Starting /dee2/code/volunteer_pipeline.sh SRR13079637
    current disk space = 414794264576
    free memory = 73650308 
SRR13079637 SRAfilesize
0e767f5a6e4cc901a38b8e25b827138d  SRR13079637.sra
SRR13079637.sra file validated
SRR13079637 is paired end
SRR13079637 is conventional basespace
SRR13079637 read1 length is 41 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR13079637_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	41
%GC	50
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.8325	32.0	32.0	32.0	32.0	32.0
2	31.33975	32.0	32.0	32.0	32.0	32.0
3	31.48	32.0	32.0	32.0	32.0	32.0
4	31.463	32.0	32.0	32.0	32.0	32.0
5	31.41175	32.0	32.0	32.0	32.0	32.0
6	35.113	36.0	36.0	36.0	36.0	36.0
7	35.087	36.0	36.0	36.0	36.0	36.0
8	34.941	36.0	36.0	36.0	36.0	36.0
9	34.885	36.0	36.0	36.0	32.0	36.0
10	34.983	36.0	36.0	36.0	36.0	36.0
11	35.04375	36.0	36.0	36.0	36.0	36.0
12	34.97	36.0	36.0	36.0	36.0	36.0
13	34.9555	36.0	36.0	36.0	36.0	36.0
14	34.965	36.0	36.0	36.0	36.0	36.0
15	34.938	36.0	36.0	36.0	32.0	36.0
16	34.9325	36.0	36.0	36.0	36.0	36.0
17	34.9795	36.0	36.0	36.0	36.0	36.0
18	35.14825	36.0	36.0	36.0	36.0	36.0
19	35.136	36.0	36.0	36.0	36.0	36.0
20	34.98075	36.0	36.0	36.0	36.0	36.0
21	34.982	36.0	36.0	36.0	36.0	36.0
22	35.041	36.0	36.0	36.0	36.0	36.0
23	34.826	36.0	36.0	36.0	32.0	36.0
24	34.97025	36.0	36.0	36.0	36.0	36.0
25	34.8375	36.0	36.0	36.0	36.0	36.0
26	34.9425	36.0	36.0	36.0	36.0	36.0
27	34.888	36.0	36.0	36.0	36.0	36.0
28	35.0125	36.0	36.0	36.0	36.0	36.0
29	34.928	36.0	36.0	36.0	36.0	36.0
30	35.06875	36.0	36.0	36.0	36.0	36.0
31	34.76325	36.0	36.0	36.0	32.0	36.0
32	34.81925	36.0	36.0	36.0	32.0	36.0
33	34.77775	36.0	36.0	36.0	32.0	36.0
34	34.885	36.0	36.0	36.0	36.0	36.0
35	34.88075	36.0	36.0	36.0	32.0	36.0
36	34.7395	36.0	36.0	36.0	32.0	36.0
37	34.733	36.0	36.0	36.0	32.0	36.0
38	34.6915	36.0	36.0	36.0	32.0	36.0
39	34.64225	36.0	36.0	36.0	32.0	36.0
40	34.85875	36.0	36.0	36.0	36.0	36.0
41	34.4805	36.0	36.0	36.0	32.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
20	1.0
21	1.0
22	5.0
23	4.0
24	9.0
25	5.0
26	27.0
27	33.0
28	47.0
29	63.0
30	83.0
31	106.0
32	178.0
33	258.0
34	634.0
35	2546.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	13.950000000000001	38.925	27.450000000000003	19.675
2	27.525	27.224999999999998	20.849999999999998	24.4
3	22.575	20.724999999999998	33.800000000000004	22.900000000000002
4	34.975	18.675	20.974999999999998	25.374999999999996
5	27.800000000000004	31.25	19.45	21.5
6	28.21026282853567	25.90738423028786	19.374217772215268	26.5081351689612
7	28.375	30.65	21.775	19.2
8	19.3	22.25	23.1	35.35
9	20.625	24.05	37.775	17.549999999999997
10	40.949999999999996	18.95	24.325	15.775
11	40.75	23.175	18.25	17.825
12	34.2	23.724999999999998	24.099999999999998	17.974999999999998
13	28.7	22.875	31.85	16.575
14	38.675	21.925	25.224999999999998	14.174999999999999
15	21.575	24.9	29.925	23.599999999999998
16	27.325	26.55	31.35	14.774999999999999
17	24.325	19.7	29.75	26.224999999999998
18	20.599999999999998	28.375	33.475	17.549999999999997
19	31.574999999999996	22.125	29.925	16.375
20	25.35	20.65	37.35	16.650000000000002
21	29.349999999999998	17.675	32.475	20.5
22	26.25	33.074999999999996	24.825	15.85
23	29.275000000000002	43.025000000000006	11.65	16.05
24	39.375	36.55	13.200000000000001	10.875
25	23.1	40.949999999999996	20.65	15.299999999999999
26	18.4	22.475	30.3	28.825
27	28.1	18.525	15.8	37.574999999999996
28	46.725	16.0	14.000000000000002	23.275000000000002
29	42.525	30.25	11.0	16.225
30	31.5	45.85	7.475	15.174999999999999
31	33.225	43.75	10.674999999999999	12.35
32	38.175	41.25	7.6499999999999995	12.925
33	31.900000000000002	45.0	8.175	14.924999999999999
34	37.7	28.9	7.225	26.174999999999997
35	22.35	33.300000000000004	8.275	36.075
36	18.099999999999998	42.15	9.049999999999999	30.7
37	15.575	35.875	9.700000000000001	38.85
38	18.35	39.074999999999996	8.95	33.625
39	28.075	22.325	10.225	39.375
40	36.1	19.775000000000002	21.4	22.725
41	21.075	16.175	33.2	29.549999999999997
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	0.5
2	1.0
3	1.0
4	0.5
5	0.0
6	1.0
7	2.0
8	2.0
9	1.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	3.0
29	6.0
30	8.0
31	10.0
32	10.0
33	12.0
34	14.0
35	24.0
36	34.0
37	34.0
38	53.0
39	72.0
40	126.0
41	180.0
42	180.0
43	228.5
44	277.0
45	415.5
46	554.0
47	554.0
48	551.5
49	549.0
50	690.0
51	831.0
52	749.0
53	667.0
54	667.0
55	491.5
56	316.0
57	278.0
58	240.0
59	240.0
60	192.5
61	145.0
62	105.5
63	66.0
64	66.0
65	42.0
66	18.0
67	11.0
68	4.0
69	4.0
70	2.5
71	1.0
72	1.0
73	1.0
74	1.5
75	2.0
76	2.0
77	1.5
78	1.0
79	0.5
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.5
88	1.0
89	2.0
90	3.0
91	2.0
92	1.0
93	1.0
94	0.5
95	0.0
96	0.0
97	0.0
98	0.0
99	1.5
100	3.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.125
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
41	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	55.50000000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	84.68468468468468	47.0
2	7.117117117117116	7.9
3	2.4324324324324325	4.05
4	1.5315315315315314	3.4000000000000004
5	0.945945945945946	2.625
6	0.5855855855855856	1.95
7	0.40540540540540543	1.575
8	0.36036036036036034	1.6
9	0.22522522522522523	1.125
>10	1.4414414414414414	16.0
>50	0.18018018018018017	6.550000000000001
