Starting /dee2/code/volunteer_pipeline.sh SRR13079636
    current disk space = 414790111232
    free memory = 73710472 
SRR13079636 SRAfilesize
dd4d2fb00403d0fa8702018b50b7257a  SRR13079636.sra
SRR13079636.sra file validated
SRR13079636 is paired end
SRR13079636 is conventional basespace
SRR13079636 read1 length is 41 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR13079636_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	30.93475	32.0	32.0	32.0	32.0	32.0
2	31.4315	32.0	32.0	32.0	32.0	32.0
3	31.493	32.0	32.0	32.0	32.0	32.0
4	31.50175	32.0	32.0	32.0	32.0	32.0
5	31.388	32.0	32.0	32.0	32.0	32.0
6	35.20275	36.0	36.0	36.0	36.0	36.0
7	35.06725	36.0	36.0	36.0	36.0	36.0
8	34.98575	36.0	36.0	36.0	36.0	36.0
9	34.947	36.0	36.0	36.0	36.0	36.0
10	35.0575	36.0	36.0	36.0	36.0	36.0
11	35.127	36.0	36.0	36.0	36.0	36.0
12	35.164	36.0	36.0	36.0	36.0	36.0
13	34.997	36.0	36.0	36.0	36.0	36.0
14	35.047	36.0	36.0	36.0	36.0	36.0
15	35.05675	36.0	36.0	36.0	36.0	36.0
16	34.8885	36.0	36.0	36.0	36.0	36.0
17	34.96175	36.0	36.0	36.0	36.0	36.0
18	35.06775	36.0	36.0	36.0	36.0	36.0
19	35.138	36.0	36.0	36.0	36.0	36.0
20	34.98725	36.0	36.0	36.0	36.0	36.0
21	35.15625	36.0	36.0	36.0	36.0	36.0
22	35.148	36.0	36.0	36.0	36.0	36.0
23	34.9995	36.0	36.0	36.0	32.0	36.0
24	35.076	36.0	36.0	36.0	36.0	36.0
25	34.95475	36.0	36.0	36.0	36.0	36.0
26	35.071	36.0	36.0	36.0	36.0	36.0
27	35.02875	36.0	36.0	36.0	36.0	36.0
28	35.006	36.0	36.0	36.0	36.0	36.0
29	34.97275	36.0	36.0	36.0	36.0	36.0
30	35.08075	36.0	36.0	36.0	36.0	36.0
31	34.90525	36.0	36.0	36.0	32.0	36.0
32	34.92375	36.0	36.0	36.0	36.0	36.0
33	34.81825	36.0	36.0	36.0	32.0	36.0
34	34.89175	36.0	36.0	36.0	36.0	36.0
35	34.9285	36.0	36.0	36.0	36.0	36.0
36	34.8175	36.0	36.0	36.0	36.0	36.0
37	34.825	36.0	36.0	36.0	32.0	36.0
38	34.96525	36.0	36.0	36.0	32.0	36.0
39	34.84975	36.0	36.0	36.0	32.0	36.0
40	34.88475	36.0	36.0	36.0	36.0	36.0
41	34.622	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	2.0
23	6.0
24	12.0
25	7.0
26	12.0
27	28.0
28	41.0
29	70.0
30	75.0
31	105.0
32	150.0
33	248.0
34	616.0
35	2626.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.45	43.5	26.275	17.775
2	27.474999999999998	28.199999999999996	19.625	24.7
3	21.4	21.975	36.625	20.0
4	36.525	17.549999999999997	18.725	27.200000000000003
5	26.6	32.300000000000004	19.1	22.0
6	27.53188297074269	28.40710177544386	18.629657414353588	25.431357839459867
7	28.425	32.4	20.599999999999998	18.575
8	18.45	21.525	23.325000000000003	36.7
9	19.8	24.575	38.875	16.75
10	43.95	16.45	23.425	16.175
11	41.575	22.625	17.549999999999997	18.25
12	34.849999999999994	23.45	25.924999999999997	15.775
13	29.099999999999998	21.8	32.5	16.6
14	39.300000000000004	21.45	25.45	13.8
15	19.325	24.725	31.45	24.5
16	25.124999999999996	25.525	34.0	15.35
17	24.275	17.0	30.975	27.750000000000004
18	20.474999999999998	27.950000000000003	35.5	16.075
19	31.8	19.375	32.175	16.650000000000002
20	21.925	20.325	40.2	17.549999999999997
21	31.025000000000002	17.625	31.6	19.75
22	27.075	31.075000000000003	25.25	16.6
23	27.075	45.475	12.275	15.174999999999999
24	40.425	36.199999999999996	13.525	9.85
25	22.725	42.8	21.3	13.175
26	16.925	22.925	32.800000000000004	27.35
27	26.85	18.2	16.6	38.35
28	48.05	14.875	13.525	23.549999999999997
29	45.300000000000004	30.125	10.35	14.224999999999998
30	30.175	47.5	6.925000000000001	15.4
31	32.275	47.15	9.6	10.975
32	40.849999999999994	39.425	7.074999999999999	12.65
33	33.175	46.175	6.925000000000001	13.725000000000001
34	40.8	28.875	6.7	23.625
35	22.975	32.25	6.8500000000000005	37.925
36	17.65	44.675	8.575000000000001	29.099999999999998
37	16.775000000000002	35.875	6.925000000000001	40.425
38	19.125	42.175000000000004	6.375	32.324999999999996
39	26.200000000000003	23.175	8.75	41.875
40	37.55	18.775	18.775	24.9
41	18.675	15.45	37.275000000000006	28.599999999999998
>>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	0.5
7	1.0
8	1.0
9	1.0
10	1.0
11	1.0
12	1.0
13	0.5
14	0.0
15	0.0
16	0.5
17	1.0
18	1.0
19	1.0
20	1.0
21	1.5
22	2.0
23	2.0
24	2.0
25	2.0
26	2.5
27	3.0
28	3.5
29	4.0
30	6.0
31	8.0
32	8.0
33	9.5
34	11.0
35	19.5
