Dear all,
I am using prinseq (v.0.20.4, CentOS) to filter my paried end data with the following commands.
[root@localhost]# perl prinseq-lite.pl -fastq S1_read1.fq -trim_right 1 -trim_qual_right 10 -min_len 100 -derep 123 -out_format 3 -out_good S1_read1.trim -out_bad null -log
Estimate size of input data for status report (this might take a while for large files)
done
Parse and process input data
done
Check for duplicates
done
Write results to output file(s)
done
Clean up empty files
done
Input and filter stats:
Input sequences: 489,463
Input bases: 49,435,763
Input mean length: 101.00
Good sequences: 292,060 (59.67%)
Good bases: 29,206,000
Good mean length: 100.00
Bad sequences: 197,403 (40.33%)
Bad bases: 19,937,703
Bad mean length: 101.00
Sequences filtered by specified parameters:
derep: 197403
Output: log file and S1_read.trim.fastq
[root@localhost]# perl prinseq-lite.pl -fastq S1_read2.fq -trim_right 1 -trim_qual_right 10 -min_len 100 -derep 123 -out_format 3 -out_good S1_read2.trim -out_bad null -log
Estimate size of input data for status report (this might take a while for large files)
done
Parse and process input data
done
Clean up empty files
Use of uninitialized value $fhmappings in unlink at ../prinseq-lite-0.20.4/prinseq-lite.pl line 1833.
done
Input and filter stats:
Input sequences: 489,463
Input bases: 46,498,985
Input mean length: 95.00
Good sequences: 0 (0.00%)
Bad sequences: 489,463 (100.00%)
Bad bases: 46,498,985
Bad mean length: 95.00
Sequences filtered by specified parameters:
min_len: 489463
Output: only log file
Could anybody let me know what the problem is and how to solve it?
I am using prinseq (v.0.20.4, CentOS) to filter my paried end data with the following commands.
[root@localhost]# perl prinseq-lite.pl -fastq S1_read1.fq -trim_right 1 -trim_qual_right 10 -min_len 100 -derep 123 -out_format 3 -out_good S1_read1.trim -out_bad null -log
Estimate size of input data for status report (this might take a while for large files)
done
Parse and process input data
done
Check for duplicates
done
Write results to output file(s)
done
Clean up empty files
done
Input and filter stats:
Input sequences: 489,463
Input bases: 49,435,763
Input mean length: 101.00
Good sequences: 292,060 (59.67%)
Good bases: 29,206,000
Good mean length: 100.00
Bad sequences: 197,403 (40.33%)
Bad bases: 19,937,703
Bad mean length: 101.00
Sequences filtered by specified parameters:
derep: 197403
Output: log file and S1_read.trim.fastq
[root@localhost]# perl prinseq-lite.pl -fastq S1_read2.fq -trim_right 1 -trim_qual_right 10 -min_len 100 -derep 123 -out_format 3 -out_good S1_read2.trim -out_bad null -log
Estimate size of input data for status report (this might take a while for large files)
done
Parse and process input data
done
Clean up empty files
Use of uninitialized value $fhmappings in unlink at ../prinseq-lite-0.20.4/prinseq-lite.pl line 1833.
done
Input and filter stats:
Input sequences: 489,463
Input bases: 46,498,985
Input mean length: 95.00
Good sequences: 0 (0.00%)
Bad sequences: 489,463 (100.00%)
Bad bases: 46,498,985
Bad mean length: 95.00
Sequences filtered by specified parameters:
min_len: 489463
Output: only log file
Could anybody let me know what the problem is and how to solve it?
Comment