Starting /dee2/code/volunteer_pipeline.sh SRR5031004
    current disk space = 160554237952
    free memory = 73948928 
SRR5031004 SRAfilesize
8c6cdb5b454982dfba17404f875aa8a1  SRR5031004.sra
SRR5031004.sra file validated
SRR5031004 is single end
SRR5031004 is conventional basespace
SRR5031004 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031004_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.248	33.0	31.0	34.0	31.0	34.0
2	32.5395	34.0	31.0	34.0	31.0	34.0
3	32.5985	34.0	31.0	34.0	31.0	34.0
4	36.15175	37.0	35.0	37.0	35.0	37.0
5	36.125	37.0	35.0	37.0	35.0	37.0
6	35.92525	37.0	35.0	37.0	35.0	37.0
7	35.89875	37.0	35.0	37.0	35.0	37.0
8	35.909	37.0	35.0	37.0	35.0	37.0
9	37.493	39.0	37.0	39.0	35.0	39.0
10	37.4825	39.0	37.0	39.0	34.0	39.0
11	36.978	39.0	37.0	39.0	33.0	39.0
12	37.564	39.0	37.0	39.0	35.0	39.0
13	37.48	39.0	37.0	39.0	34.0	39.0
14	38.901	40.0	38.0	41.0	35.0	41.0
15	38.89425	40.0	38.0	41.0	35.0	41.0
16	38.84275	40.0	38.0	41.0	35.0	41.0
17	39.0045	40.0	38.0	41.0	35.0	41.0
18	38.8705	40.0	38.0	41.0	35.0	41.0
19	38.69275	40.0	38.0	41.0	34.0	41.0
20	38.64125	40.0	38.0	41.0	34.0	41.0
21	38.71525	40.0	38.0	41.0	35.0	41.0
22	38.66625	40.0	38.0	41.0	34.0	41.0
23	38.32675	40.0	38.0	41.0	34.0	41.0
24	38.65775	40.0	38.0	41.0	34.0	41.0
25	38.7585	40.0	38.0	41.0	35.0	41.0
26	38.44675	40.0	38.0	41.0	34.0	41.0
27	38.6365	40.0	38.0	41.0	34.0	41.0
28	38.3835	40.0	38.0	41.0	34.0	41.0
29	38.0315	40.0	38.0	41.0	33.0	41.0
30	38.07425	40.0	38.0	41.0	32.0	41.0
31	38.3375	40.0	38.0	41.0	33.0	41.0
32	38.42325	40.0	38.0	41.0	34.0	41.0
33	37.58525	40.0	37.0	41.0	32.0	41.0
34	37.59125	40.0	37.0	41.0	33.0	41.0
35	37.61975	39.0	37.0	40.0	32.0	41.0
36	37.64175	39.0	37.0	41.0	33.0	41.0
37	37.096	39.0	36.0	41.0	31.0	41.0
38	37.146	39.0	36.0	40.0	31.0	41.0
39	37.64075	39.0	37.0	41.0	33.0	41.0
40	37.669	40.0	37.0	41.0	33.0	41.0
41	37.85925	40.0	37.0	41.0	33.0	41.0
42	37.73025	40.0	37.0	41.0	33.0	41.0
43	37.686	40.0	37.0	41.0	33.0	41.0
44	37.7425	40.0	37.0	41.0	33.0	41.0
45	37.69125	40.0	37.0	41.0	33.0	41.0
46	37.375	40.0	36.0	41.0	32.0	41.0
47	36.43975	39.0	35.0	41.0	30.0	41.0
48	36.3575	39.0	35.0	41.0	30.0	41.0
49	36.527	39.0	35.0	41.0	31.0	41.0
50	35.9265	38.0	34.0	40.0	30.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
10	1.0
11	0.0
12	0.0
13	1.0
14	1.0
15	0.0
16	1.0
17	0.0
18	2.0
19	2.0
20	2.0
21	2.0
22	7.0
23	3.0
24	7.0
25	19.0
26	11.0
27	14.0
28	20.0
29	42.0
30	55.0
31	70.0
32	88.0
33	127.0
34	168.0
35	202.0
36	331.0
37	466.0
38	827.0
39	1531.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.25	24.375	43.875	20.5
2	25.03128911138924	24.430538172715895	19.59949937421777	30.9386733416771
3	24.85	17.775	23.025000000000002	34.35
4	36.85	23.75	16.650000000000002	22.75
5	23.674999999999997	36.425000000000004	26.424999999999997	13.475000000000001
6	34.300000000000004	13.3	33.425	18.975
7	18.625	22.15	22.0	37.225
8	24.45	24.75	20.275000000000002	30.525000000000002
9	23.724999999999998	29.475	25.95	20.849999999999998
10	22.3	22.325	27.800000000000004	27.575
11	32.125	11.675	18.05	38.15
12	19.425	19.650000000000002	29.175	31.75
13	31.3	15.299999999999999	34.175	19.225
14	28.125	30.55	20.75	20.575
15	36.25	22.525000000000002	25.4	15.825
16	20.849999999999998	16.5	25.35	37.3
17	27.750000000000004	21.349999999999998	36.475	14.424999999999999
18	25.724999999999998	16.150000000000002	29.975	28.15
19	37.425000000000004	14.475	29.299999999999997	18.8
20	41.85	15.950000000000001	27.6	14.6