36	28.0
37	28.0
38	46.5
39	65.0
40	121.5
41	178.0
42	178.0
43	254.0
44	330.0
45	421.0
46	512.0
47	512.0
48	560.5
49	609.0
50	751.0
51	893.0
52	739.0
53	585.0
54	585.0
55	465.0
56	345.0
57	272.5
58	200.0
59	200.0
60	161.0
61	122.0
62	90.0
63	58.0
64	58.0
65	39.0
66	20.0
67	13.5
68	7.0
69	7.0
70	7.0
71	7.0
72	4.0
73	1.0
74	0.5
75	0.0
76	0.0
77	0.0
78	0.0
79	1.0
80	2.0
81	2.0
82	1.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.5
90	1.0
91	0.5
92	0.0
93	0.0
94	0.0
95	0.0
96	0.5
97	1.0
98	1.0
99	0.5
100	0.0
>>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	0.025
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	52.55
#Duplication Level	Percentage of deduplicated	Percentage of total
1	83.15889628924833	43.7
2	7.849666983824928	8.25
3	2.759276879162702	4.35
4	1.569933396764986	3.3000000000000003
5	1.1893434823977165	3.125
6	0.3805899143672693	1.2
7	0.6184586108468125	2.275
8	0.3330161750713606	1.4000000000000001
9	0.285442435775452	1.35
>10	1.569933396764986	17.1
>50	0.19029495718363465	6.9
>100	0.09514747859181732	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
ACTCAAACTGGGGGCTCTTTTAGATCGGAAGAGCACACGTC	166	4.15	No Hit
ACTCAAACTGGGGGCTCTTTTGAGATCGGAAGAGCACACGT	116	2.9000000000000004	No Hit
AGTGCCGCAGAGTTTGTAGTGTAGATCGGAAGAGCACACGT	100	2.5	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGT	68	1.7000000000000002	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCT	57	1.425	TruSeq Adapter, Index 20 (100% over 40bp)
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCACACGT	51	1.275	No Hit
TGGAAGACTAGTGATTTTGTTGTTAGATCGGAAGAGCACAC	44	1.0999999999999999	No Hit
AGTGCCGCAGAGTTTGTAGTGAGATCGGAAGAGCACACGTC	44	1.0999999999999999	No Hit
ACTCAAACTGTGTGACATTTTAGATCGGAAGAGCACACGTC	42	1.05	No Hit
TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTT	35	0.8750000000000001	No Hit
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCACACGT	34	0.8500000000000001	No Hit
AAGGGATTCTGATGTTGGTCACACTAGATCGGAAGAGCACA	32	0.8	No Hit
AGTGCCGCAGAGTTTGTAGTGCAGATCGGAAGAGCACACGT	32	0.8	No Hit
TATGGCACTGGTAGAATTCACTAGATCGGAAGAGCACACGT	26	0.65	No Hit
TTTGGCAATGGTAGAACTCACACCAGATCGGAAGAGCACAC	24	0.6	No Hit
ATGGCACTGGTAGAATTCACTGAGATCGGAAGAGCACACGT	23	0.575	No Hit
TATTGCACTTGTCCCGGCCTGTAGATCGGAAGAGCACACGT	23	0.575	No Hit
AAAGTGCTTCCCTTTTGTGTGTAGATCGGAAGAGCACACGT	21	0.525	No Hit
TTCAAGTAATCCAGGATAGGCCAGATCGGAAGAGCACACGT	20	0.5	No Hit
TTTGGCAATGGTAGAACTCACACCGAGATCGGAAGAGCACA	20	0.5	No Hit
AAACATTCGCGGTGCACTTCTTAGATCGGAAGAGCACACGT	19	0.475	No Hit
AAAGTGCCGCCAGGTTTTGAGTGTAGATCGGAAGAGCACAC	19	0.475	No Hit
TATGGCACTGGTAGAATTCACTGAGATCGGAAGAGCACACG	18	0.44999999999999996	No Hit
AAGGGATTCTGATGTTGGTCACACTCAGATCGGAAGAGCAC	17	0.42500000000000004	No Hit
CCTGCATGATGACGAACAAATACTGACTAGATCGGAAGAGC	15	0.375	No Hit
CATCAAAGTGGAGGCCCTCTCTAGATCGGAAGAGCACACGT	15	0.375	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAGATCGG	15	0.375	No Hit
CAACGGAATCCCAAAAGCAGCTGAGATCGGAAGAGCACACG	15	0.375	No Hit
CATTGCACTTGTCTCGGTCTGAAGATCGGAAGAGCACACGT	15	0.375	No Hit
AACTGTGGTAATTCTAGAGCTAATACATGCCGAGATCGGAA	14	0.35000000000000003	No Hit
TGGAAGACTAGTGATTTTGTTGTCAGATCGGAAGAGCACAC	14	0.35000000000000003	No Hit
ACTCAAACTGGGGGCTCTTTCAGATCGGAAGAGCACACGTC	13	0.325	No Hit
AGTGCCGCAGAGTTTGTAGTAAGATCGGAAGAGCACACGTC	12	0.3	No Hit
TGTAAACATCCTACACTCTCAGCAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
AAAGTGCTACTACTTTTGAGTCTAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
AAGTGCCGCCAGGTTTTGAGTGTAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAG	10	0.25	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACACGTCT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CTGCATGATGACGAACAAATACTGACTAGATCGGAAGAGCA	10	0.25	No Hit
TTTGGCAATGGTAGAACTCACACTAGATCGGAAGAGCACAC	9	0.22499999999999998	No Hit
AGTGCCGCAGAGTTTGTAGTGAAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
CACCCGTAGAACCGACCTTGCGAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
ACTCAAACTGGGGGCTCTTTTGTAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
ACTCAAACTGTGTGACATTTAGATCGGAAGAGCACACGTCT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TATGCAAGGGCAAGCTCTCTTCAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
