Starting /dee2/code/volunteer_pipeline.sh SRR13079633
    current disk space = 414751191040
    free memory = 73649776 
SRR13079633 SRAfilesize
b97a63326d37d23c144eb7d945f7af40  SRR13079633.sra
SRR13079633.sra file validated
SRR13079633 is paired end
SRR13079633 is conventional basespace
SRR13079633 read1 length is 41 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR13079633_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.1165	32.0	32.0	32.0	32.0	32.0
2	31.4445	32.0	32.0	32.0	32.0	32.0
3	31.47725	32.0	32.0	32.0	32.0	32.0
4	31.45425	32.0	32.0	32.0	32.0	32.0
5	31.2955	32.0	32.0	32.0	32.0	32.0
6	35.05625	36.0	36.0	36.0	36.0	36.0
7	35.1335	36.0	36.0	36.0	36.0	36.0
8	35.05225	36.0	36.0	36.0	36.0	36.0
9	34.9435	36.0	36.0	36.0	36.0	36.0
10	35.05675	36.0	36.0	36.0	36.0	36.0
11	34.99775	36.0	36.0	36.0	36.0	36.0
12	35.05375	36.0	36.0	36.0	36.0	36.0
13	34.98775	36.0	36.0	36.0	36.0	36.0
14	35.019	36.0	36.0	36.0	36.0	36.0
15	35.1185	36.0	36.0	36.0	36.0	36.0
16	35.05225	36.0	36.0	36.0	36.0	36.0
17	34.92825	36.0	36.0	36.0	32.0	36.0
18	35.13575	36.0	36.0	36.0	36.0	36.0
19	35.1255	36.0	36.0	36.0	36.0	36.0
20	35.058	36.0	36.0	36.0	36.0	36.0
21	35.082	36.0	36.0	36.0	36.0	36.0
22	35.15825	36.0	36.0	36.0	36.0	36.0
23	34.8965	36.0	36.0	36.0	32.0	36.0
24	35.1135	36.0	36.0	36.0	36.0	36.0
25	34.8985	36.0	36.0	36.0	36.0	36.0
26	35.00675	36.0	36.0	36.0	36.0	36.0
27	34.97125	36.0	36.0	36.0	36.0	36.0
28	34.98275	36.0	36.0	36.0	32.0	36.0
29	34.763	36.0	36.0	36.0	32.0	36.0
30	35.148	36.0	36.0	36.0	36.0	36.0
31	34.8715	36.0	36.0	36.0	32.0	36.0
32	34.95525	36.0	36.0	36.0	36.0	36.0
33	34.6505	36.0	36.0	36.0	32.0	36.0
34	34.965	36.0	36.0	36.0	36.0	36.0
35	34.74575	36.0	36.0	36.0	32.0	36.0
36	34.738	36.0	36.0	36.0	32.0	36.0
37	34.86825	36.0	36.0	36.0	32.0	36.0
38	34.80125	36.0	36.0	36.0	32.0	36.0
39	34.79625	36.0	36.0	36.0	32.0	36.0
40	34.87375	36.0	36.0	36.0	36.0	36.0
41	34.56725	36.0	36.0	36.0	32.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	1.0
22	3.0
23	2.0
24	2.0
25	13.0
26	21.0
27	30.0
28	49.0
29	71.0
30	76.0
31	117.0
32	157.0
33	248.0
34	606.0
35	2604.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.175	39.025	24.95	24.85
2	32.0	25.674999999999997	19.925	22.400000000000002
3	20.625	21.275	32.0	26.1
4	38.45	16.400000000000002	19.525000000000002	25.624999999999996
5	24.3	34.449999999999996	19.325	21.925
6	26.471324818432258	24.167292762334082	19.083395942900076	30.277986476333584
7	29.5	28.575	18.2	23.724999999999998
8	18.85	20.599999999999998	27.0	33.550000000000004
9	19.8	24.025	36.35	19.825
10	40.675	23.35	20.849999999999998	15.125
11	41.675000000000004	22.75	17.549999999999997	18.025
12	33.025	27.675	22.6	16.7
13	29.049999999999997	20.9	34.575	15.475
14	34.125	22.05	25.575	18.25
15	20.775	25.95	29.875	23.400000000000002
16	30.275000000000002	23.95	32.125	13.65
17	24.825	23.474999999999998	27.250000000000004	24.45
18	20.65	28.299999999999997	32.675	18.375
19	33.1	22.8	27.075	17.025000000000002
20	23.225	22.85	37.9	16.025
21	33.875	18.2	29.95	17.974999999999998
22	28.4	31.424999999999997	23.65	16.525000000000002
23	26.625	42.725	11.55	19.1
24	39.975	36.449999999999996	11.799999999999999	11.774999999999999
25	23.875	41.925000000000004	18.35	15.85
26	18.224999999999998	20.674999999999997	28.799999999999997	32.300000000000004
27	25.75	18.275	15.525	40.45
28	43.2	15.775	14.224999999999998	26.8
29	43.325	28.975	11.225	16.475
30	30.099999999999998	42.6	8.9	18.4
31	33.1	40.35	12.325	14.224999999999998
32	37.724999999999994	40.325	6.825	15.125
33	31.6	44.375	9.049999999999999	14.975
34	34.35	30.025000000000002	7.725	27.900000000000002
35	19.2	31.474999999999998	11.450000000000001	37.875
36	18.475	39.900000000000006	8.9	32.725
37	18.4	35.725	8.95	36.925000000000004
38	19.575	38.375	10.674999999999999	31.374999999999996
39	29.425	21.725	10.325	38.525
40	33.85	19.475	22.675	24.0
41	21.9	16.150000000000002	32.574999999999996	29.375
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.5
5	1.0
6	0.5
7	0.0
8	0.0
9	0.0
10	0.0
11	0.5
12	1.0
13	0.5
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	2.0