>100	0.09009009009009009	6.225
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
ACTCAAACTGGGGGCTCTTTTAGATCGGAAGAGCACACGTC	148	3.6999999999999997	No Hit
AGTGCCGCAGAGTTTGTAGTGTAGATCGGAAGAGCACACGT	101	2.5250000000000004	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGT	74	1.8499999999999999	No Hit
ACTCAAACTGGGGGCTCTTTTGAGATCGGAAGAGCACACGT	68	1.7000000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCACACGT	61	1.525	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGG	59	1.4749999999999999	TruSeq Adapter, Index 21 (100% over 40bp)
TGGAAGACTAGTGATTTTGTTGTTAGATCGGAAGAGCACAC	46	1.15	No Hit
AGTGCCGCAGAGTTTGTAGTGAGATCGGAAGAGCACACGTC	46	1.15	No Hit
ACTCAAACTGTGTGACATTTTAGATCGGAAGAGCACACGTC	43	1.075	No Hit
TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTT	40	1.0	No Hit
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCACACGT	28	0.7000000000000001	No Hit
TTTGGCAATGGTAGAACTCACACCAGATCGGAAGAGCACAC	26	0.65	No Hit
AAGGGATTCTGATGTTGGTCACACTAGATCGGAAGAGCACA	25	0.625	No Hit
TATGGCACTGGTAGAATTCACTAGATCGGAAGAGCACACGT	24	0.6	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACACGTCT	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TATTGCACTTGTCCCGGCCTGTAGATCGGAAGAGCACACGT	22	0.5499999999999999	No Hit
AAAGTGCCGCCAGGTTTTGAGTGTAGATCGGAAGAGCACAC	19	0.475	No Hit
CGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTT	19	0.475	No Hit
TTTGGCAATGGTAGAACTCACACCGAGATCGGAAGAGCACA	19	0.475	No Hit
AAGTGCCGCCAGGTTTTGAGTGTAGATCGGAAGAGCACACG	19	0.475	No Hit
AGTGCCGCAGAGTTTGTAGTGCAGATCGGAAGAGCACACGT	18	0.44999999999999996	No Hit
ATGGCACTGGTAGAATTCACTGAGATCGGAAGAGCACACGT	17	0.42500000000000004	No Hit
CCTGCATGATGACGAACAAATACTGACTAGATCGGAAGAGC	16	0.4	No Hit
ACTCAAACTGGGGGCTCTTTCAGATCGGAAGAGCACACGTC	16	0.4	No Hit
CATTGCACTTGTCTCGGTCTGAAGATCGGAAGAGCACACGT	16	0.4	No Hit
TTCAAGTAATCCAGGATAGGCCAGATCGGAAGAGCACACGT	15	0.375	No Hit
AAAGTGCTTCCCTTTTGTGTGTAGATCGGAAGAGCACACGT	15	0.375	No Hit
TATGGCACTGGTAGAATTCACTGAGATCGGAAGAGCACACG	15	0.375	No Hit
AACTGTGGTAATTCTAGAGCTAATACATGCCGAGATCGGAA	13	0.325	No Hit
CAACGGAATCCCAAAAGCAGCTGAGATCGGAAGAGCACACG	13	0.325	No Hit
TAAAGTGCTTATAGTGCAGGTAGAGATCGGAAGAGCACACG	12	0.3	No Hit
TTTGGCAATGGTAGAACTCACACTAGATCGGAAGAGCACAC	11	0.27499999999999997	No Hit
GCCTGCTGGGGTGGAACCTGGTAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
AAAGTGCTTCCACTTTGTGTGCAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
ACTCAAACTGGGGGCTCTTTTAAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
AAACATTCGCGGTGCACTTCTTAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
TGGAAGACTAGTGATTTTGTTGTAGATCGGAAGAGCACACG	10	0.25	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGC	10	0.25	No Hit
GAATGTTGCTCGGTGAACCCCTAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGAGATCGGAA	9	0.22499999999999998	No Hit
AAAGTGCTACTACTTTTGAGTCTAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TGGTAGACTATGGAACGTAGGAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
AGTGCCGCAGAGTTTGTAGTGGAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
TCAGTGCACTACAGAACTTTGCAGATCGGAAGAGCACACGT	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTCAGATCGGAAGAGCAC	8	0.2	No Hit
CATTGCACTTGTCTCGGTCTGAGATCGGAAGAGCACACGTC	8	0.2	No Hit
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTA	8	0.2	No Hit
CAACGGAATCCCAAAAGCAGCTAGATCGGAAGAGCACACGT	8	0.2	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAGATCGG	8	0.2	No Hit
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GCCCTCTTTCCGTGTGGATTTAAGAATTTTAGATCGGAAGA	8	0.2	No Hit
CATCAAAGTGGAGGCCCTCTCTAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
CGCGACCTCAGATCAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CACATTACACGGTCGACCTCTAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
AAGTGCTACTACTTTTGAGTCTAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
AAACAAACATGGTGCACTTCTTAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
CAAAGTGCTGTTCGTGCAGGTAGAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
GAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTAGATCG	7	0.17500000000000002	No Hit
ACTCAAACTGTGTGACATTTAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAA	6	0.15	No Hit
CAAAGTGCTTACAGTGCAGGTAGAGATCGGAAGAGCACACG	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCGAGATCGGAAGAGCACACGT	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCGAGATCGGAAGAGCACACGT	6	0.15	No Hit
TAGCTTATCAGACTGATGTTGAAGATCGGAAGAGCACACGT	6	0.15	No Hit
AGCAGCATTGTACAGGGCTATGAAGATCGGAAGAGCACACG	6	0.15	No Hit
TATGGCACTGGTAGAATTCACCAGATCGGAAGAGCACACGT	6	0.15	No Hit
CTCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCA	6	0.15	No Hit
TGAGGTTGGTGTACTGTGTGTGAAGATCGGAAGAGCACACG	6	0.15	No Hit
ACTGGACTTGGAGTCAGAAGGCAGATCGGAAGAGCACACGT	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCACACGT	6	0.15	No Hit
TAGTAGACCGTATAGCGTACGAGATCGGAAGAGCACACGTC	6	0.15	No Hit
CTGCATGATGACGAACAAATACTGACTAGATCGGAAGAGCA	6	0.15	No Hit
TATACAAGGGCAAGCTCTCTGTAGATCGGAAGAGCACACGT	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACAGATCGGAAGAGCACACGT	5	0.125	No Hit
GGCAGAGGAGGGCTGTTCTTCCCAGATCGGAAGAGCACACG	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTAGATCGGAAG	5	0.125	No Hit
AGACGATGATGACTGCTTTTCTGAGTTAGATCGGAAGAGCA	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TAGGTAGTTTCATGTTGTTGGGAGATCGGAAGAGCACACGT	5	0.125	No Hit