AAGGGATTCTGATGTTGGTCACACAGATCGGAAGAGCACAC	8	0.2	No Hit
TAGGTAGTTTCATGTTGTTGGGAGATCGGAAGAGCACACGT	8	0.2	No Hit
TTTGGCAATGGTAGAACTCACACAGATCGGAAGAGCACACG	8	0.2	No Hit
AAGTGCTACTACTTTTGAGTCTAGATCGGAAGAGCACACGT	8	0.2	No Hit
AAAGTGCTTCCCTTTTGTGTGCAGATCGGAAGAGCACACGT	8	0.2	No Hit
TATGGCACTGGTAGAATTCACCAGATCGGAAGAGCACACGT	8	0.2	No Hit
TAAAGTGCTTATAGTGCAGGTAGAGATCGGAAGAGCACACG	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
AAAGTGCTTCCACTTTGTGTGCAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
TGGAAGACTAGTGATTTTGTTGTAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
ACTCAAACTGGGGGCTCTTTTAAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGC	7	0.17500000000000002	No Hit
TGGTAGACTATGGAACGTAGGAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
ACTCAAACTGTGTGACATTTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
TTTGGCACTAGCACATTTTTGCTAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
AGTGCCGCAGAGTTTGTAGTGGAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
CGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTT	7	0.17500000000000002	No Hit
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
GAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTAGATCG	7	0.17500000000000002	No Hit
AACATTCATTGTTGTCGGTGGGTAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
AGTAATGATGATTTCTGGTGATTCTGAGTAGATCGGAAGAG	6	0.15	No Hit
AGTGCCGCAGAGTTTGTAGTAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGTAAACATCCTTGACTGGAAGCTAGATCGGAAGAGCACAC	6	0.15	No Hit
ATGGCACTGGTAGAATTCACTAGATCGGAAGAGCACACGTC	6	0.15	No Hit
CAACGGAATCCCAAAAGCAGCTAGATCGGAAGAGCACACGT	6	0.15	No Hit
AATTGCACGGTATCCATCTGTAAGATCGGAAGAGCACACGT	6	0.15	No Hit
AAAGTGCCGCCAGGTTTTGAGTAGATCGGAAGAGCACACGT	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCAAGATCGGAAGAGCACACGT	6	0.15	No Hit
TGTGACTGGTTGACCAGAGGGGAGATCGGAAGAGCACACGT	5	0.125	No Hit
GCCTGCTGGGGTGGAACCTGGTAGATCGGAAGAGCACACGT	5	0.125	No Hit
GGCAGAGGAGGGCTGTTCTTCCCAGATCGGAAGAGCACACG	5	0.125	No Hit
CAAAGTGCTTACAGTGCAGGTAGAGATCGGAAGAGCACACG	5	0.125	No Hit
AAAGTGCTACTACTTTTGAGTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACAAGATCGGAAGAGCACACG	5	0.125	No Hit
ACTCAAACTGGGGGCTCTTTAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CACATTACACGGTCGACCTCTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
ATCATGATGGGCTCCTCGGTGTAGATCGGAAGAGCACACGT	5	0.125	No Hit
AGCAGCATTGTACAGGGCTATGAAGATCGGAAGAGCACACG	5	0.125	No Hit
TTCAAGTAATTCAGGATAGGTTAGATCGGAAGAGCACACGT	5	0.125	No Hit
TGGAAGACTAGTGATTTTGTTGAGATCGGAAGAGCACACGT	5	0.125	No Hit
AAACAAACATGGTGCACTTCTTAGATCGGAAGAGCACACGT	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGTAAACATCCTACACTCTCAGCTAGATCGGAAGAGCACAC	5	0.125	No Hit
ATAACTGTGGTAATTCTAGAGCTAATACATGCCGAGATCGG	5	0.125	No Hit
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCACACGT	5	0.125	No Hit
CAAAGTGCTCATAGTGCAGGTAGAGATCGGAAGAGCACACG	5	0.125	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAA	5	0.125	No Hit
CAAAGTGCTGTTCGTGCAGGTAGAGATCGGAAGAGCACACG	5	0.125	No Hit
CCTGCATGATGACGAACAAATACTGACCAGATCGGAAGAGC	5	0.125	No Hit
AGCAGGCTCACTCTTTAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AAAGGTGATCGTTTTAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AATATAACACAGATGGCCTGTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
AACTGTGGTAATTCTAGAGCTAATACATGCCAGATCGGAAG	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	1.575	0.0	0.0	0.0	0.0
2	1.575	0.0	0.0	0.0	0.0
3	1.6	0.0	0.0	0.0	0.0
4	1.6	0.0	0.0	0.0	0.0
5	1.6	0.0	0.0	0.0	0.0
6	1.625	0.0	0.0	0.0	0.0
7	1.65	0.0	0.0	0.0	0.0
8	1.775	0.0	0.0	0.0	0.0
9	2.05	0.0	0.0	0.0	0.0
10	2.3	0.0	0.0	0.0	0.0
11	2.85	0.0	0.0	0.0	0.0
12	3.65	0.0	0.0	0.0	0.0
13	4.5	0.0	0.0	0.0	0.0
14	5.525	0.0	0.0	0.0	0.0
15	6.75	0.0	0.0	0.0	0.0
16	8.5	0.0	0.0	0.0	0.0
17	9.475	0.0	0.0	0.0	0.0
18	10.65	0.0	0.0	0.0	0.0
19	12.175	0.0	0.0	0.0	0.0
20	12.975	0.0	0.0	0.0	0.0
21	16.1	0.0	0.0	0.0	0.0
22	29.225	0.0	0.0	0.0	0.0
23	53.7	0.0	0.0	0.0	0.0
24	62.575	0.0	0.0	0.0	0.0
25	68.575	0.0	0.0	0.0	0.0
26	71.65	0.0	0.0	0.0	0.0
27	73.5	0.0	0.0	0.0	0.0