27	4.0
28	3.0
29	2.0
30	5.0
31	8.0
32	8.0
33	10.0
34	12.0
35	21.5
36	31.0
37	31.0
38	50.5
39	70.0
40	130.0
41	190.0
42	190.0
43	235.5
44	281.0
45	369.5
46	458.0
47	458.0
48	462.0
49	466.0
50	636.5
51	807.0
52	710.0
53	613.0
54	613.0
55	479.5
56	346.0
57	373.0
58	400.0
59	400.0
60	280.0
61	160.0
62	132.0
63	104.0
64	104.0
65	65.0
66	26.0
67	18.0
68	10.0
69	10.0
70	5.5
71	1.0
72	1.5
73	2.0
74	1.5
75	1.0
76	1.0
77	1.0
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	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.5
97	1.0
98	1.0
99	2.5
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	0.17500000000000002
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	53.449999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	84.2376052385407	45.025
2	7.3433115060804495	7.85
3	2.7595884003741813	4.425
4	1.3564078578110383	2.9000000000000004
5	0.7015902712815716	1.875
6	0.4677268475210477	1.5
7	0.4677268475210477	1.7500000000000002
8	0.37418147801683815	1.6
9	0.2806361085126286	1.35
>10	1.7773620205799812	18.55
>50	0.1403180542563143	6.65
>100	0.09354536950420954	6.525
>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	151	3.775	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGT	110	2.75	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCG	94	2.35	TruSeq Adapter, Index 16 (97% over 39bp)
AGTGCCGCAGAGTTTGTAGTGTAGATCGGAAGAGCACACGT	89	2.225	No Hit
ACTCAAACTGGGGGCTCTTTTGAGATCGGAAGAGCACACGT	83	2.075	No Hit
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCACACGT	44	1.0999999999999999	No Hit
TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTT	43	1.075	No Hit
AGTGCCGCAGAGTTTGTAGTGAGATCGGAAGAGCACACGTC	42	1.05	No Hit
TGGAAGACTAGTGATTTTGTTGTTAGATCGGAAGAGCACAC	37	0.9249999999999999	No Hit
CGCGACCTCAGATCAGATCGGAAGAGCACACGTCTGAACTC	34	0.8500000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TATGGCACTGGTAGAATTCACTAGATCGGAAGAGCACACGT	31	0.775	No Hit
ACTCAAACTGTGTGACATTTTAGATCGGAAGAGCACACGTC	31	0.775	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTAGATCGGAAG	28	0.7000000000000001	No Hit
TATTGCACTTGTCCCGGCCTGTAGATCGGAAGAGCACACGT	25	0.625	No Hit
AACTGTGGTAATTCTAGAGCTAATACATGCCGAGATCGGAA	24	0.6	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACACGTCT	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AAGTGCCGCCAGGTTTTGAGTGTAGATCGGAAGAGCACACG	23	0.575	No Hit
CGCGACCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AAAGTGCTTCCCTTTTGTGTGTAGATCGGAAGAGCACACGT	20	0.5	No Hit
AGTGCCGCAGAGTTTGTAGTGCAGATCGGAAGAGCACACGT	18	0.44999999999999996	No Hit
AAAGTGCCGCCAGGTTTTGAGTGTAGATCGGAAGAGCACAC	18	0.44999999999999996	No Hit
AAGGGATTCTGATGTTGGTCACACTAGATCGGAAGAGCACA	16	0.4	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGC	16	0.4	No Hit
TTTGGCAATGGTAGAACTCACACCAGATCGGAAGAGCACAC	15	0.375	No Hit
AAAGTGCTTCCACTTTGTGTGCAGATCGGAAGAGCACACGT	14	0.35000000000000003	No Hit
ACTCAAACTGGGGGCTCTTTCAGATCGGAAGAGCACACGTC	14	0.35000000000000003	No Hit
CGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTT	14	0.35000000000000003	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAGATCGG	14	0.35000000000000003	No Hit
TTTGGCAATGGTAGAACTCACACCGAGATCGGAAGAGCACA	14	0.35000000000000003	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATAGATCG	13	0.325	No Hit
TATGGCACTGGTAGAATTCACTGAGATCGGAAGAGCACACG	13	0.325	No Hit
CATTGCACTTGTCTCGGTCTGAAGATCGGAAGAGCACACGT	13	0.325	No Hit
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCACACGT	13	0.325	No Hit
CATCAAAGTGGAGGCCCTCTCTAGATCGGAAGAGCACACGT	12	0.3	No Hit
TTCAAGTAATCCAGGATAGGCCAGATCGGAAGAGCACACGT	12	0.3	No Hit
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGCACACG	12	0.3	No Hit
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
ATGGCACTGGTAGAATTCACTGAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
AGTGCCGCAGAGTTTGTAGTAAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGAGATCGGAAG	10	0.25	No Hit
TTTGGCACTAGCACATTTTTGCTAGATCGGAAGAGCACACG	10	0.25	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTAGATC	10	0.25	No Hit
CTGCATGATGACGAACAAATACTGACTAGATCGGAAGAGCA	10	0.25	No Hit