TTTGGCAATGGTAGAACTCACACAGATCGGAAGAGCACACG	5	0.125	No Hit
TGTAAACATCCTTGACTGGAAGCTAGATCGGAAGAGCACAC	5	0.125	No Hit
ATGGCACTGGTAGAATTCACTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
AAAGTGCTTCCCTTTTGTGTGCAGATCGGAAGAGCACACGT	5	0.125	No Hit
ACTCAAACTGTGTGACATTTCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
AATTGCACGGTATCCATCTGTAAGATCGGAAGAGCACACGT	5	0.125	No Hit
TGTAAACATCCTACACTCTCAGCTAGATCGGAAGAGCACAC	5	0.125	No Hit
TCGTATCCCTAATACATATTCAAAAAAAAAAGAGCACACGT	5	0.125	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAA	5	0.125	No Hit
CGGCGTCATGCAGGAGTTGATTAGATCGGAAGAGCACACGT	5	0.125	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGAGATCGGAAGA	5	0.125	No Hit
CGCGACCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAAACATACACGGGAAACCTCTAGATCGGAAGAGCACACG	5	0.125	No Hit
GCCCTCTTTCCGTGTGGATTTAAGAATTTTTAGATCGGAAG	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	1.7	0.0	0.0	0.0	0.0
2	1.725	0.0	0.0	0.0	0.0
3	1.725	0.0	0.0	0.0	0.0
4	1.725	0.0	0.0	0.0	0.0
5	1.75	0.0	0.0	0.0	0.0
6	1.775	0.0	0.0	0.0	0.0
7	1.85	0.0	0.0	0.0	0.0
8	2.025	0.0	0.0	0.0	0.0
9	2.35	0.0	0.0	0.0	0.0
10	2.95	0.0	0.0	0.0	0.0
11	3.575	0.0	0.0	0.0	0.0
12	4.75	0.0	0.0	0.0	0.0
13	5.975	0.0	0.0	0.0	0.0
14	7.15	0.0	0.0	0.0	0.0
15	8.6	0.0	0.0	0.0	0.0
16	9.7	0.0	0.0	0.0	0.0
17	10.875	0.0	0.0	0.0	0.0
18	12.125	0.0	0.0	0.0	0.0
19	13.875	0.0	0.0	0.0	0.0
20	14.925	0.0	0.0	0.0	0.0
21	18.3	0.0	0.0	0.0	0.0
22	32.025	0.0	0.0	0.0	0.0
23	53.425	0.0	0.0	0.0	0.0
24	61.6	0.0	0.0	0.0	0.0
25	67.65	0.0	0.0	0.0	0.0
26	70.325	0.0	0.0	0.0	0.0
27	71.55	0.0	0.0	0.0	0.0
28	72.975	0.0	0.0	0.0	0.0
29	74.5	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTTTGTA	30	9.417061E-6	35.000004	12
TTGTAGT	30	9.417061E-6	35.000004	14
TGCCGCA	30	9.417061E-6	35.000004	3
CCGCAGA	30	9.417061E-6	35.000004	5
GAGTTTG	30	9.417061E-6	35.000004	10
CAGAGTT	30	9.417061E-6	35.000004	8
ACTCAAA	30	9.417061E-6	35.000004	1
AGAGTTT	30	9.417061E-6	35.000004	9
TCAAACT	30	9.417061E-6	35.000004	3
TGTAGTG	30	9.417061E-6	35.000004	15
GCAGAGT	30	9.417061E-6	35.000004	7
CGCAGAG	30	9.417061E-6	35.000004	6
GCCGCAG	30	9.417061E-6	35.000004	4
AGTTTGT	30	9.417061E-6	35.000004	11
TTTGTAG	30	9.417061E-6	35.000004	13
CTCAAAC	30	9.417061E-6	35.000004	2
CGTTTCG	20	0.0021434545	35.0	34
AAACTGG	25	1.4254966E-4	35.0	5
TAGTGTA	20	0.0021434545	35.0	17
GTCACGT	20	0.0021434545	35.0	30
>>END_MODULE
SRR13079637 read2 length is 41 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR13079637_2.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	41
%GC	50
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.74525	32.0	32.0	32.0	32.0	32.0
2	30.5155	32.0	32.0	32.0	32.0	32.0
3	30.6185	32.0	32.0	32.0	32.0	32.0
4	30.588	32.0	32.0	32.0	32.0	32.0
5	30.46975	32.0	32.0	32.0	32.0	32.0
6	33.89675	36.0	36.0	36.0	32.0	36.0
7	33.98725	36.0	36.0	36.0	32.0	36.0
8	33.842	36.0	36.0	36.0	32.0	36.0
9	33.83025	36.0	36.0	36.0	32.0	36.0
10	33.9555	36.0	36.0	36.0	32.0	36.0
11	34.10925	36.0	36.0	36.0	32.0	36.0
12	33.89725	36.0	36.0	36.0	32.0	36.0
13	34.15075	36.0	36.0	36.0	32.0	36.0
14	33.875	36.0	36.0	36.0	32.0	36.0
15	33.858	36.0	36.0	36.0	32.0	36.0
16	33.9515	36.0	36.0	36.0	32.0	36.0
17	34.1305	36.0	36.0	36.0	32.0	36.0
18	33.86875	36.0	36.0	36.0	32.0	36.0
19	33.92075	36.0	36.0	36.0	32.0	36.0
20	33.86925	36.0	36.0	36.0	32.0	36.0
21	34.11	36.0	36.0	36.0	32.0	36.0
22	33.86175	36.0	36.0	36.0	32.0	36.0
23	34.183	36.0	36.0	36.0	32.0	36.0
24	33.71	36.0	36.0	36.0	32.0	36.0
25	33.9705	36.0	36.0	36.0	32.0	36.0
26	33.92075	36.0	36.0	36.0	32.0	36.0
27	34.023	36.0	36.0	36.0	32.0	36.0
28	33.8265	36.0	36.0	36.0	32.0	36.0
29	34.012	36.0	36.0	36.0	32.0	36.0
30	33.87875	36.0	36.0	36.0	32.0	36.0
31	33.7245	36.0	36.0	36.0	32.0	36.0
32	34.25475	36.0	36.0	36.0	32.0	36.0
33	34.13625	36.0	36.0	36.0	32.0	36.0
34	33.89975	36.0	36.0	36.0	32.0	36.0
35	33.8255	36.0	36.0	36.0	32.0	36.0
36	33.7475	36.0	36.0	36.0	32.0	36.0
37	33.6475	36.0	36.0	36.0	32.0	36.0
38	33.661	36.0	36.0	36.0	27.0	36.0
39	33.65525	36.0	36.0	36.0	27.0	36.0
40	33.3205	36.0	36.0	36.0	21.0	36.0
41	32.69175	36.0	36.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
16	3.0
17	1.0
18	3.0
19	6.0
20	9.0
21	12.0
22	16.0
23	19.0
24	26.0
25	44.0
26	56.0
27	90.0
28	97.0
29	123.0
30	135.0
31	189.0
32	250.0
33	377.0
34	830.0
35	1714.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	19.925	46.875	13.600000000000001	19.6
2	25.05	34.9	8.774999999999999	31.275
3	15.0	39.725	21.725	23.549999999999997
4	18.575	32.875	16.7	31.85
5	25.4	35.4	21.8	17.4
6	28.65	27.975	16.75	26.625
7	19.075	30.3	22.575	28.050000000000004
8	20.5	30.425	18.575	30.5
9	16.6	29.4	20.674999999999997	33.324999999999996
10	14.499999999999998	25.900000000000002	26.174999999999997	33.425
11	24.0	20.775	20.225	35.0
12	19.75	19.2	24.875	36.175000000000004
13	22.2	33.175	17.45	27.175
14	26.1	23.799999999999997	26.375	23.724999999999998
15	24.65	20.724999999999998	25.924999999999997	28.7
16	27.125	23.849999999999998	27.675	21.349999999999998
17	27.425	21.425	30.3	20.849999999999998
18	31.3	19.75	23.7	25.25
19	23.775	27.375	18.224999999999998	30.625000000000004
20	27.625	25.900000000000002	26.950000000000003	19.525000000000002
21	21.2	17.65	33.2	27.950000000000003
22	26.3	24.05	31.85	17.8
23	40.0	27.250000000000004	17.125	15.625
24	19.85	41.6	24.325	14.224999999999998
