=======
Atropos
=======

Atropos version: 1.1.14+0.gb71f62e.dirty
Python version: 3.5.3
Command line parameters: trim -p Hm2_GTGAAA_L005/cutadapt/Hm2_GTGAAA_L005_R2_.cutadapt.fastq.gz -pe1 Hm2_GTGAAA_L005/bwa_bam_to_fastq/Hm2_GTGAAA_L005_R1_.unmapped.fastq.gz -pe2 Hm2_GTGAAA_L005/bwa_bam_to_fastq/Hm2_GTGAAA_L005_R2_.unmapped.fastq.gz -T 4 --process-timeout 600 --report-formats json txt --report-file Hm2_GTGAAA_L005/logs/cutadapt/cutadapt -b file:/home/cokelaer/Work/github/sequana/sequana/resources/data/adapters/adapters_Nextera_fwd.fa -B file:/home/cokelaer/Work/github/sequana/sequana/resources/data/adapters/adapters_Nextera_rev.fa -m 20 -q 30 -O 6 --trim-n -o Hm2_GTGAAA_L005/cutadapt/Hm2_GTGAAA_L005_R1_.cutadapt.fastq.gz

Sample ID: Hm2_GTGAAA_L005_R
Input format: FASTQ, Paired, w/ Qualities
Input files:
  /home/cokelaer/Temp/test/analysis/Hm2_GTGAAA_L005/bwa_bam_to_fastq/Hm2_GTGAAA_L005_R1_.unmapped.fastq.gz
  /home/cokelaer/Temp/test/analysis/Hm2_GTGAAA_L005/bwa_bam_to_fastq/Hm2_GTGAAA_L005_R2_.unmapped.fastq.gz

Start time: 2017-09-23T23:52:24.109433
Wallclock time: 0.86 s (9 us/read; 7.00 M reads/minute)
CPU time (main process): 0.85 s

--------
Trimming
--------

Pairs                                  records   fraction
----------------------------------- ---------- ----------
Total read pairs processed:             99,854
  Read 1 with adapter:                   8,767       8.8%
  Read 2 with adapter:                   9,218       9.2%
Pairs that were too short:               3,942       3.9%
Pairs written (passing filters):        95,912      96.1%

Base pairs                                  bp   fraction
----------------------------------- ---------- ----------
Total bp processed:                 20,170,508
  Read 1:                           10,085,254
  Read 2:                           10,085,254
Quality-trimmed                      1,802,413       8.9%
  Read 1:                              739,488       7.3%
  Read 2:                            1,062,925      10.5%
End Ns trimmed                              19       0.0%
  Read 1:                                   16       0.0%
  Read 2:                                    3       0.0%
Total bp written (filtered):        17,790,287      88.2%
  Read 1:                            8,857,103      87.8%
  Read 2:                            8,933,184      88.6%

----------------------------------------------------
First read: Adapter Universal_Adapter|name:universal
----------------------------------------------------

Sequence                                                   Type           Length Trimmed (x)
---------------------------------------------------------- -------------- ------ -----------
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT variable 5'/3'     58          68

18 times, it overlapped the 5' end of a read
50 times, it overlapped the 3' end or was within the read

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50-58 bp: 5

Overview of removed sequences (5'):
length count expect max.err error counts
                            0 1         
------ ----- ------ ------- ------------
     6     7  146.3       0 7           
     7     3   36.6       0 3           
    10     1    4.6       1 0 1         
    11     1    2.3       1 0 1         
    12     1    1.1       1 1           
    13     1    0.3       1 1           
    17     1    0.0       1 1           
    18     1    0.0       1 1           
    19     2    0.0       1 2           


Overview of removed sequences (3' or within):
length count expect max.err error counts
                            0  1        
------ ----- ------ ------- ------------
     6    40  146.3       0 40          
     7     4   36.6       0 4           
     8     1   18.3       0 1           
    10     5    4.6       1 0  5        

--------------------------------------------------------------------
First read: Adapter Nextera_transposase_seq_1|name:transposase_seq_1
--------------------------------------------------------------------

Sequence                          Type           Length Trimmed (x)
--------------------------------- -------------- ------ -----------
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG variable 5'/3'     33          37

29 times, it overlapped the 5' end of a read
8 times, it overlapped the 3' end or was within the read

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-33 bp: 3

Overview of removed sequences (5'):
length count  expect max.err error counts
                             0  1        
------ ----- ------- ------- ------------
     6    17 1,170.2       0 17          
     7    11   585.1       0 11          
    10     1    36.6       1 0  1        


Overview of removed sequences (3' or within):
length count  expect max.err error counts
                             0 1         
------ ----- ------- ------- ------------
     6     5 1,170.2       0 5           
     7     2   585.1       0 2           
    10     1    36.6       1 0 1         

--------------------------------------------------------------------
First read: Adapter Nextera_transposase_seq_2|name:transposase_seq_2
--------------------------------------------------------------------

Sequence                           Type           Length Trimmed (x)
---------------------------------- -------------- ------ -----------
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG variable 5'/3'     34          18

0 times, it overlapped the 5' end of a read
18 times, it overlapped the 3' end or was within the read

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-34 bp: 3

Overview of removed sequences (5'):
    length      count     expect    max.err error c...
                                                      
---------- ---------- ---------- ---------- ----------


Overview of removed sequences (3' or within):
length count  expect max.err error counts
                             0           
------ ----- ------- ------- ------------
     6    13 1,170.2       0 13          
     7     5   292.5       0 5           

-------------------------------------------------------------
First read: Adapter Nextera_index_N501|name:N501|seq:TAGATCGC
-------------------------------------------------------------

Sequence                                            Type           Length Trimmed (x)
--------------------------------------------------- -------------- ------ -----------
AATGATACGGCGACCACCGAGATCTACACTAGATCGCTCGTCGGCAGCGTC variable 5'/3'     51          36

36 times, it overlapped the 5' end of a read
0 times, it overlapped the 3' end or was within the read

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50-51 bp: 5

Overview of removed sequences (5'):
length count expect max.err error counts
                            0  1        
------ ----- ------ ------- ------------
     6    26  146.3       0 26          
     7     8   36.6       0 8           
    11     2    2.3       1 0  2        


Overview of removed sequences (3' or within):
    length      count     expect    max.err error c...
                                                      
---------- ---------- ---------- ---------- ----------

-------------------------------------------------------------
First read: Adapter Nextera_index_N502|name:N502|seq:CTCTCTAT
-------------------------------------------------------------

Sequence                                            Type           Length Trimmed (x)
--------------------------------------------------- -------------- ------ -----------
AATGATACGGCGACCACCGAGATCTACACCTCTCTATTCGTCGGCAGCGTC variable 5'/3'     51           0