ACTCAAACTGGGGGCTCTTTAGATCGGAAGAGCACACGTCT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AAGTGCTACTACTTTTGAGTCTAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
AAAGTGCTACTACTTTTGAGTCTAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TATGGCACTGGTAGAATTCACCAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAA	9	0.22499999999999998	No Hit
CGCGACCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGGAAGACTAGTGATTTTGTTGTAGATCGGAAGAGCACACG	8	0.2	No Hit
ACTCAAACTGGGGGCTCTTTTAAGATCGGAAGAGCACACGT	8	0.2	No Hit
TAAAGTGCTTATAGTGCAGGTAGAGATCGGAAGAGCACACG	8	0.2	No Hit
TAACTGTGGTAATTCTAGAGCTAATACATGCCGAGATCGGA	8	0.2	No Hit
ATAACTGTGGTAATTCTAGAGCTAATACATGCCGAGATCGG	8	0.2	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGAAGATC	8	0.2	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGAGATCGGA	8	0.2	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAGAT	8	0.2	No Hit
TTTGGCAATGGTAGAACTCACACTAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
TCAGTGCACTACAGAACTTTGCAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGAGATCGGAA	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTAGATCG	7	0.17500000000000002	No Hit
CAACGGAATCCCAAAAGCAGCTGAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
CGGCGTCATGCAGGAGTTGATTAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
CGCGACCTCAGATCAGACAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ACTCAAACTGTGTGACATTTAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AAGGGATTCTGATGTTGGTCACACTCAGATCGGAAGAGCAC	6	0.15	No Hit
CGCGACCTCAGATCAGACGCAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CATTGCACTTGTCTCGGTCTGAGATCGGAAGAGCACACGTC	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAGCTAGATCGGAAGAGCACAC	6	0.15	No Hit
AAAGTGCTACTACTTTTGAGTAGATCGGAAGAGCACACGTC	6	0.15	No Hit
AGCAGCATTGTACAGGGCTATGAAGATCGGAAGAGCACACG	6	0.15	No Hit
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTA	6	0.15	No Hit
AAAGTGCCGCCAGGTTTTGAGTGGAGATCGGAAGAGCACAC	6	0.15	No Hit
ACTGGACTTGGAGTCAGAAGGCAGATCGGAAGAGCACACGT	6	0.15	No Hit
AACTGTGGTAATTCTAGAGCTAATACATGCCAAGATCGGAA	6	0.15	No Hit
CCTGCATGATGACGAACAAATACTGACTAGATCGGAAGAGC	5	0.125	No Hit
ATGGCACTGGTAGAATTCACTAAGATCGGAAGAGCACACGT	5	0.125	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAG	5	0.125	No Hit
ACTCAAACTGTGTGACATTCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCAGATCGGAAGA	5	0.125	No Hit
ATGGCACTGGTAGAATTCACTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CAACGGAATCCCAAAAGCAGCTAGATCGGAAGAGCACACGT	5	0.125	No Hit
TGGTAGACTATGGAACGTAGGAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CATCAAAGTGGAGGCCCTCTCCAGATCGGAAGAGCACACGT	5	0.125	No Hit
TGACTGTGATGAATCTTACTCTGAGTCACAGATCGGAAGAG	5	0.125	No Hit
AGTGCCGCAGAGTTTGTAGTGGAGATCGGAAGAGCACACGT	5	0.125	No Hit
CGCGACCTCAGATAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAG	5	0.125	No Hit
AAGTGCCGCCAGGTTTTGAGTGCAGATCGGAAGAGCACACG	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAGATCGGA	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	2.575	0.0	0.0	0.0	0.0
2	2.625	0.0	0.0	0.0	0.0
3	2.675	0.0	0.0	0.0	0.0
4	2.675	0.0	0.0	0.0	0.0
5	2.75	0.0	0.0	0.0	0.0
6	2.825	0.0	0.0	0.0	0.0
7	2.9	0.0	0.0	0.0	0.0
8	3.225	0.0	0.0	0.0	0.0
9	3.575	0.0	0.0	0.0	0.0
10	5.05	0.0	0.0	0.0	0.0
11	5.9	0.0	0.0	0.0	0.0
12	7.075	0.0	0.0	0.0	0.0
13	8.325	0.0	0.0	0.0	0.0
14	9.6	0.0	0.0	0.0	0.0
15	11.925	0.0	0.0	0.0	0.0
16	13.45	0.0	0.0	0.0	0.0
17	14.5	0.0	0.0	0.0	0.0
18	15.6	0.0	0.0	0.0	0.0
19	17.475	0.0	0.0	0.0	0.0
20	18.8	0.0	0.0	0.0	0.0
21	21.9	0.0	0.0	0.0	0.0
22	34.3	0.0	0.0	0.0	0.0
23	53.875	0.0	0.0	0.0	0.0
24	61.45	0.0	0.0	0.0	0.0
25	66.375	0.0	0.0	0.0	0.0
26	68.375	0.0	0.0	0.0	0.0
27	69.55	0.0	0.0	0.0	0.0
28	70.8	0.0	0.0	0.0	0.0
29	71.825	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCGACC	45	2.588422E-9	35.000004	1
AAACTGG	35	6.175269E-7	35.000004	5
GCGACCT	45	2.588422E-9	35.000004	2
AACTGGG	35	6.175269E-7	35.000004	6
CTGGGGG	30	9.417061E-6	35.000004	8
CTCTTTT	30	9.417061E-6	35.000004	15
ATCAGAC	30	9.417061E-6	35.000004	12
ACTCAAA	45	2.588422E-9	35.000004	1
TGGGGGC	30	9.417061E-6	35.000004	9
TCAAACT	45	2.588422E-9	35.000004	3