25	19.475	19.5	31.825	29.2
26	26.05	17.05	23.225	33.675
27	36.9	13.125	31.075000000000003	18.9
28	23.325000000000003	12.125	37.425000000000004	27.125
29	34.53363340835209	12.328082020505127	17.60440110027507	35.533883470867714
30	48.25	16.475	18.15	17.125
31	40.575	27.85	13.25	18.325
32	25.674999999999997	31.825	17.45	25.05
33	20.724999999999998	25.25	23.1	30.925000000000004
34	30.65	16.25	35.875	17.224999999999998
35	31.4	19.475	31.45	17.675
36	21.775	25.025	41.225	11.975
37	30.2	34.2	19.3	16.3
38	39.825	33.425	16.45	10.299999999999999
39	21.825	49.1	12.0	17.075000000000003
40	19.375	43.675000000000004	15.225	21.725
41	21.25	24.275	23.0	31.474999999999998
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	2.0
2	4.0
3	4.0
4	3.5
5	3.0
6	2.0
7	1.0
8	1.0
9	1.5
10	2.0
11	1.5
12	1.0
13	0.5
14	0.0
15	0.0
16	0.5
17	1.0
18	0.5
19	0.0
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	0.0
26	2.0
27	4.0
28	3.0
29	2.0
30	6.5
31	11.0
32	11.0
33	14.5
34	18.0
35	23.0
36	28.0
37	28.0
38	47.5
39	67.0
40	139.0
41	211.0
42	211.0
43	255.5
44	300.0
45	435.0
46	570.0
47	570.0
48	694.0
49	818.0
50	821.0
51	824.0
52	625.0
53	426.0
54	426.0
55	334.5
56	243.0
57	209.0
58	175.0
59	175.0
60	158.5
61	142.0
62	114.5
63	87.0
64	87.0
65	57.5
66	28.0
67	19.5
68	11.0
69	11.0
70	8.5
71	6.0
72	8.0
73	10.0
74	5.0
75	0.0
76	0.0
77	0.0
78	0.0
79	0.5
80	1.0
81	1.0
82	0.5
83	0.0
84	0.0
85	0.0
86	0.0
87	0.5
88	1.0
89	0.5
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	2.0
100	4.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.025
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
41	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	57.95
#Duplication Level	Percentage of deduplicated	Percentage of total
1	85.41846419327005	49.5
2	7.1182053494391715	8.25
3	2.459016393442623	4.275
4	1.3373597929249352	3.1
5	0.6902502157031924	2.0
6	0.6471095772217429	2.25
7	0.3882657463330457	1.575
8	0.30198446937014667	1.4000000000000001
9	0.1725625539257981	0.8999999999999999
>10	1.2079378774805867	13.700000000000001
>50	0.12942191544434856	4.425
>100	0.12942191544434856	8.625
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAACT	143	3.5749999999999997	No Hit
ACAAACCCTTGTGTCGAGGGCTGACTTTCAATAGATCGCAG	101	2.5250000000000004	No Hit
ACACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	101	2.5250000000000004	No Hit
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTG	60	1.5	Illumina RNA PCR Primer (100% over 36bp)
AGCCTATCCTGGATTACTTGAAGATCGTCGGACTGTAGAAC	60	1.5	No Hit
CAAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAAC	57	1.425	No Hit
AACAACAAAATCACTAGTCTTCCAGATCGTCGGACTGTAGA	44	1.0999999999999999	No Hit
CACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAACT	43	1.075	No Hit
AAAATGTCACACAGTTTGAGTGATCGTCGGACTGTAGAACT	38	0.95	No Hit
ACAAAGTTCTGTAGTGCACTGAGATCGTCGGACTGTAGAAC	30	0.75	No Hit
GGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAGA	26	0.65	No Hit
AGTGTGACCAACATCAGAATCCCTTGATCGTCGGACTGTAG	24	0.6	No Hit
ACAGGCCGGGACAAGTGCAATAGATCGTCGGACTGTAGAAC	23	0.575	No Hit
AGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAAC	22	0.5499999999999999	No Hit
ACGTCTGATCTGAGGTCGCGGATCGTCGGACTGTAGAACTC	22	0.5499999999999999	Illumina DpnII expression Sequencing Primer (100% over 21bp)
GCAAACCCTTGTGTCGAGGGCTGACTTTCAATAGATCGCAG	22	0.5499999999999999	No Hit
ACACTCAAAACCTGGCGGCACTTGATCGTCGGACTGTAGAA	19	0.475	No Hit
ACACTCAAAACCTGGCGGCACTTTGATCGTCGGACTGTAGA	18	0.44999999999999996	No Hit
ACACACAAAAGGGAAGCACTTTGATCGTCGGACTGTAGAAC	17	0.42500000000000004	No Hit
GCACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	17	0.42500000000000004	No Hit
CAGTGAATTCTACCAGTGCCATGATCGTCGGACTGTAGAAC	16	0.4	No Hit
AGTCAGTATTTGTTCGTCATCATGCAGGGATCGTCGGACTG	16	0.4	No Hit
CGGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAG	15	0.375	No Hit
GAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAACT	15	0.375	No Hit
TCAGACCGAGACAAGTGCAATGGATCGTCGGACTGTAGAAC	14	0.35000000000000003	No Hit
GGCCTATCCTGGATTACTTGAAGATCGTCGGACTGTAGAAC	14	0.35000000000000003	No Hit
CTACCTGCACTATAAGCACTTTAGATCGTCGGACTGTAGAA	13	0.325	No Hit
CAGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAA	13	0.325	No Hit
ACCAGGTTCCACCCCAGCAGGCGATCGTCGGACTGTAGAAC	12	0.3	No Hit
CAGCTGCTTTTGGGATTCCGTTGGATCGTCGGACTGTAGAA	12	0.3	No Hit
AAGAAGTGCACCGCGAATGTTTGATCGTCGGACTGTAGAAC	11	0.27499999999999997	No Hit
AGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAGA	11	0.27499999999999997	No Hit
CGGCATGTATTAGCTCTAGAATTACCACAGTTGATCGTCGG	11	0.27499999999999997	No Hit
ACAACAAAATCACTAGTCTTCCAGATCGTCGGACTGTAGAA	10	0.25	No Hit
CAGACCGAGACAAGTGCAATGGATCGTCGGACTGTAGAACT	9	0.22499999999999998	No Hit
AGACTCAAAAGTAGTAGCACTTTGATCGTCGGACTGTAGAA	9	0.22499999999999998	No Hit
AAATGACGCTCAAACAGGCATGCCCCCTGGAATACCAAGGG	9	0.22499999999999998	No Hit
CGCACGAGCCGAGTGATCCACCGCTAAGAGTCGATCGTCGG	9	0.22499999999999998	No Hit
TAAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAAC	8	0.2	No Hit
CCTACGTTCCATAGTCTACCAGATCGTCGGACTGTAGAACT	8	0.2	No Hit
GCAAAGTTCTGTAGTGCACTGAGATCGTCGGACTGTAGAAC	8	0.2	No Hit
AGCTGCTTTTGGGATTCCGTTGGATCGTCGGACTGTAGAAC	8	0.2	No Hit
GCACACAAAGTGGAAGCACTTTGATCGTCGGACTGTAGAAC	8	0.2	No Hit
AGGGGTTCACCGAGCAACATTCGATCGTCGGACTGTAGAAC	8	0.2	No Hit
GCAGAACTTAGCCACTGTGAAGATCGTCGGACTGTAGAACT	8	0.2	No Hit
