Sir,
I wanted to use prinseq to filter my fastq files. After running this command it seemed everything going perfect but when loading completed 100% there was output. What I am missing??
[zillur@workstation01 Strain_GI]$ perl /home/zillur/Desktop/zillur/Tools/prinseq-lite-0.20.4/prinseq-lite.pl -verbose -fastq SRR901607_1.fastq -fastq2 SRR901607_2.fastq -min_qual_score 36 -ns_max_n 0 -noniupac -derep 124 -out_good GI_qual_fltr -out_bad null
This gave me the following output but no filtered fastq files.
[zillur@workstation01 Strain_GI]$ perl /home/zillur/Desktop/zillur/Tools/prinseq-lite-0.20.4/prinseq-lite.pl -verbose -fastq SRR901607_1.fastq -fastq2 SRR901607_2.fastq -min_qual_score 36 -ns_max_n 0 -noniupac -derep 124 -out_good GI_qual_fltr -out_bad null
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Estimate size of input data for status report (this might take a while for large files)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
done
Parse and process input data
status: 0 %perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
done
Clean up empty files
Use of uninitialized value $fhmappings in unlink at /home/zillur/Desktop/zillur/Tools/prinseq-lite-0.20.4/prinseq-lite.pl line 1833.
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
done
Input and filter stats:
Input sequences (file 1): 26,419,950
Input bases (file 1): 2,668,414,950
Input mean length (file 1): 101.00
Input sequences (file 2): 26,419,950
Input bases (file 2): 2,668,414,950
Input mean length (file 2): 101.00
Good sequences (pairs): 0
Good sequences (singletons file 1): 0 (0.00%)
Good sequences (singletons file 2): 0 (0.00%)
Bad sequences (file 1): 26,419,950 (100.00%)
Bad bases (file 1): 2,668,414,950
Bad mean length (file 1): 101.00
Bad sequences (file 2): 0 (0.00%)
Sequences filtered by specified parameters:
min_qual_score: 52839900
[zillur@workstation01 Strain_GI]$ ls
SRR901607_1.fastq SRR901607_2.fastq
I wanted to use prinseq to filter my fastq files. After running this command it seemed everything going perfect but when loading completed 100% there was output. What I am missing??
[zillur@workstation01 Strain_GI]$ perl /home/zillur/Desktop/zillur/Tools/prinseq-lite-0.20.4/prinseq-lite.pl -verbose -fastq SRR901607_1.fastq -fastq2 SRR901607_2.fastq -min_qual_score 36 -ns_max_n 0 -noniupac -derep 124 -out_good GI_qual_fltr -out_bad null
This gave me the following output but no filtered fastq files.
[zillur@workstation01 Strain_GI]$ perl /home/zillur/Desktop/zillur/Tools/prinseq-lite-0.20.4/prinseq-lite.pl -verbose -fastq SRR901607_1.fastq -fastq2 SRR901607_2.fastq -min_qual_score 36 -ns_max_n 0 -noniupac -derep 124 -out_good GI_qual_fltr -out_bad null
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Estimate size of input data for status report (this might take a while for large files)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
done
Parse and process input data
status: 0 %perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
done
Clean up empty files
Use of uninitialized value $fhmappings in unlink at /home/zillur/Desktop/zillur/Tools/prinseq-lite-0.20.4/prinseq-lite.pl line 1833.
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
done
Input and filter stats:
Input sequences (file 1): 26,419,950
Input bases (file 1): 2,668,414,950
Input mean length (file 1): 101.00
Input sequences (file 2): 26,419,950
Input bases (file 2): 2,668,414,950
Input mean length (file 2): 101.00
Good sequences (pairs): 0
Good sequences (singletons file 1): 0 (0.00%)
Good sequences (singletons file 2): 0 (0.00%)
Bad sequences (file 1): 26,419,950 (100.00%)
Bad bases (file 1): 2,668,414,950
Bad mean length (file 1): 101.00
Bad sequences (file 2): 0 (0.00%)
Sequences filtered by specified parameters:
min_qual_score: 52839900
[zillur@workstation01 Strain_GI]$ ls
SRR901607_1.fastq SRR901607_2.fastq
Comment