GGGGGCT	30	9.417061E-6	35.000004	10
CCTCAGA	45	2.588422E-9	35.000004	6
CAGATCA	35	6.175269E-7	35.000004	9
ACCTCAG	45	2.588422E-9	35.000004	5
GGGGCTC	30	9.417061E-6	35.000004	11
GCTCTTT	30	9.417061E-6	35.000004	14
GACCTCA	45	2.588422E-9	35.000004	4
ACTGGGG	30	9.417061E-6	35.000004	7
CAAACTG	45	2.588422E-9	35.000004	4
AGATCAG	35	6.175269E-7	35.000004	10
>>END_MODULE
SRR13079633 read2 length is 41 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR13079633_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	30.9105	32.0	32.0	32.0	32.0	32.0
2	30.82825	32.0	32.0	32.0	32.0	32.0
3	30.78025	32.0	32.0	32.0	32.0	32.0
4	30.6385	32.0	32.0	32.0	32.0	32.0
5	30.51675	32.0	32.0	32.0	32.0	32.0
6	34.11075	36.0	36.0	36.0	32.0	36.0
7	34.08975	36.0	36.0	36.0	32.0	36.0
8	34.0845	36.0	36.0	36.0	32.0	36.0
9	34.116	36.0	36.0	36.0	32.0	36.0
10	34.03475	36.0	36.0	36.0	32.0	36.0
11	34.145	36.0	36.0	36.0	32.0	36.0
12	33.95075	36.0	36.0	36.0	32.0	36.0
13	34.2165	36.0	36.0	36.0	32.0	36.0
14	34.151	36.0	36.0	36.0	32.0	36.0
15	33.91725	36.0	36.0	36.0	32.0	36.0
16	34.18225	36.0	36.0	36.0	32.0	36.0
17	34.15425	36.0	36.0	36.0	32.0	36.0
18	34.27875	36.0	36.0	36.0	32.0	36.0
19	34.1025	36.0	36.0	36.0	32.0	36.0
20	34.017	36.0	36.0	36.0	32.0	36.0
21	34.26075	36.0	36.0	36.0	32.0	36.0
22	34.10825	36.0	36.0	36.0	32.0	36.0
23	34.373	36.0	36.0	36.0	32.0	36.0
24	33.98025	36.0	36.0	36.0	32.0	36.0
25	34.0865	36.0	36.0	36.0	32.0	36.0
26	34.1495	36.0	36.0	36.0	32.0	36.0
27	34.0835	36.0	36.0	36.0	32.0	36.0
28	33.972	36.0	36.0	36.0	32.0	36.0
29	34.27625	36.0	36.0	36.0	32.0	36.0
30	34.166	36.0	36.0	36.0	32.0	36.0
31	33.8905	36.0	36.0	36.0	32.0	36.0
32	34.34025	36.0	36.0	36.0	32.0	36.0
33	34.2745	36.0	36.0	36.0	32.0	36.0
34	34.1635	36.0	36.0	36.0	32.0	36.0
35	33.88525	36.0	36.0	36.0	32.0	36.0
36	33.95725	36.0	36.0	36.0	32.0	36.0
37	33.86775	36.0	36.0	36.0	32.0	36.0
38	34.01475	36.0	36.0	36.0	32.0	36.0
39	33.958	36.0	36.0	36.0	32.0	36.0
40	33.62125	36.0	36.0	36.0	27.0	36.0
41	33.132	36.0	36.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
15	3.0
16	0.0
17	0.0
18	5.0
19	5.0
20	8.0
21	11.0
22	5.0
23	14.0
24	37.0
25	40.0
26	55.0
27	63.0
28	80.0
29	112.0
30	148.0
31	148.0
32	221.0
33	358.0
34	878.0
35	1809.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	21.725	44.35	15.4	18.525
2	23.549999999999997	36.025	9.45	30.975
3	15.525	39.775	22.0	22.7
4	19.7	32.025	15.7	32.574999999999996
5	25.1	36.15	21.224999999999998	17.525
6	26.075	27.55	17.150000000000002	29.225
7	21.2	30.575000000000003	18.6	29.625
8	23.474999999999998	28.999999999999996	16.875	30.65
9	21.349999999999998	28.025	20.225	30.4
10	16.275000000000002	25.7	25.25	32.775
11	23.175	19.950000000000003	21.15	35.725
12	20.25	19.6	26.025	34.125
13	24.4	29.075	16.875	29.65
14	28.275	23.45	26.3	21.975
15	26.174999999999997	20.7	26.5	26.625
16	28.775000000000002	20.424999999999997	27.1	23.7
17	27.975	22.6	30.349999999999998	19.075
18	32.95	20.525	22.95	23.575
19	26.450000000000003	24.425	18.325	30.8
20	27.675	26.825	26.400000000000002	19.1
21	19.075	18.075	33.125	29.725
22	26.224999999999998	20.65	35.949999999999996	17.175
23	41.0	25.15	19.025	14.825
24	19.225	43.6	23.125	14.05
25	18.3	21.5	30.375000000000004	29.825000000000003
26	25.55	16.175	24.25	34.025
27	36.65	14.499999999999998	30.775000000000002	18.075
28	23.05	11.700000000000001	37.2	28.050000000000004
29	33.4333583395849	14.103525881470366	17.554388597149288	34.90872718179545
30	46.650000000000006	17.575	17.349999999999998	18.425
31	39.6	30.075000000000003	13.900000000000002	16.425
32	26.625	30.55	19.525000000000002	23.3
33	19.0	28.449999999999996	21.975	30.575000000000003
34	30.7	16.25	36.375	16.675
35	30.599999999999998	19.75	29.65	20.0
36	22.35	24.075	41.25	12.325
37	29.349999999999998	32.074999999999996	20.1	18.475
38	40.725	31.65	16.35	11.275
39	23.275000000000002	45.925	12.975	17.825
40	18.975	42.525	16.150000000000002	22.35
41	25.15	22.7	21.975	30.175
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	1.0
1	0.5
2	0.0
3	0.0
4	0.5
5	1.0
6	1.5
7	2.0
8	2.0
9	2.0
10	2.0
11	2.0
12	2.0