AAAGCCTACAGCACCCGGTATTCCCAGGCGGTCTCGATCGT	7	0.17500000000000002	No Hit
CCACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	7	0.17500000000000002	No Hit
TCACACACAGTACACCAACCTCAGATCGTCGGACTGTAGAA	7	0.17500000000000002	No Hit
TTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCGTC	7	0.17500000000000002	No Hit
AAGAAGTGCACCATGTTTGTTTGATCGTCGGACTGTAGAAC	7	0.17500000000000002	No Hit
GAAATGTCACACAGTTTGAGTGATCGTCGGACTGTAGAACT	7	0.17500000000000002	No Hit
AGAGAGGGCCTCCACTTTGATGGATCGTCGGACTGTAGAAC	7	0.17500000000000002	No Hit
GAGTGTGACCAACATCAGAATCCCTTGATCGTCGGACTGTA	7	0.17500000000000002	No Hit
AAAATTCTTAAATCCACACGGAAAGAGGGCGATCGTCGGAC	7	0.17500000000000002	No Hit
CGCCTATCCTGGATTACTTGAAGATCGTCGGACTGTAGAAC	6	0.15	No Hit
CGCAAGGTCGGTTCTACGGGTGGATCGTCGGACTGTAGAAC	6	0.15	No Hit
AGCTGAGAGTGTAGGATGTTTACAGATCGTCGGACTGTAGA	6	0.15	No Hit
CTACCTGCACGAACAGCACTTTGGATCGTCGGACTGTAGAA	6	0.15	No Hit
CGTACGCTATACGGTCTACTAGATCGTCGGACTGTAGAACT	6	0.15	No Hit
CTACCTGCACTGTAAGCACTTTGGATCGTCGGACTGTAGAA	6	0.15	No Hit
GATCTGAGGTCGCGGATCGTCGGACTGTAGAACTCTGAACG	6	0.15	Illumina DpnII expression Sequencing Primer (96% over 26bp)
GCCTTCTGACTCCAAGTCCAGTGATCGTCGGACTGTAGAAC	6	0.15	No Hit
ACTTGGTTCCGCGGCTTCACGAGGGCGATTCAGGTACGCAC	6	0.15	No Hit
AAATGTCACACAGTTTGAGTGATCGTCGGACTGTAGAACTC	6	0.15	Illumina DpnII expression Sequencing Primer (100% over 21bp)
GGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAAC	6	0.15	No Hit
GCAAGGTCGGTTCTACGGGTGGATCGTCGGACTGTAGAACT	6	0.15	No Hit
AGTCAGTATTTGTTCGTCATCATGCAGGATCGTCGGACTGT	6	0.15	No Hit
GCACACAAAAGGGAAGCACTTTGATCGTCGGACTGTAGAAC	6	0.15	No Hit
GTCAACATCAGTCTGATAAGCTAGATCGTCGGACTGTAGAA	6	0.15	No Hit
AGAGGTCGACCGTGTAATGTGGATCGTCGGACTGTAGAACT	5	0.125	No Hit
CCCAACAACATGAAACTACCTAGATCGTCGGACTGTAGAAC	5	0.125	No Hit
CACGAGCCGAGTGATCCACCGCTAAGAGTCGATCGTCGGAC	5	0.125	No Hit
GTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAGAA	5	0.125	No Hit
TCATAGCCCTGTACAATGCTGCTGATCGTCGGACTGTAGAA	5	0.125	No Hit
AACTCAGAAAAGCAGTCATCATCGTCTGATCGTCGGACTGT	5	0.125	No Hit
AGACTCAAAAGTAGTAGCACTTGATCGTCGGACTGTAGAAC	5	0.125	No Hit
AACTGTACAAACTACTACCTCAGATCGTCGGACTGTAGAAC	5	0.125	No Hit
TCTGAGGTCGCGGATCGTCGGACTGTAGAACTCTGAACGTG	5	0.125	Illumina DpnII expression Sequencing Primer (96% over 29bp)
ACTCAGAAAATACCTTTCTCCACAGCTATCAGACTGGGGCG	5	0.125	No Hit
ACAGAGAGCTTGCCCTTGTATAGATCGTCGGACTGTAGAAC	5	0.125	No Hit
AAAAATTCTTAAATCCACACGGAAAGAGGGCGATCGTCGGA	5	0.125	No Hit
GGGAAGAACAGCCCTCCTCTGCCGATCGTCGGACTGTAGAA	5	0.125	No Hit
AGCTTCCAGTCAAGGATGTTTACAGATCGTCGGACTGTAGA	5	0.125	No Hit
AGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCGTCGGA	5	0.125	No Hit
TACAGATGGATACCGTGCAATTGATCGTCGGACTGTAGAAC	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.0	1.675	0.0	0.0
2	0.0	0.0	1.675	0.0	0.0
3	0.0	0.0	1.675	0.0	0.0
4	0.0	0.0	1.675	0.0	0.0
5	0.0	0.0	1.7	0.0	0.0
6	0.0	0.0	1.725	0.0	0.0
7	0.0	0.0	1.8	0.0	0.0
8	0.0	0.0	1.975	0.0	0.0
9	0.0	0.0	2.275	0.0	0.0
10	0.0	0.0	2.85	0.0	0.0
11	0.0	0.0	3.425	0.0	0.0
12	0.0	0.0	4.55	0.0	0.0
13	0.0	0.0	5.725	0.0	0.0
14	0.0	0.0	6.775	0.0	0.0
15	0.0	0.0	8.1	0.0	0.0
16	0.0	0.0	9.2	0.0	0.0
17	0.0	0.0	10.375	0.0	0.0
18	0.0	0.0	11.6	0.0	0.0
19	0.0	0.0	13.3	0.0	0.0
20	0.0	0.0	14.25	0.0	0.0
21	0.0	0.0	17.525	0.0	0.0
22	0.0	0.0	30.7	0.0	0.0
23	0.0	0.0	51.3	0.0	0.0
24	0.0	0.0	59.25	0.0	0.0
25	0.0	0.0	65.125	0.0	0.0
26	0.0	0.0	67.65	0.0	0.0
27	0.0	0.0	68.85	0.0	0.0
28	0.0	0.0	70.225	0.0	0.0
29	0.0	0.0	71.7	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGATC	20	0.0021434545	35.0	29
ATCTCGG	20	0.0021434545	35.0	33
GTGTAGA	20	0.0021434545	35.0	27
ACACTAC	20	0.0021434545	35.0	1
TCTCGGT	20	0.0021434545	35.0	34
GATCTCG	20	0.0021434545	35.0	32
TGTAGAT	20	0.0021434545	35.0	28
CTCGGTG	20	0.0021434545	35.0	35
CGTGTAG	20	0.0021434545	35.0	26
AGATCTC	20	0.0021434545	35.0	31
TAGATCT	25	0.0063971295	27.999998	30
GCGGCAC	35	0.0010258359	25.000002	15
CGGCACT	35	0.0010258359	25.000002	16
CTGATCG	45	0.0044288943	19.444445	21
GTAGAAC	245	0.0	14.285714	35
TAGAACT	145	7.836061E-7	13.275863	35
TGATCGT	145	7.836061E-7	13.275863	22
TGTAGAA	265	0.0	13.207547	34
CTGTAGA	290	0.0	12.068966	33
ACTGTAG	300	0.0	11.666667	32
>>END_MODULE
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942371 spots for SRR13079637.sra
Written 942371 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
Read 942368 spots for SRR13079637.sra
Written 942368 spots for SRR13079637.sra
SRR ids: ['SRR13079637.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_zzpjh05r
SRR13079637.sra spots: 11308419
blocks: [[1, 942368], [942369, 1884736], [1884737, 2827104], [2827105, 3769472], [3769473, 4711840], [4711841, 5654208], [5654209, 6596576], [6596577, 7538944], [7538945, 8481312], [8481313, 9423680], [9423681, 10366048], [10366049, 11308419]]
SRR13079637 file size 1380808
SRR13079637 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR13079637 SRR13079637_1.fastq SRR13079637_2.fastq
Input file:	SRR13079637_1.fastq
Paired file:	SRR13079637_2.fastq
trimmed:	SRR13079637-trimmed-pair1.fastq, SRR13079637-trimmed-pair2.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- paired 3' end adapter sequence (-y):	AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
-- 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)
-- number of concurrent threads (-t):	12
Tue Apr 20 16:39:22 2021 >> started