28	75.225	0.0	0.0	0.0	0.0
29	77.225	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTTTGTA	35	6.175269E-7	35.000004	12
AAACTGG	35	6.175269E-7	35.000004	5
TTGTAGT	35	6.175269E-7	35.000004	14
AACTGGG	35	6.175269E-7	35.000004	6
CTGGGGG	35	6.175269E-7	35.000004	8
TGCCGCA	35	6.175269E-7	35.000004	3
CTCTTTT	30	9.417061E-6	35.000004	15
CCGCAGA	35	6.175269E-7	35.000004	5
GAGTTTG	35	6.175269E-7	35.000004	10
CAGAGTT	35	6.175269E-7	35.000004	8
TTTTAGA	30	9.417061E-6	35.000004	18
ACTCAAA	45	2.588422E-9	35.000004	1
TGGGGGC	35	6.175269E-7	35.000004	9
AGAGTTT	35	6.175269E-7	35.000004	9
TCAAACT	45	2.588422E-9	35.000004	3
GGGGGCT	35	6.175269E-7	35.000004	10
GGCTCTT	35	6.175269E-7	35.000004	13
TGTAGTG	35	6.175269E-7	35.000004	15
GCAGAGT	35	6.175269E-7	35.000004	7
CGCAGAG	35	6.175269E-7	35.000004	6
>>END_MODULE
SRR13079636 read2 length is 41 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR13079636_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	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.90875	32.0	32.0	32.0	32.0	32.0
2	30.8525	32.0	32.0	32.0	32.0	32.0
3	30.803	32.0	32.0	32.0	32.0	32.0
4	30.783	32.0	32.0	32.0	32.0	32.0
5	30.8355	32.0	32.0	32.0	32.0	32.0
6	34.1315	36.0	36.0	36.0	32.0	36.0
7	34.2305	36.0	36.0	36.0	32.0	36.0
8	34.122	36.0	36.0	36.0	32.0	36.0
9	34.27275	36.0	36.0	36.0	32.0	36.0
10	34.23475	36.0	36.0	36.0	32.0	36.0
11	34.232	36.0	36.0	36.0	32.0	36.0
12	34.1655	36.0	36.0	36.0	32.0	36.0
13	34.35275	36.0	36.0	36.0	32.0	36.0
14	34.1335	36.0	36.0	36.0	32.0	36.0
15	34.08825	36.0	36.0	36.0	32.0	36.0
16	34.2615	36.0	36.0	36.0	32.0	36.0
17	34.29225	36.0	36.0	36.0	32.0	36.0
18	34.44275	36.0	36.0	36.0	32.0	36.0
19	34.242	36.0	36.0	36.0	32.0	36.0
20	34.19425	36.0	36.0	36.0	32.0	36.0
21	34.24775	36.0	36.0	36.0	32.0	36.0
22	34.135	36.0	36.0	36.0	32.0	36.0
23	34.42525	36.0	36.0	36.0	32.0	36.0
24	34.09375	36.0	36.0	36.0	32.0	36.0
25	34.23075	36.0	36.0	36.0	32.0	36.0
26	34.22925	36.0	36.0	36.0	32.0	36.0
27	34.20275	36.0	36.0	36.0	32.0	36.0
28	34.10075	36.0	36.0	36.0	32.0	36.0
29	34.34925	36.0	36.0	36.0	32.0	36.0
30	34.1305	36.0	36.0	36.0	32.0	36.0
31	34.141	36.0	36.0	36.0	32.0	36.0
32	34.28	36.0	36.0	36.0	32.0	36.0
33	34.3295	36.0	36.0	36.0	32.0	36.0
34	34.2235	36.0	36.0	36.0	32.0	36.0
35	34.13425	36.0	36.0	36.0	32.0	36.0
36	34.0935	36.0	36.0	36.0	32.0	36.0
37	34.0915	36.0	36.0	36.0	32.0	36.0
38	34.15075	36.0	36.0	36.0	32.0	36.0
39	34.19475	36.0	36.0	36.0	32.0	36.0
40	33.628	36.0	36.0	36.0	27.0	36.0
41	33.25375	36.0	36.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
14	1.0
15	1.0
16	1.0
17	6.0
18	1.0
19	6.0
20	7.0
21	11.0
22	12.0
23	18.0
24	24.0
25	48.0
26	40.0
27	60.0
28	72.0
29	103.0
30	122.0
31	168.0
32	216.0
33	310.0
34	765.0
35	2008.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	20.95	44.625	14.325	20.1
2	24.325	36.825	9.575	29.275000000000002
3	16.075	40.875	20.075000000000003	22.975
4	18.4	33.725	15.975	31.900000000000002
5	24.95	37.375	22.175	15.5
6	29.475	29.125	15.65	25.75
7	20.3	32.5	20.225	26.974999999999998
8	21.8	32.475	17.625	28.1
9	16.475	30.225	20.075000000000003	33.225
10	12.725	27.0	25.525	34.75
11	20.575	20.424999999999997	21.825	37.175000000000004
12	18.9	19.275000000000002	24.099999999999998	37.724999999999994
13	21.075	32.375	17.1	29.45
14	26.275	23.974999999999998	25.55	24.2
15	26.75	21.475	26.275	25.5
16	26.35	22.925	28.825	21.9
17	26.450000000000003	21.45	31.525	20.575
18	31.324999999999996	19.925	25.55	23.200000000000003
19	23.150000000000002	27.325	17.1	32.425
20	25.525	28.175	27.025	19.275000000000002
21	19.625	18.475	34.775	27.125
22	24.65	23.425	32.9	19.025
23	42.425000000000004	26.200000000000003	16.875	14.499999999999998
24	19.35	44.3	22.8	13.55
25	17.95	20.025000000000002	34.25	27.775
26	25.2	15.950000000000001	22.95	35.9
27	38.324999999999996	13.625000000000002	29.475	18.575
28	23.025000000000002	11.825	39.2	25.95
29	33.59179589794897	10.430215107553776	18.684342171085543	37.293646823411706
30	50.8	15.575	17.025000000000002	16.6
31	44.574999999999996	25.5	13.0	16.925
32	25.25	34.625	15.525	24.6
33	21.099999999999998	23.724999999999998	21.125	34.050000000000004