21	25.374999999999996	20.724999999999998	25.05	28.849999999999998
22	29.925	14.649999999999999	41.675000000000004	13.750000000000002
23	26.075	14.575	40.075	19.275000000000002
24	48.725	14.649999999999999	26.0	10.625
25	47.55	23.799999999999997	15.725	12.925
26	28.749999999999996	40.25	16.425	14.575
27	18.95	41.8	21.575	17.675
28	15.25	22.75	42.775	19.225
29	16.825000000000003	12.75	52.1	18.325
30	13.750000000000002	7.675	31.275	47.3
31	16.35	6.0249999999999995	44.925	32.7
32	29.099999999999998	6.575	22.400000000000002	41.925000000000004
33	48.6	11.3	15.1	25.0
34	53.900000000000006	9.325	19.45	17.325
35	61.0	8.875	17.775	12.35
36	41.349999999999994	9.125	34.449999999999996	15.075
37	42.9	13.750000000000002	21.3	22.05
38	25.924999999999997	20.7	12.375	41.0
39	17.549999999999997	22.925	13.55	45.975
40	18.575	43.075	15.85	22.5
41	24.625	43.775	10.674999999999999	20.925
42	43.125	27.200000000000003	16.875	12.8
43	47.599999999999994	26.8	10.85	14.75
44	33.425	41.8	9.2	15.575
45	22.2	45.050000000000004	15.625	17.125
46	19.650000000000002	24.2	16.0	40.150000000000006
47	12.2	16.05	38.65	33.1
48	15.125	13.225000000000001	21.224999999999998	50.425
49	17.1	17.849999999999998	16.225	48.825
50	19.55	32.425	14.899999999999999	33.125
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
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	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	0.5
28	0.0
29	0.5
30	1.0
31	10.0
32	19.0
33	17.0
34	15.0
35	16.0
36	17.0
37	23.5
38	30.0
39	39.0
40	48.0
41	44.5
42	41.0
43	64.5
44	88.0
45	115.5
46	143.0
47	244.5
48	346.0
49	443.5
50	541.0
51	639.5
52	738.0
53	592.5
54	447.0
55	503.5
56	560.0
57	453.0
58	346.0
59	231.0
60	116.0
61	86.0
62	56.0
63	137.0
64	218.0
65	133.0
66	48.0
67	36.0
68	24.0
69	28.0
70	32.0
71	70.0
72	108.0
73	59.5
74	11.0
75	6.5
76	2.0
77	1.5
78	1.0
79	1.0
80	1.0
81	1.0
82	1.0
83	0.5
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	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.125
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	0.0
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
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	36.95
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.69553450608932	27.6
2	10.419485791610285	7.7
3	4.2625169147496615	4.725
4	2.3004059539918806	3.4000000000000004
5	1.3531799729364005	2.5
6	1.0825439783491204	2.4
7	1.0825439783491204	2.8000000000000003
8	0.40595399188092013	1.2
9	0.5412719891745602	1.7999999999999998
>10	3.3152909336941816	26.224999999999998
>50	0.3382949932341001	10.424999999999999
>100	0.20297699594046006	9.225
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	135	3.375	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	130	3.25	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	104	2.6	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	100	2.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	91	2.275	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	90	2.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	82	2.0500000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	54	1.35	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	48	1.2	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGG	48	1.2	RNA PCR Primer, Index 2 (97% over 35bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	47	1.175	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	45	1.