Tue Apr 20 16:39:34 2021 >> done (12.505s)
11308419 read pairs processed; of these:
 1641375 (14.51%) short read pairs filtered out after trimming by size control
  288738 ( 2.55%) empty read pairs filtered out after trimming by size control
 9378306 (82.93%) read pairs available; of these:
 8237087 (87.83%) trimmed read pairs available after processing
 1141219 (12.17%) untrimmed read pairs available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 174822	  1.86%
 19	 152848	  1.63%
 20	 381841	  4.07%
 21	1411457	 15.05%
 22	2554193	 27.24%
 23	 955540	 10.19%
 24	 616648	  6.58%
 25	 270574	  2.89%
 26	 146752	  1.56%
 27	 132141	  1.41%
 28	 145824	  1.55%
 29	 124806	  1.33%
 30	 116432	  1.24%
 31	 172402	  1.84%
 32	 186629	  1.99%
 33	 135354	  1.44%
 34	 124395	  1.33%
 35	  99407	  1.06%
 36	  80272	  0.86%
 37	  76704	  0.82%
 38	  63457	  0.68%
 39	  58119	  0.62%
 40	  56470	  0.60%
 41	1141219	 12.17%
9378306 reads passed initial QC


criterion=sequence-density
sequence-density=7.80
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=4
prefix-density=0.01
prefix-fanout=1.0
sequence=ACTCAAACTGGGGGCTCTTTTG