13	2.0
14	2.0
15	2.0
16	1.5
17	1.0
18	1.0
19	1.0
20	1.0
21	1.5
22	2.0
23	1.0
24	0.0
25	0.0
26	0.5
27	1.0
28	1.5
29	2.0
30	5.5
31	9.0
32	9.0
33	11.5
34	14.0
35	24.0
36	34.0
37	34.0
38	53.5
39	73.0
40	141.5
41	210.0
42	210.0
43	247.5
44	285.0
45	399.0
46	513.0
47	513.0
48	651.5
49	790.0
50	803.5
51	817.0
52	604.5
53	392.0
54	392.0
55	356.0
56	320.0
57	242.0
58	164.0
59	164.0
60	162.5
61	161.0
62	121.0
63	81.0
64	81.0
65	73.5
66	66.0
67	50.0
68	34.0
69	34.0
70	21.0
71	8.0
72	6.5
73	5.0
74	3.0
75	1.0
76	1.0
77	0.5
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	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.5
95	1.0
96	0.5
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	55.625
#Duplication Level	Percentage of deduplicated	Percentage of total
1	85.34831460674157	47.475
2	6.921348314606742	7.7
3	2.4719101123595504	4.125
4	1.303370786516854	2.9000000000000004
5	0.7191011235955056	2.0
6	0.5393258426966292	1.7999999999999998
7	0.5393258426966292	2.1
8	0.1797752808988764	0.8
9	0.1348314606741573	0.675
>10	1.6179775280898878	16.725
>50	0.1348314606741573	6.65
>100	0.0898876404494382	7.049999999999999
>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	139	3.4750000000000005	No Hit
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTG	100	2.5	Illumina RNA PCR Primer (100% over 36bp)
ACACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	88	2.1999999999999997	No Hit
CAAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAAC	78	1.95	No Hit
CACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAACT	42	1.05	No Hit
AGCCTATCCTGGATTACTTGAAGATCGTCGGACTGTAGAAC	42	1.05	No Hit
AACAACAAAATCACTAGTCTTCCAGATCGTCGGACTGTAGA	35	0.8750000000000001	No Hit
AGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAAC	31	0.775	No Hit
AAAATGTCACACAGTTTGAGTGATCGTCGGACTGTAGAACT	31	0.775	No Hit
GATCTGAGGTCGCGGATCGTCGGACTGTAGAACTCTGAACG	30	0.75	Illumina DpnII expression Sequencing Primer (96% over 26bp)
AGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCGTCGGA	27	0.675	No Hit
ACAGGCCGGGACAAGTGCAATAGATCGTCGGACTGTAGAAC	24	0.6	No Hit
CGGCATGTATTAGCTCTAGAATTACCACAGTTGATCGTCGG	24	0.6	No Hit
ACACTCAAAACCTGGCGGCACTTGATCGTCGGACTGTAGAA	23	0.575	No Hit
ACGTCTGATCTGAGGTCGCGGATCGTCGGACTGTAGAACTC	23	0.575	Illumina DpnII expression Sequencing Primer (100% over 21bp)
GCAAACCCTTGTGTCGAGGGCTGACTTTCAATAGATCGCAG	20	0.5	No Hit
GAGGTCGCGGATCGTCGGACTGTAGAACTCTGAACGTGTAG	19	0.475	Illumina DpnII expression Sequencing Primer (96% over 30bp)
ACACACAAAAGGGAAGCACTTTGATCGTCGGACTGTAGAAC	19	0.475	No Hit
ACACTCAAAACCTGGCGGCACTTTGATCGTCGGACTGTAGA	17	0.42500000000000004	No Hit
GCACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	17	0.42500000000000004	No Hit
GGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAGA	15	0.375	No Hit
ACAAAGTTCTGTAGTGCACTGAGATCGTCGGACTGTAGAAC	15	0.375	No Hit
GCACACAAAGTGGAAGCACTTTGATCGTCGGACTGTAGAAC	15	0.375	No Hit
AGTGTGACCAACATCAGAATCCCTTGATCGTCGGACTGTAG	14	0.35000000000000003	No Hit
TCAGACCGAGACAAGTGCAATGGATCGTCGGACTGTAGAAC	14	0.35000000000000003	No Hit
CGGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAG	13	0.325	No Hit
TTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCGTC	13	0.325	No Hit
ATTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCGT	13	0.325	No Hit
GAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAACT	13	0.325	No Hit
CAGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAA	12	0.3	No Hit
GTCAACATCAGTCTGATAAGCTAGATCGTCGGACTGTAGAA	12	0.3	No Hit
GCAGAACTTAGCCACTGTGAAGATCGTCGGACTGTAGAACT	12	0.3	No Hit
CAGTGAATTCTACCAGTGCCATGATCGTCGGACTGTAGAAC	11	0.27499999999999997	No Hit
TACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAACT	11	0.27499999999999997	No Hit
AGAGAGGGCCTCCACTTTGATGGATCGTCGGACTGTAGAAC	11	0.27499999999999997	No Hit
GGCCTATCCTGGATTACTTGAAGATCGTCGGACTGTAGAAC	11	0.27499999999999997	No Hit
AATTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCG	10	0.25	No Hit
AGACTCAAAAGTAGTAGCACTTGATCGTCGGACTGTAGAAC	10	0.25	No Hit
CACGAGCCGAGTGATCCACCGCTAAGAGTCGGATCGTCGGA	10	0.25	No Hit
AGCAAAAATGTGCTAGTGCCAAAGATCGTCGGACTGTAGAA	10	0.25	No Hit
AAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAACTC	9	0.22499999999999998	Illumina DpnII expression Sequencing Primer (100% over 21bp)
GGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAAC	9	0.22499999999999998	No Hit
AGTCAGTATTTGTTCGTCATCATGCAGGATCGTCGGACTGT	9	0.22499999999999998	No Hit
TCGACGCACGAGCCGAGTGATCCACCGCTAAGAGTCGATCG	8	0.2	No Hit
AGACTCAAAAGTAGTAGCACTTTGATCGTCGGACTGTAGAA	8	0.2	No Hit
AAATGACGCTCAAACAGGCATGCCCCCTGGAATACCAAGGG	8	0.2	No Hit
AAATTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATC	8	0.2	No Hit
ACAACAAAATCACTAGTCTTCCAGATCGTCGGACTGTAGAA	7	0.17500000000000002	No Hit
TAAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAAC	7	0.17500000000000002	No Hit
CGGCATGTATTAGCTCTAGAATTACCACAGTTATGATCGTC	7	0.17500000000000002	No Hit
CGGCATGTATTAGCTCTAGAATTACCACAGTTAGATCGTCG	7	0.17500000000000002	No Hit
AAATGTCACACAGTTTGAGTGATCGTCGGACTGTAGAACTC	7	0.17500000000000002	Illumina DpnII expression Sequencing Primer (100% over 21bp)
AACTGTACAAACTACTACCTCAGATCGTCGGACTGTAGAAC	7	0.17500000000000002	No Hit
TCTGAGGTCGCGGATCGTCGGACTGTAGAACTCTGAACGTG	7	0.17500000000000002	Illumina DpnII expression Sequencing Primer (96% over 29bp)
AGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAGA	7	0.17500000000000002	No Hit
CTACCTGCACTATAAGCACTTTAGATCGTCGGACTGTAGAA	7	0.17500000000000002	No Hit
CAGCTGCTTTTGGGATTCCGTTGGATCGTCGGACTGTAGAA	7	0.17500000000000002	No Hit
CGCACGAGCCGAGTGATCCACCGCTAAGAGTCGATCGTCGG	7	0.17500000000000002	No Hit
CGCACGAGCCGAGTGATCCACCGCTAAGAGTCGGATCGTCG	7	0.17500000000000002	No Hit
GCTTAAATTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCG	6	0.15	No Hit
AGTGAATTCTACCAGTGCCATGATCGTCGGACTGTAGAACT	6	0.15	No Hit
TCATAGCCCTGTACAATGCTGCTGATCGTCGGACTGTAGAA	6	0.15	No Hit
GCCTTCTGACTCCAAGTCCAGTGATCGTCGGACTGTAGAAC	6	0.15	No Hit
GCAAAGTTCTGTAGTGCACTGAGATCGTCGGACTGTAGAAC	6	0.15	No Hit
GTCTGATCTGAGGTCGCGGATCGTCGGACTGTAGAACTCTG	6	0.15	Illumina DpnII expression Sequencing Primer (100% over 23bp)
AGCTTCCAGTCGGGGATGTTTACAGATCGTCGGACTGTAGA	6	0.15	No Hit
CCACTCAAAACCTGGCGGCACTTTGATCGTCGGACTGTAGA	6	0.15	No Hit
ACTCAAAAGTAGTAGCACTTTGATCGTCGGACTGTAGAACT	6	0.15	No Hit
TGGCATGTATTAGCTCTAGAATTACCACAGTTGATCGTCGG	6	0.15	No Hit
AATCAACTCCTGCATGACGCCGGATCGTCGGACTGTAGAAC	6	0.15	No Hit
GAGTGTGACCAACATCAGAATCCCTTGATCGTCGGACTGTA	6	0.15	No Hit
TGCTTAAATTCAGCGGGTCGCCACGTCTGATCTGAGGTCGC	5	0.125	No Hit
TCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCGTCG	5	0.125	No Hit
CAGACCGAGACAAGTGCAATGGATCGTCGGACTGTAGAACT	5	0.125	No Hit
AAAGCCTACAGCACCCGGTATTCCCAGGCGGTCTCCCATCC	5	0.125	No Hit
AGTCAGTATTTGTTCGTCATCATGCAGGGATCGTCGGACTG	5	0.125	No Hit
GTGACCAACATCAGAATCCCTTGATCGTCGGACTGTAGAAC	5	0.125	No Hit
CATCAGAATCGTTGGTATTCATCAACAAGCTCAGTTGTCCC	5	0.125	No Hit
CCACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	5	0.125	No Hit
GCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCGTCGGAC	5	0.125	No Hit
GAATGTCACACAGTTTGAGTGATCGTCGGACTGTAGAACTC	5	0.125	Illumina DpnII expression Sequencing Primer (100% over 21bp)
ATCTGAGGTCGCGGATCGTCGGACTGTAGAACTCTGAACGT	5	0.125	Illumina DpnII expression Sequencing Primer (96% over 28bp)
ATACAGATGGATACCGTGCAATGATCGTCGGACTGTAGAAC	5	0.125	No Hit
AATCTGAGGTCGCGGATCGTCGGACTGTAGAACTCTGAACG	5	0.125	Illumina DpnII expression Sequencing Primer (96% over 26bp)
GCGTCTGATCTGAGGTCGCGGATCGTCGGACTGTAGAACTC	5	0.125	Illumina DpnII expression Sequencing Primer (100% over 21bp)
TAGTGAATTCTACCAGTGCCATGATCGTCGGACTGTAGAAC	5	0.125	No Hit
GTGACTCAGAGTAAGATTCATCACAGTCAGATCGTCGGACT	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	2.575	0.0	0.0
2	0.0	0.0	2.6	0.0	0.0
3	0.0	0.0	2.625	0.0	0.0
4	0.0	0.0	2.625	0.0	0.0
5	0.0	0.0	2.725	0.0	0.0
6	0.0	0.0	2.8	0.0	0.0
7	0.0	0.0	2.875	0.0	0.0
8	0.0	0.0	3.2	0.0	0.0
9	0.0	0.0	3.525	0.0	0.0
10	0.0	0.0	5.05	0.0	0.0
11	0.0	0.0	5.85	0.0	0.0
12	0.0	0.0	6.975	0.0	0.0
13	0.0	0.0	8.175	0.0	0.0
14	0.0	0.0	9.375	0.0	0.0
15	0.0	0.0	11.525	0.0	0.0
16	0.0	0.0	12.95	0.0	0.0
17	0.0	0.0	13.975	0.0	0.0
18	0.0	0.0	15.0	0.0	0.0
19	0.0	0.0	16.9	0.0	0.0
20	0.0	0.0	18.225	0.0	0.0
21	0.0	0.0	21.15	0.0	0.0
22	0.0	0.0	32.975	0.0	0.0