34	29.675	14.149999999999999	38.550000000000004	17.625
35	34.9	17.675	30.45	16.975
36	22.3	23.5	42.3	11.899999999999999
37	28.65	36.0	20.575	14.774999999999999
38	42.075	32.35	15.975	9.6
39	21.7	51.05	11.450000000000001	15.8
40	18.025	47.099999999999994	14.774999999999999	20.1
41	19.3	24.55	21.575	34.575
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	3.0
1	2.5
2	2.0
3	2.0
4	1.5
5	1.0
6	0.5
7	0.0
8	0.0
9	0.0
10	0.0
11	1.0
12	2.0
13	3.0
14	4.0
15	4.0
16	2.5
17	1.0
18	2.0
19	3.0
20	3.0
21	2.5
22	2.0
23	1.5
24	1.0
25	1.0
26	2.5
27	4.0
28	5.5
29	7.0
30	8.0
31	9.0
32	9.0
33	10.5
34	12.0
35	19.0
36	26.0
37	26.0
38	35.5
39	45.0
40	136.0
41	227.0
42	227.0
43	271.5
44	316.0
45	443.0
46	570.0
47	570.0
48	714.5
49	859.0
50	846.0
51	833.0
52	624.5
53	416.0
54	416.0
55	331.5
56	247.0
57	208.0
58	169.0
59	169.0
60	139.5
61	110.0
62	91.5
63	73.0
64	73.0
65	49.0
66	25.0
67	18.0
68	11.0
69	11.0
70	9.5
71	8.0
72	6.0
73	4.0
74	3.0
75	2.0
76	2.0
77	1.5
78	1.0
79	1.0
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	1.5
90	2.0
91	1.0
92	0.0
93	0.0
94	0.5
95	1.0
96	0.5
97	0.0
98	0.0
99	1.0
100	2.0
>>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	0.05
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	55.074999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	84.61189287335452	46.6
2	7.535179300953246	8.3
3	2.4058102587380845	3.975
4	1.407172038129823	3.1
5	0.9532455742169769	2.625
6	0.2723558783477077	0.8999999999999999
7	0.49931911030413073	1.925
8	0.3177485247389923	1.4000000000000001
9	0.22696323195642307	1.125
>10	1.5433499773036767	17.175
>50	0.09078529278256922	3.5249999999999995
>100	0.13617793917385385	9.35
>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	160	4.0	No Hit
CAAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAAC	113	2.825	No Hit
ACACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	101	2.5250000000000004	No Hit
ACAAACCCTTGTGTCGAGGGCTGACTTTCAATAGATCGCAG	80	2.0	No Hit
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTG	61	1.525	Illumina RNA PCR Primer (100% over 36bp)
AGCCTATCCTGGATTACTTGAAGATCGTCGGACTGTAGAAC	49	1.225	No Hit
AACAACAAAATCACTAGTCTTCCAGATCGTCGGACTGTAGA	44	1.0999999999999999	No Hit
CACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAACT	42	1.05	No Hit
AAAATGTCACACAGTTTGAGTGATCGTCGGACTGTAGAACT	39	0.975	No Hit
GCACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	31	0.775	No Hit
ACAAAGTTCTGTAGTGCACTGAGATCGTCGGACTGTAGAAC	30	0.75	No Hit
AGTGTGACCAACATCAGAATCCCTTGATCGTCGGACTGTAG	30	0.75	No Hit
AGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAAC	27	0.675	No Hit
CAGTGAATTCTACCAGTGCCATGATCGTCGGACTGTAGAAC	25	0.625	No Hit
GCAAACCCTTGTGTCGAGGGCTGACTTTCAATAGATCGCAG	25	0.625	No Hit
GGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAGA	21	0.525	No Hit
ACAGGCCGGGACAAGTGCAATAGATCGTCGGACTGTAGAAC	20	0.5	No Hit
GGCCTATCCTGGATTACTTGAAGATCGTCGGACTGTAGAAC	20	0.5	No Hit
CGGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAG	19	0.475	No Hit
AAGAAGTGCACCGCGAATGTTTGATCGTCGGACTGTAGAAC	18	0.44999999999999996	No Hit
ACACACAAAAGGGAAGCACTTTGATCGTCGGACTGTAGAAC	17	0.42500000000000004	No Hit
CAGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAA	16	0.4	No Hit
AGTCAGTATTTGTTCGTCATCATGCAGGGATCGTCGGACTG	15	0.375	No Hit
ACACTCAAAACCTGGCGGCACTTTGATCGTCGGACTGTAGA	15	0.375	No Hit
TCAGACCGAGACAAGTGCAATGGATCGTCGGACTGTAGAAC	15	0.375	No Hit
GAGTGTGACCAACATCAGAATCCCTTGATCGTCGGACTGTA	15	0.375	No Hit
CAGCTGCTTTTGGGATTCCGTTGGATCGTCGGACTGTAGAA	14	0.35000000000000003	No Hit
AGAGAGGGCCTCCACTTTGATGGATCGTCGGACTGTAGAAC	14	0.35000000000000003	No Hit
TTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCGTC	13	0.325	No Hit
CGGCATGTATTAGCTCTAGAATTACCACAGTTGATCGTCGG	13	0.325	No Hit
GACAACAAAATCACTAGTCTTCCAGATCGTCGGACTGTAGA	13	0.325	No Hit
GAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAACT	13	0.325	No Hit
ACGTCTGATCTGAGGTCGCGGATCGTCGGACTGTAGAACTC	12	0.3	Illumina DpnII expression Sequencing Primer (100% over 21bp)
ACACTCAAAACCTGGCGGCACTTGATCGTCGGACTGTAGAA	11	0.27499999999999997	No Hit
GCTGAGAGTGTAGGATGTTTACAGATCGTCGGACTGTAGAA	11	0.27499999999999997	No Hit