criterion=fanout-score
sequence-density=0.99
sequence-density-rank=11
fanout-score=41.85
fanout-score-rank=1
prefix-density=1.17
prefix-fanout=35.3
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGAATCG


criterion=sequence-density
sequence-density=2.97
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=11
prefix-density=0.00
prefix-fanout=1.0
sequence=ACACTACAAACTCTGCGGCACT


criterion=fanout-score
sequence-density=0.78
sequence-density-rank=7
fanout-score=37.26
fanout-score-rank=1
prefix-density=0.86
prefix-fanout=33.5
sequence=GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCC
Potential 3prime adapter identified. Now checking if in reference sequence
/dee2/code/volunteer_pipeline.sh: line 802: -f: command not found
/dee2/code/volunteer_pipeline.sh: line 803: -f: command not found
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x ACTCAAACTGGGGGCTCTTTTG -y ACACTACAAACTCTGCGGCACT -o SRR13079637 SRR13079637_1.fastq SRR13079637_2.fastq
Input file:	SRR13079637_1.fastq
Paired file:	SRR13079637_2.fastq
trimmed:	SRR13079637-trimmed-pair1.fastq, SRR13079637-trimmed-pair2.fastq

Parameters used:
-- 3' end adapter sequence (-x):	ACTCAAACTGGGGGCTCTTTTG
-- paired 3' end adapter sequence (-y):	ACACTACAAACTCTGCGGCACT
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- number of concurrent threads (-t):	12
Tue Apr 20 16:40:17 2021 >> started