23	0.0	0.0	51.95	0.0	0.0
24	0.0	0.0	59.275	0.0	0.0
25	0.0	0.0	63.975	0.0	0.0
26	0.0	0.0	65.925	0.0	0.0
27	0.0	0.0	67.075	0.0	0.0
28	0.0	0.0	68.3	0.0	0.0
29	0.0	0.0	69.275	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCTCGGT	30	9.417061E-6	35.000004	34
CTCGGTG	30	9.417061E-6	35.000004	35
CTCTGCG	20	0.0021434545	35.0	11
CTACAAA	20	0.0021434545	35.0	4
ACAAACT	20	0.0021434545	35.0	6
AAACCCT	20	0.0021434545	35.0	3
AAACTCT	20	0.0021434545	35.0	8
GGCACTG	20	0.0021434545	35.0	17
TGACTTT	20	0.0021434545	35.0	22
CTGACTT	20	0.0021434545	35.0	21
ACTCTGC	20	0.0021434545	35.0	10
GGCTGAC	20	0.0021434545	35.0	19
ACTTTCA	20	0.0021434545	35.0	24
TCTGCGG	20	0.0021434545	35.0	12
CTGCGGC	20	0.0021434545	35.0	13
TACAAAC	20	0.0021434545	35.0	5
GCTGACT	20	0.0021434545	35.0	20
GCACTGA	20	0.0021434545	35.0	18
CAAACTC	20	0.0021434545	35.0	7
GACTTTC	20	0.0021434545	35.0	23
>>END_MODULE
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814730 spots for SRR13079633.sra
Written 814730 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
Read 814724 spots for SRR13079633.sra
Written 814724 spots for SRR13079633.sra
SRR ids: ['SRR13079633.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_k9xehi7f
SRR13079633.sra spots: 9776694
blocks: [[1, 814724], [814725, 1629448], [1629449, 2444172], [2444173, 3258896], [3258897, 4073620], [4073621, 4888344], [4888345, 5703068], [5703069, 6517792], [6517793, 7332516], [7332517, 8147240], [8147241, 8961964], [8961965, 9776694]]
SRR13079633 file size 1191274
SRR13079633 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR13079633 SRR13079633_1.fastq SRR13079633_2.fastq
Input file:	SRR13079633_1.fastq
Paired file:	SRR13079633_2.fastq
trimmed:	SRR13079633-trimmed-pair1.fastq, SRR13079633-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 16:35:14 2021 >> started

Tue Apr 20 16:35:25 2021 >> done (10.785s)
9776694 read pairs processed; of these:
1350557 (13.81%) short read pairs filtered out after trimming by size control
 230556 ( 2.36%) empty read pairs filtered out after trimming by size control
8195581 (83.83%) read pairs available; of these:
6997056 (85.38%) trimmed read pairs available after processing
1198525 (14.62%) untrimmed read pairs available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 145863	  1.78%
 19	 127266	  1.55%
 20	 342265	  4.18%
 21	1098381	 13.40%
 22	1929256	 23.54%
 23	 758526	  9.26%
 24	 492586	  6.01%
 25	 208317	  2.54%
 26	 118301	  1.44%
 27	 118831	  1.45%
 28	 132311	  1.61%
 29	 112955	  1.38%
 30	 120833	  1.47%
 31	 231718	  2.83%
 32	 213950	  2.61%
 33	 154733	  1.89%
 34	 150874	  1.84%
 35	 122434	  1.49%
 36	 112148	  1.37%
 37	  96428	  1.18%
 38	  75879	  0.93%
 39	  68926	  0.84%
 40	  64275	  0.78%
 41	1198525	 14.62%
8195581 reads passed initial QC


criterion=sequence-density
sequence-density=7.64
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=0.88
sequence-density-rank=13
fanout-score=39.91
fanout-score-rank=1
prefix-density=1.03
prefix-fanout=34.1
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCGCATCT


criterion=sequence-density
sequence-density=2.78
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=13
prefix-density=0.00
prefix-fanout=1.0
sequence=ACACTACAAACTCTGCGGCACT


criterion=fanout-score
sequence-density=0.64
sequence-density-rank=8
fanout-score=34.17
fanout-score-rank=1
prefix-density=0.72
prefix-fanout=30.3
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 SRR13079633 SRR13079633_1.fastq SRR13079633_2.fastq
Input file:	SRR13079633_1.fastq
Paired file:	SRR13079633_2.fastq
trimmed:	SRR13079633-trimmed-pair1.fastq, SRR13079633-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 16:36:02 2021 >> started

Tue Apr 20 16:36:08 2021 >> done (5.176s)
5463721 read pairs processed; of these:
   2044 ( 0.04%) short read pairs filtered out after trimming by size control
 690289 (12.63%) empty read pairs filtered out after trimming by size control
4771388 (87.33%) read pairs available; of these:
    151 ( 0.00%) trimmed read pairs available after processing