GGCGAGAATTCTACCACTGAACCACCAATGCGATCGTCGGA	10	0.25	No Hit
AGACTCAAAAGTAGTAGCACTTTGATCGTCGGACTGTAGAA	10	0.25	No Hit
AGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAGA	10	0.25	No Hit
AGTCAGTATTTGTTCGTCATCATGCAGGATCGTCGGACTGT	10	0.25	No Hit
CGCAAGGTCGGTTCTACGGGTGGATCGTCGGACTGTAGAAC	9	0.22499999999999998	No Hit
ACAAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAA	9	0.22499999999999998	No Hit
GGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAAC	9	0.22499999999999998	No Hit
TCACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	9	0.22499999999999998	No Hit
GAAGAGAGCTTGCCCTTGCATAGATCGTCGGACTGTAGAAC	9	0.22499999999999998	No Hit
ACAACAAAATCACTAGTCTTCCAGATCGTCGGACTGTAGAA	8	0.2	No Hit
GTGACCAACATCAGAATCCCTTGATCGTCGGACTGTAGAAC	8	0.2	No Hit
CCCAACAACATGAAACTACCTAGATCGTCGGACTGTAGAAC	8	0.2	No Hit
TACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAACT	8	0.2	No Hit
GTGTGACCAACATCAGAATCCCTTGATCGTCGGACTGTAGA	8	0.2	No Hit
CTACCTGCACTATAAGCACTTTAGATCGTCGGACTGTAGAA	8	0.2	No Hit
GCACACAAAAGGGAAGCACTTTGATCGTCGGACTGTAGAAC	8	0.2	No Hit
AAAGCCTACAGCACCCGGTATTCCCAGGCGGTCTCGATCGT	7	0.17500000000000002	No Hit
AGTGAATTCTACCAGTGCCATGATCGTCGGACTGTAGAACT	7	0.17500000000000002	No Hit
CCACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAAC	7	0.17500000000000002	No Hit
GTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAGAA	7	0.17500000000000002	No Hit
AGACTCAAAAGTAGTAGCACTTGATCGTCGGACTGTAGAAC	7	0.17500000000000002	No Hit
AAATGTCACACAGTTTGAGTGATCGTCGGACTGTAGAACTC	7	0.17500000000000002	Illumina DpnII expression Sequencing Primer (100% over 21bp)
GCACACAAAGTGGAAGCACTTTGATCGTCGGACTGTAGAAC	7	0.17500000000000002	No Hit
GAAATGTCACACAGTTTGAGTGATCGTCGGACTGTAGAACT	7	0.17500000000000002	No Hit
GTCAACATCAGTCTGATAAGCTAGATCGTCGGACTGTAGAA	7	0.17500000000000002	No Hit
AGCAAAAATGTGCTAGTGCCAAAGATCGTCGGACTGTAGAA	7	0.17500000000000002	No Hit
TACAGATGGATACCGTGCAATTGATCGTCGGACTGTAGAAC	7	0.17500000000000002	No Hit
TAAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAAC	6	0.15	No Hit
ACTCAGAATCACCAGAAATCATCATTACTGATCGTCGGACT	6	0.15	No Hit
ACCCACCGACAACAATGAATGTTGATCGTCGGACTGTAGAA	6	0.15	No Hit
AACTGTACAAACTACTACCTCAGATCGTCGGACTGTAGAAC	6	0.15	No Hit
AGCTGCTTTTGGGATTCCGTTGGATCGTCGGACTGTAGAAC	6	0.15	No Hit
ACTACAAACTCTGCGGCACTGATCGTCGGACTGTAGAACTC	6	0.15	Illumina DpnII expression Sequencing Primer (100% over 21bp)
AGAGGTCGACCGTGTAATGTGGATCGTCGGACTGTAGAACT	5	0.125	No Hit
AAAACGATCACCTTTGATCGTCGGACTGTAGAACTCTGAAC	5	0.125	Illumina DpnII expression Sequencing Primer (100% over 26bp)
AGCTGAGAGTGTAGGATGTTTACAGATCGTCGGACTGTAGA	5	0.125	No Hit
ACTCAAAACCTGGCGGCACTTTGATCGTCGGACTGTAGAAC	5	0.125	No Hit
CGAATCCACCACGAACAACTTCGATCGTCGGACTGTAGAAC	5	0.125	No Hit
CTACCTGCACTGTAAGCACTTTGGATCGTCGGACTGTAGAA	5	0.125	No Hit
TAGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTAGAA	5	0.125	No Hit
ACCAGGTTCCACCCCAGCAGGCGATCGTCGGACTGTAGAAC	5	0.125	No Hit
AAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGAACTC	5	0.125	Illumina DpnII expression Sequencing Primer (100% over 21bp)
AACCTATCCTGAATTACTTGAAGATCGTCGGACTGTAGAAC	5	0.125	No Hit
GGTCAGTATTTGTTCGTCATCATGCAGGGATCGTCGGACTG	5	0.125	No Hit
CCTACGTTCCATAGTCTACCAGATCGTCGGACTGTAGAACT	5	0.125	No Hit
ACTTGGTTCCGCGGCTTCACGAGGGCGATTCAGGTACGCAC	5	0.125	No Hit
AAATGACGCTCAAACAGGCATGCCCCCTGGAATACCAAGGG	5	0.125	No Hit
AGGGGTTCACCGAGCAACATTCGATCGTCGGACTGTAGAAC	5	0.125	No Hit
GGGAAGAACAGCCCTCCTCTGCCGATCGTCGGACTGTAGAA	5	0.125	No Hit
CAACAAAATCACTAGTCTTCCAGATCGTCGGACTGTAGAAC	5	0.125	No Hit
ACTCAAAAGTAGTAGCACTTTGATCGTCGGACTGTAGAACT	5	0.125	No Hit
AGCTTCCAGTCAAGGATGTTTACAGATCGTCGGACTGTAGA	5	0.125	No Hit
TGCAAGGTCGGTTCTACGGGTGGATCGTCGGACTGTAGAAC	5	0.125	No Hit
GACCAACATCAGAATCCCTTGATCGTCGGACTGTAGAACTC	5	0.125	Illumina DpnII expression Sequencing Primer (100% over 21bp)
>>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	1.6	0.0	0.0
2	0.0	0.0	1.6	0.0	0.0
3	0.0	0.0	1.625	0.0	0.0
4	0.0	0.0	1.625	0.0	0.0
5	0.0	0.0	1.625	0.0	0.0
6	0.0	0.0	1.625	0.0	0.0
7	0.0	0.0	1.65	0.0	0.0
8	0.0	0.0	1.775	0.0	0.0
9	0.0	0.0	2.05	0.0	0.0
10	0.0	0.0	2.275	0.0	0.0
11	0.0	0.0	2.825	0.0	0.0