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	32	0.8	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTC	26	0.65	RNA PCR Primer, Index 24 (100% over 44bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	26	0.65	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	23	0.575	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	21	0.525	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	20	0.5	RNA PCR Primer, Index 1 (100% over 31bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGC	19	0.475	RNA PCR Primer, Index 24 (100% over 50bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	18	0.44999999999999996	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	17	0.42500000000000004	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	17	0.42500000000000004	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	15	0.375	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	15	0.375	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	12	0.3	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	12	0.3	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	12	0.3	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	10	0.25	RNA PCR Primer, Index 6 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 24bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	9	0.22499999999999998	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	8	0.2	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	8	0.2	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	8	0.2	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACGG	7	0.17500000000000002	RNA PCR Primer, Index 11 (97% over 35bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTGGAATT	7	0.17500000000000002	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTGGGCTACACATTTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	6	0.15	RNA PCR Primer, Index 6 (100% over 34bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGG	6	0.15	RNA PCR Primer, Index 2 (97% over 35bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGC	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCTC	5	0.125	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
GAATGTTGCTCGGTGAACCCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAG	5	0.125	RNA PCR Primer, Index 24 (100% over 38bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATGGAAT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	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	0.5	0.0	0.0	0.0
2	0.0	0.525	0.0	0.0	0.0
3	0.0	0.625	0.0	0.0	0.0
4	0.0	0.65	0.0	0.0	0.0
5	0.0	0.775	0.0	0.0	0.0
6	0.0	0.925	0.0	0.0	0.0
7	0.0	1.675	0.0	0.0	0.0
8	0.0	1.875	0.0	0.0	0.0
9	0.0	1.925	0.0	0.0	0.0
10	0.0	2.1	0.0	0.0	0.0
11	0.0	2.25	0.0	0.0	0.0
12	0.0	2.45	0.0	0.0	0.0
13	0.0	2.7	0.0	0.0	0.0
14	0.0	2.9	0.0	0.0	0.0
15	0.0	3.25	0.0	0.0	0.0
16	0.0	5.175	0.0	0.0	0.0
17	0.0	5.95	0.0	0.0	0.0
18	0.0	7.7	0.0	0.0	0.0
19	0.0	8.125	0.0	0.0	0.0
20	0.0	9.375	0.0	0.0	0.0
21	0.0	14.625	0.0	0.0	0.0
22	0.0	23.075	0.0	0.0	0.0
23	0.0	48.325	0.0	0.0	0.0
24	0.0	59.75	0.0	0.0	0.0
25	0.0	64.725	0.0	0.0	0.0
26	0.0	66.525	0.0	0.0	0.0
27	0.0	67.475	0.0	0.0	0.0
28	0.0	68.225	0.0	0.0	0.0
29	0.0	68.875	0.0	0.0	0.0
30	0.0	69.275	0.0	0.0	0.0
31	0.0	70.325	0.0	0.0	0.0
32	0.0	71.975	0.0	0.0	0.0
33	0.0	72.875	0.0	0.0	0.0
34	0.0	77.85	0.0	0.0	0.0
35	0.0	79.5	0.0	0.0	0.0
36	0.0	80.525	0.0	0.0	0.0
37	0.0	82.25	0.0	0.0	0.0
38	0.0	82.775	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GCGACCC	20	6.952051E-4	44.000004	22
GGCGACC	20	6.952051E-4	44.000004	21
