30.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 30.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 32.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 32.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 32.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 34.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 34.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 34.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 36.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 36.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 36.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 38.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 38.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 38.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 40.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 40.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 40.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 42.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 42.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 42.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 44.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 44.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 44.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 46.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 46.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 46.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 48.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 48.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 48.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 50.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 50.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 50.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 52.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 52.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 52.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 54.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 54.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 54.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 56.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 56.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 56.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 58.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 58.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 58.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 60.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 60.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 60.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 62.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 62.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 62.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 64.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 64.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 64.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 66.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 66.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 66.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 68.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 68.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 68.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 70.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 70.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 70.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 72.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 72.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 72.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 74.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 74.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 74.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 76.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 76.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 76.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 78.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 78.
........
........
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 9982.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 9984.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 9984.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 9984.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 9986.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 9986.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 9986.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 9988.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 9988.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 9988.
Use of uninitialized value $markov_qual in addition (+) at trim_reads.pl line 252, line 9990.
Use of uninitialized value $rand_length in substr at trim_reads.pl line 258, line 9990.
Use of uninitialized value $rand_length in numeric lt (<) at trim_reads.pl line 259, line 9990.

Any ideas?
I will now try it using DRISEE.
Kind regards,
Rudy

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