4771237 (100.00%) untrimmed read pairs available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  96424	  2.02%
 19	  83356	  1.75%
 20	 211328	  4.43%
 21	 428525	  8.98%
 22	 948279	 19.87%
 23	 487136	 10.21%
 24	 326519	  6.84%
 25	 137873	  2.89%
 26	  78423	  1.64%
 27	  78978	  1.66%
 28	  88043	  1.85%
 29	  75562	  1.58%
 30	  80557	  1.69%
 31	 154783	  3.24%
 32	 142768	  2.99%
 33	 103470	  2.17%
 34	 100466	  2.11%
 35	  81600	  1.71%
 36	  74489	  1.56%
 37	  64042	  1.34%
 38	  49792	  1.04%
 39	  46106	  0.97%
 40	  42645	  0.89%
 41	 790224	 16.56%


criterion=sequence-density
sequence-density=2.56
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=7
prefix-density=0.00
prefix-fanout=1.0
sequence=TTTGGCAATGGTAGAACTCACACCG


criterion=fanout-score
sequence-density=1.13
sequence-density-rank=11
fanout-score=45.03
fanout-score-rank=1
prefix-density=1.31
prefix-fanout=38.5
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCGCATCT


criterion=sequence-density
sequence-density=1.50
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AGCCTATCCTGGATTACTTGAAGATCGTCGG


criterion=fanout-score
sequence-density=0.76
sequence-density-rank=6
fanout-score=42.52
fanout-score-rank=1
prefix-density=0.89
prefix-fanout=36.1
sequence=GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCC
SRR13079633 testing PE reads STAR mapping to Ensembl genome
                                 Started job on |	Apr 20 16:37:04
                             Started mapping on |	Apr 20 16:37:04
                                    Finished on |	Apr 20 16:37:36
       Mapping speed, Million of reads per hour |	844.12

                          Number of input reads |	7503248
                      Average input read length |	55
                                    UNIQUE READS:
                   Uniquely mapped reads number |	4730291
                        Uniquely mapped reads % |	63.04%
                          Average mapped length |	50.82
                       Number of splices: Total |	22715
            Number of splices: Annotated (sjdb) |	10190
                       Number of splices: GT/AG |	19469
                       Number of splices: GC/AG |	842
                       Number of splices: AT/AC |	17
               Number of splices: Non-canonical |	2387
                      Mismatch rate per base, % |	0.29%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.30
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1172446
             % of reads mapped to multiple loci |	15.63%
        Number of reads mapped to too many loci |	83516
             % of reads mapped to too many loci |	1.11%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	18.06%
                     % of reads unmapped: other |	2.16%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1600511	1600511	1600511
N_multimapping	1172446	1172446	1172446
N_noFeature	985166	1131758	3329327
N_ambiguous	1909231	709899	365937
UnstrandedReadsAssigned:1835894 PositiveStrandReadsAssigned:2888634 NegativeStrandReadsAssigned:1035027
Dataset is classified unstranded
MeadianReadLen=24 20thPercentileLength=22 echo kmer=19
SRR13079633 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: SRR13079633-trimmed-pair1.fastq
                             SRR13079633-trimmed-pair2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 7,503,248 reads, 1,782,296 reads pseudoaligned
[quant] estimated average fragment length: 28.454
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,232 rounds

 109283 SRR13079633.ke.tsv
  52636 SRR13079633.se.tsv
 161919 total
==> SRR13079633.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSMUST00000177564.1	16	17	0	0
ENSMUST00000196221.1	9	10	0	0
ENSMUST00000179664.1	11	12	0	0
ENSMUST00000178537.1	12	13	0	0
ENSMUST00000178862.1	14	15	0	0
ENSMUST00000179520.1	11	12	0	0
ENSMUST00000179883.1	16	17	0	0
ENSMUST00000195858.1	10	11	0	0
ENSMUST00000179932.1	12	13	0	0

==> SRR13079633.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR13079633 completed mapping pipeline successfully