ACCCGCT	20	6.952051E-4	44.000004	25
ACATTCA	20	6.952051E-4	44.000004	2
CCCGCTG	20	6.952051E-4	44.000004	26
CTTGGCT	45	2.728484E-10	44.000004	16
CGTGGCG	20	6.952051E-4	44.000004	18
AGACGTG	20	6.952051E-4	44.000004	15
GCTGTCG	20	6.952051E-4	44.000004	11
GACGTGG	20	6.952051E-4	44.000004	16
GGCTTTG	20	6.952051E-4	44.000004	19
TCAGACG	20	6.952051E-4	44.000004	13
CAGACGT	20	6.952051E-4	44.000004	14
TTGGCTT	40	5.315087E-9	44.000004	17
GTGGCGA	20	6.952051E-4	44.000004	19
TGGCGAC	20	6.952051E-4	44.000004	20
GACCCGC	20	6.952051E-4	44.000004	24
CTTTGGA	20	6.952051E-4	44.000004	21
CTGTCGG	20	6.952051E-4	44.000004	12
GCTTTGG	20	6.952051E-4	44.000004	20
>>END_MODULE
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
Read 313526 spots for SRR5031004.sra
Written 313526 spots for SRR5031004.sra
Read 313520 spots for SRR5031004.sra
Written 313520 spots for SRR5031004.sra
SRR ids: ['SRR5031004.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_m6q0zjmp
SRR5031004.sra spots: 3762246
blocks: [[1, 313520], [313521, 627040], [627041, 940560], [940561, 1254080], [1254081, 1567600], [1567601, 1881120], [1881121, 2194640], [2194641, 2508160], [2508161, 2821680], [2821681, 3135200], [3135201, 3448720], [3448721, 3762246]]
SRR5031004 file size 651020
SRR5031004 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031004 SRR5031004_1.fastq
Input file:	SRR5031004_1.fastq
trimmed:	SRR5031004-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- 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)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 07:04:31 2020 >> started

Wed Mar  4 07:04:33 2020 >> done (2.470s)
3762246 reads processed; of these:
    424 ( 0.01%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
3761812 (99.99%) reads available; of these:
 247864 ( 6.59%) trimmed reads available after processing
3513948 (93.41%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    131	  0.00%
 19	    138	  0.00%
 20	    255	  0.01%
 21	    329	  0.01%
 22	    526	  0.01%
 23	    637	  0.02%
 24	    710	  0.02%
 25	   1111	  0.03%
 26	    748	  0.02%
 27	    899	  0.02%
 28	   1089	  0.03%
 29	   1429	  0.04%
 30	   1097	  0.03%
 31	   1301	  0.03%
 32	   1615	  0.04%
 33	   1607	  0.04%
 34	   1941	  0.05%
 35	   3284	  0.09%
 36	   3410	  0.09%
 37	   3663	  0.10%
 38	   4023	  0.11%
 39	   4532	  0.12%
 40	   5183	  0.14%
 41	   5218	  0.14%
 42	   6698	  0.18%
 43	  10537	  0.28%
 44	  13797	  0.37%
 45	  18152	  0.48%
 46	  27599	  0.73%
 47	  29172	  0.78%
 48	  41729	  1.11%
 49	  55304	  1.47%
 50	3513948	 93.41%
3761812 reads passed initial QC


criterion=sequence-density
sequence-density=81.35
sequence-density-rank=1
fanout-score=21.44
fanout-score-rank=1
prefix-density=83.94
prefix-fanout=20.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=81.35
sequence-density-rank=1
fanout-score=21.44
fanout-score-rank=1
prefix-density=83.94
prefix-fanout=20.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC -o SRR5031004 -
Input file:	STDIN
trimmed:	SRR5031004-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC
-- 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):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 07:04:51 2020 >> started

Wed Mar  4 07:04:57 2020 >> done (6.058s)
3670061 reads processed; of these:
 257729 ( 7.02%) short reads filtered out after trimming by size control
  26711 ( 0.73%) empty reads filtered out after trimming by size control