12	0.0	0.0	3.625	0.0	0.0
13	0.0	0.0	4.4	0.0	0.0
14	0.0	0.0	5.35	0.0	0.0
15	0.0	0.0	6.45	0.0	0.0
16	0.0	0.0	8.175	0.0	0.0
17	0.0	0.0	9.1	0.0	0.0
18	0.0	0.0	10.175	0.0	0.0
19	0.0	0.0	11.675	0.0	0.0
20	0.0	0.0	12.525	0.0	0.0
21	0.0	0.0	15.55	0.0	0.0
22	0.0	0.0	28.3	0.0	0.0
23	0.0	0.0	52.35	0.0	0.0
24	0.0	0.0	60.85	0.0	0.0
25	0.0	0.0	66.575	0.0	0.0
26	0.0	0.0	69.575	0.0	0.0
27	0.0	0.0	71.375	0.0	0.0
28	0.0	0.0	73.025	0.0	0.0
29	0.0	0.0	74.925	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTGCAAT	20	0.0021434545	35.0	15
ACACTAC	20	0.0021434545	35.0	1
AGCCCCC	35	2.707939E-5	30.000002	6
TTTGAGT	35	2.707939E-5	30.000002	15
CTCTGCG	35	2.707939E-5	30.000002	11
CTACAAA	35	2.707939E-5	30.000002	4
ACAAACT	35	2.707939E-5	30.000002	6
AAACTCT	35	2.707939E-5	30.000002	8
CAGTTTG	35	2.707939E-5	30.000002	12
GGCACTG	35	2.707939E-5	30.000002	17
CCCAGTT	35	2.707939E-5	30.000002	10
GTTTGAG	35	2.707939E-5	30.000002	14
AAGAGCC	35	2.707939E-5	30.000002	3
ACTCTGC	35	2.707939E-5	30.000002	10
TCTGCGG	35	2.707939E-5	30.000002	12
CTGCGGC	35	2.707939E-5	30.000002	13
AGAGCCC	35	2.707939E-5	30.000002	4
TACAAAC	35	2.707939E-5	30.000002	5
CACTACA	35	2.707939E-5	30.000002	2
CCCCCAG	35	2.707939E-5	30.000002	8
>>END_MODULE
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867800 spots for SRR13079636.sra
Written 867800 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
Read 867792 spots for SRR13079636.sra
Written 867792 spots for SRR13079636.sra
SRR ids: ['SRR13079636.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ydkpnlrh
SRR13079636.sra spots: 10413512
blocks: [[1, 867792], [867793, 1735584], [1735585, 2603376], [2603377, 3471168], [3471169, 4338960], [4338961, 5206752], [5206753, 6074544], [6074545, 6942336], [6942337, 7810128], [7810129, 8677920], [8677921, 9545712], [9545713, 10413512]]
SRR13079636 file size 1269819
SRR13079636 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR13079636 SRR13079636_1.fastq SRR13079636_2.fastq
Input file:	SRR13079636_1.fastq
Paired file:	SRR13079636_2.fastq
trimmed:	SRR13079636-trimmed-pair1.fastq, SRR13079636-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 (11.728s)
10413512 read pairs processed; of these:
 1321023 (12.69%) short read pairs filtered out after trimming by size control
  247374 ( 2.38%) empty read pairs filtered out after trimming by size control
 8845115 (84.94%) read pairs available; of these:
 7989629 (90.33%) trimmed read pairs available after processing
  855486 ( 9.67%) untrimmed read pairs available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 155869	  1.76%
 19	 137662	  1.56%
 20	 351144	  3.97%
 21	1355487	 15.32%
 22	2451476	 27.72%
 23	 907331	 10.26%
 24	 615996	  6.96%
 25	 279977	  3.17%
 26	 152186	  1.72%
 27	 140234	  1.59%
 28	 159672	  1.81%
 29	 137896	  1.56%
 30	 127716	  1.44%
 31	 183596	  2.08%
 32	 213928	  2.42%
 33	 145956	  1.65%
 34	 135068	  1.53%
 35	  93783	  1.06%
 36	  62107	  0.70%
 37	  56011	  0.63%
 38	  45643	  0.52%
 39	  41098	  0.46%
 40	  39793	  0.45%
 41	 855486	  9.67%
8845115 reads passed initial QC


criterion=sequence-density
sequence-density=8.18
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=5
prefix-density=0.01
prefix-fanout=1.0
sequence=ACTCAAACTGGGGGCTCTTTTG


criterion=fanout-score
sequence-density=0.84
sequence-density-rank=12
fanout-score=40.42
fanout-score-rank=1
prefix-density=1.01
prefix-fanout=33.7
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCTTATCT


criterion=sequence-density
sequence-density=3.02
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=12
prefix-density=0.00
prefix-fanout=1.0
sequence=ACACTACAAACTCTGCGGCACT


criterion=fanout-score
sequence-density=0.73
sequence-density-rank=5
fanout-score=36.20
fanout-score-rank=1
prefix-density=0.81
prefix-fanout=32.6
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 SRR13079636 SRR13079636_1.fastq SRR13079636_2.fastq
Input file:	SRR13079636_1.fastq
Paired file:	SRR13079636_2.fastq
trimmed:	SRR13079636-trimmed-pair1.fastq, SRR13079636-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 16:40:23 2021 >> done (5.185s)