Tue Apr 20 16:40:22 2021 >> done (5.063s)
6252204 read pairs processed; of these:
   2878 ( 0.05%) short read pairs filtered out after trimming by size control
 814222 (13.02%) empty read pairs filtered out after trimming by size control
5435104 (86.93%) read pairs available; of these:
    139 ( 0.00%) trimmed read pairs available after processing
5434965 (100.00%) untrimmed read pairs available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 115885	  2.13%
 19	 100269	  1.84%
 20	 236565	  4.35%
 21	 585293	 10.77%
 22	1300031	 23.92%
 23	 613139	 11.28%
 24	 409079	  7.53%
 25	 179737	  3.31%
 26	  97699	  1.80%
 27	  88059	  1.62%
 28	  97036	  1.79%
 29	  82955	  1.53%
 30	  77504	  1.43%
 31	 115172	  2.12%
 32	 124431	  2.29%
 33	  90095	  1.66%
 34	  82993	  1.53%
 35	  66170	  1.22%
 36	  53513	  0.98%
 37	  51034	  0.94%
 38	  41820	  0.77%
 39	  38521	  0.71%
 40	  37270	  0.69%
 41	 750834	 13.81%


criterion=sequence-density
sequence-density=2.75
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=8
prefix-density=0.00
prefix-fanout=1.0
sequence=TTCAAGTAATCCAGGATAGGCTA


criterion=fanout-score
sequence-density=1.28
sequence-density-rank=9
fanout-score=47.00
fanout-score-rank=1
prefix-density=1.51
prefix-fanout=39.9
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGAATCG


criterion=sequence-density
sequence-density=1.85
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AGCCTATCCTGGATTACTTGAAGATCGTCGG


criterion=fanout-score
sequence-density=0.92
sequence-density-rank=4
fanout-score=45.45
fanout-score-rank=1
prefix-density=1.07
prefix-fanout=39.2
sequence=GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCC
SRR13079637 testing PE reads STAR mapping to Ensembl genome
                                 Started job on |	Apr 20 16:41:20
                             Started mapping on |	Apr 20 16:41:21
                                    Finished on |	Apr 20 16:42:04
       Mapping speed, Million of reads per hour |	716.75

                          Number of input reads |	8561206
                      Average input read length |	52
                                    UNIQUE READS:
                   Uniquely mapped reads number |	5712812
                        Uniquely mapped reads % |	66.73%
                          Average mapped length |	48.79
                       Number of splices: Total |	35061
            Number of splices: Annotated (sjdb) |	12961
                       Number of splices: GT/AG |	31348
                       Number of splices: GC/AG |	1088
                       Number of splices: AT/AC |	26
               Number of splices: Non-canonical |	2599
                      Mismatch rate per base, % |	0.29%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.26
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1290941
             % of reads mapped to multiple loci |	15.08%
        Number of reads mapped to too many loci |	93761
             % of reads mapped to too many loci |	1.10%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	15.77%
                     % of reads unmapped: other |	1.33%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1557454	1557454	1557454
N_multimapping	1290941	1290941	1290941
N_noFeature	989624	1111379	4054033
N_ambiguous	2329645	866600	393258
UnstrandedReadsAssigned:2393543 PositiveStrandReadsAssigned:3734833 NegativeStrandReadsAssigned:1265521
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR13079637 Starting Kallisto paired end mapping to ensembl reference transcriptome

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 19
[index] number of targets: 109,282
[index] number of k-mers: 92,755,666
[index] number of equivalence classes: 769,752
[quant] running in paired-end mode
[quant] will process pair 1: SRR13079637-trimmed-pair1.fastq
                             SRR13079637-trimmed-pair2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 8,561,206 reads, 2,013,134 reads pseudoaligned
[quant] estimated average fragment length: 27.1383
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,254 rounds

 109283 SRR13079637.ke.tsv
  52636 SRR13079637.se.tsv
 161919 total
==> SRR13079637.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSMUST00000177564.1	16	11	0	0
ENSMUST00000196221.1	9	4	0	0
ENSMUST00000179664.1	11	6	0	0
ENSMUST00000178537.1	12	7	0	0
ENSMUST00000178862.1	14	9	0	0
ENSMUST00000179520.1	11	6	0	0
ENSMUST00000179883.1	16	11	0	0
ENSMUST00000195858.1	10	5	0	0
ENSMUST00000179932.1	12	7	0	0

==> SRR13079637.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	1
ENSMUSG00000103147	0
SRR13079637 completed mapping pipeline successfully