3385621 (92.25%) reads available; of these:
3135591 (92.61%) trimmed reads available after processing
 250030 ( 7.39%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18773	  0.55%
 19	  39139	  1.16%
 20	 160948	  4.75%
 21	 333668	  9.86%
 22	 905485	 26.75%
 23	 439869	 12.99%
 24	 199151	  5.88%
 25	  60496	  1.79%
 26	  32543	  0.96%
 27	  25272	  0.75%
 28	  28797	  0.85%
 29	  23035	  0.68%
 30	  35038	  1.03%
 31	  60467	  1.79%
 32	  43859	  1.30%
 33	 191135	  5.65%
 34	  55299	  1.63%
 35	  46248	  1.37%
 36	  60245	  1.78%
 37	  24984	  0.74%
 38	  28555	  0.84%
 39	  25893	  0.76%
 40	  38999	  1.15%
 41	  50766	  1.50%
 42	  61143	  1.81%
 43	  44383	  1.31%
 44	  30334	  0.90%
 45	  41649	  1.23%
 46	  32602	  0.96%
 47	  24651	  0.73%
 48	   2477	  0.07%
 49	   4276	  0.13%
 50	 215442	  6.36%


criterion=sequence-density
sequence-density=6.30
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.37
sequence-density-rank=31
fanout-score=27.51
fanout-score-rank=1
prefix-density=10.22
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 07:05:20
                             Started mapping on |	Mar 04 07:05:21
                                    Finished on |	Mar 04 07:05:47
       Mapping speed, Million of reads per hour |	481.48

                          Number of input reads |	3477372
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1727198
                        Uniquely mapped reads % |	49.67%
                          Average mapped length |	25.67
                       Number of splices: Total |	1970
            Number of splices: Annotated (sjdb) |	250
                       Number of splices: GT/AG |	1854
                       Number of splices: GC/AG |	21
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	92
                      Mismatch rate per base, % |	0.24%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1088805
             % of reads mapped to multiple loci |	31.31%
        Number of reads mapped to too many loci |	103319
             % of reads mapped to too many loci |	2.97%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	15.30%
                     % of reads unmapped: other |	0.75%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	661369	661369	661369
N_multimapping	1088805	1088805	1088805
N_noFeature	126908	153103	1172952
N_ambiguous	956511	481389	22531
UnstrandedReadsAssigned:643779 PositiveStrandReadsAssigned:1092706 NegativeStrandReadsAssigned:531715
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031004 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[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 single-end mode
[quant] will process file 1: SRR5031004-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,477,372 reads, 842,712 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 721 rounds

 109283 SRR5031004.ke.tsv
  52636 SRR5031004.se.tsv
 161919 total
==> SRR5031004.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSMUST00000177564.1	16	4.59059	0	0
ENSMUST00000196221.1	9	3.70903	0	0
ENSMUST00000179664.1	11	4.02702	0	0
ENSMUST00000178537.1	12	4.16231	0	0
ENSMUST00000178862.1	14	4.39563	0	0
ENSMUST00000179520.1	11	4.02702	0	0
ENSMUST00000179883.1	16	4.59059	0	0
ENSMUST00000195858.1	10	3.87667	0	0
ENSMUST00000179932.1	12	4.16231	0	0

==> SRR5031004.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031004 completed mapping pipeline successfully