6317939 read pairs processed; of these:
   3014 ( 0.05%) short read pairs filtered out after trimming by size control
 855779 (13.55%) empty read pairs filtered out after trimming by size control
5459146 (86.41%) read pairs available; of these:
    141 ( 0.00%) trimmed read pairs available after processing
5459005 (100.00%) untrimmed read pairs available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 110582	  2.03%
 19	  96561	  1.77%
 20	 234660	  4.30%
 21	 597584	 10.95%
 22	1320221	 24.18%
 23	 622761	 11.41%
 24	 438695	  8.04%
 25	 198561	  3.64%
 26	 108657	  1.99%
 27	  99905	  1.83%
 28	 114086	  2.09%
 29	  98559	  1.81%
 30	  91302	  1.67%
 31	 130859	  2.40%
 32	 153103	  2.80%
 33	 104340	  1.91%
 34	  96439	  1.77%
 35	  66892	  1.23%
 36	  44245	  0.81%
 37	  39789	  0.73%
 38	  32470	  0.59%
 39	  29389	  0.54%
 40	  28374	  0.52%
 41	 601112	 11.01%


criterion=sequence-density
sequence-density=2.77
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=8
prefix-density=0.00
prefix-fanout=1.0
sequence=TTTGGCAATGGTAGAACTCACACCG


criterion=fanout-score
sequence-density=1.09
sequence-density-rank=10
fanout-score=46.35
fanout-score-rank=1
prefix-density=1.30
prefix-fanout=38.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCTTATCT


criterion=sequence-density
sequence-density=1.78
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=11
prefix-density=0.00
prefix-fanout=1.0
sequence=AGCCTATCCTGGATTACTTGAAGATCGTCGG


criterion=fanout-score
sequence-density=0.85
sequence-density-rank=4
fanout-score=43.51
fanout-score-rank=1
prefix-density=0.97
prefix-fanout=38.0
sequence=GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCC
SRR13079636 testing PE reads STAR mapping to Ensembl genome
                                 Started job on |	Apr 20 16:41:24
                             Started mapping on |	Apr 20 16:41:25
                                    Finished on |	Apr 20 16:42:02
       Mapping speed, Million of reads per hour |	777.05

                          Number of input reads |	7986322
                      Average input read length |	52
                                    UNIQUE READS:
                   Uniquely mapped reads number |	5419120
                        Uniquely mapped reads % |	67.86%
                          Average mapped length |	48.25
                       Number of splices: Total |	28462
            Number of splices: Annotated (sjdb) |	12336
                       Number of splices: GT/AG |	25143
                       Number of splices: GC/AG |	879
                       Number of splices: AT/AC |	27
               Number of splices: Non-canonical |	2413
                      Mismatch rate per base, % |	0.28%
                         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 |	1227023
             % of reads mapped to multiple loci |	15.36%
        Number of reads mapped to too many loci |	108777
             % of reads mapped to too many loci |	1.36%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	14.06%
                     % of reads unmapped: other |	1.36%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1340179	1340179	1340179
N_multimapping	1227023	1227023	1227023
N_noFeature	913118	1050512	3889206
N_ambiguous	2113363	791183	342047
UnstrandedReadsAssigned:2392639 PositiveStrandReadsAssigned:3577425 NegativeStrandReadsAssigned:1187867
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR13079636 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: SRR13079636-trimmed-pair1.fastq
                             SRR13079636-trimmed-pair2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 7,986,322 reads, 1,831,398 reads pseudoaligned
[quant] estimated average fragment length: 26.6307
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,260 rounds

 109283 SRR13079636.ke.tsv
  52636 SRR13079636.se.tsv
 161919 total
==> SRR13079636.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

==> SRR13079636.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR13079636 completed mapping pipeline successfully
