Starting /dee2/code/volunteer_pipeline.sh SRR5030970
    current disk space = 160590036992
    free memory = 73954832 
SRR5030970 SRAfilesize
9605ef9c83b7f95bf39f8a09ad06889e  SRR5030970.sra
SRR5030970.sra file validated
SRR5030970 is single end
SRR5030970 is conventional basespace
SRR5030970 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030970_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.49075	33.0	31.0	34.0	31.0	34.0
2	32.7825	34.0	31.0	34.0	31.0	34.0
3	32.6795	34.0	31.0	34.0	31.0	34.0
4	36.2585	37.0	37.0	37.0	35.0	37.0
5	36.20125	37.0	37.0	37.0	35.0	37.0
6	35.959	37.0	35.0	37.0	35.0	37.0
7	36.089	37.0	35.0	37.0	35.0	37.0
8	36.16025	37.0	36.0	37.0	35.0	37.0
9	37.8455	39.0	38.0	39.0	35.0	39.0
10	37.9565	39.0	38.0	39.0	35.0	39.0
11	37.75475	39.0	38.0	39.0	35.0	39.0
12	37.71475	39.0	38.0	39.0	35.0	39.0
13	37.7145	39.0	37.0	39.0	35.0	39.0
14	39.1075	40.0	39.0	41.0	36.0	41.0
15	39.13025	41.0	39.0	41.0	36.0	41.0
16	39.2145	40.0	39.0	41.0	36.0	41.0
17	39.24575	41.0	39.0	41.0	36.0	41.0
18	39.29475	41.0	39.0	41.0	36.0	41.0
19	38.9075	40.0	39.0	41.0	35.0	41.0
20	38.94125	40.0	38.0	41.0	35.0	41.0
21	38.68	40.0	38.0	41.0	34.0	41.0
22	38.469	40.0	38.0	41.0	34.0	41.0
23	37.90475	40.0	37.0	41.0	33.0	41.0
24	38.39225	40.0	38.0	41.0	34.0	41.0
25	38.65225	40.0	38.0	41.0	35.0	41.0
26	38.64925	40.0	38.0	41.0	34.0	41.0
27	38.85	40.0	39.0	41.0	35.0	41.0
28	38.63425	40.0	38.0	41.0	34.0	41.0
29	38.31525	40.0	38.0	41.0	33.0	41.0
30	38.44675	40.0	38.0	41.0	34.0	41.0
31	38.72575	40.0	38.0	41.0	35.0	41.0
32	38.47975	40.0	38.0	41.0	34.0	41.0
33	38.60825	40.0	38.0	41.0	35.0	41.0
34	38.62325	40.0	38.0	41.0	35.0	41.0
35	38.35475	40.0	38.0	41.0	34.0	41.0
36	37.77225	40.0	37.0	41.0	32.0	41.0
37	37.7355	40.0	37.0	41.0	32.0	41.0
38	37.60375	40.0	37.0	41.0	32.0	41.0
39	38.00475	40.0	38.0	41.0	33.0	41.0
40	37.99975	40.0	38.0	41.0	33.0	41.0
41	37.95725	40.0	38.0	41.0	33.0	41.0
42	38.09825	40.0	38.0	41.0	33.0	41.0
43	38.4135	40.0	38.0	41.0	34.0	41.0
44	38.3675	40.0	38.0	41.0	34.0	41.0
45	38.26525	40.0	38.0	41.0	34.0	41.0
46	37.58675	40.0	37.0	41.0	32.0	41.0
47	37.056	40.0	37.0	41.0	31.0	41.0
48	36.2655	39.0	35.0	41.0	29.0	41.0
49	36.616	39.0	36.0	41.0	31.0	41.0
50	36.16375	39.0	36.0	41.0	29.0	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
13	1.0
14	1.0
15	0.0
16	1.0
17	1.0
18	1.0
19	3.0
20	2.0
21	1.0
22	3.0
23	7.0
24	7.0
25	4.0
26	15.0
27	17.0
28	20.0
29	26.0
30	34.0
31	71.0
32	79.0
33	104.0
34	140.0
35	183.0
36	274.0
37	458.0
38	787.0
39	1760.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	5.977988994497249	22.56128064032016	59.329664832416206	12.131065532766383
2	21.475	28.000000000000004	24.15	26.375
3	16.7	17.525	19.05	46.725
4	25.4	39.775	11.95	22.875
5	21.11055527763882	38.86943471735868	28.51425712856428	11.505752876438219
6	37.4	14.149999999999999	36.825	11.625
7	11.475	25.8	25.25	37.475
8	23.35	43.4	12.35	20.9
9	18.099999999999998	41.85	28.725	11.325000000000001
10	17.95	20.325	27.425	34.300000000000004
11	30.225	11.075	13.5	45.2
12	15.425	14.174999999999999	24.55	45.85
13	19.2	23.275000000000002	38.475	19.05
14	41.699999999999996	22.2	24.675	11.425
15	40.1	20.3	28.799999999999997	10.8
16	11.95	27.6	20.424999999999997	40.025
17	23.575	21.775	40.9	13.750000000000002
18	29.925	19.35	27.6	23.125
19	40.2	12.45	30.475	16.875
20	54.05	16.0	20.424999999999997	9.525
21	19.625	26.200000000000003	24.6	29.575000000000003
22	32.425	11.175	50.075	6.325
23	24.55	11.475	53.349999999999994	10.625
24	56.825	11.375	27.150000000000002	4.65
25	60.12499999999999	22.775000000000002	11.55	5.55
26	27.85	55.074999999999996	11.175	5.8999999999999995
27	11.575000000000001	58.050000000000004	23.150000000000002	7.225
28	6.875000000000001	25.1	56.574999999999996	11.450000000000001
29	6.875000000000001	9.475	65.975	17.675
30	7.324999999999999	3.7249999999999996	39.375	49.575
31	12.275	3.1	49.375	35.25
32	25.074999999999996	3.5000000000000004	21.9	49.525000000000006
33	61.224999999999994	4.8	10.925	23.05
34	73.125	5.2	10.925	10.75
35	72.625	4.575	17.125	5.675
36	42.425000000000004	4.5	42.025	11.05
37	49.475	6.9	21.175	22.45
38	22.975	12.775	9.225	55.025
39	11.85	22.575	5.6000000000000005	59.975
40	12.0	55.125	6.2	26.674999999999997
41	23.425	59.425	5.7	11.450000000000001
42	55.55	31.374999999999996	6.0	7.074999999999999
43	61.425	27.575	4.725	6.275
44	29.475	55.925000000000004	4.35	10.25
45	13.0	59.5	9.625	17.875
46	7.175	27.025	17.1	48.699999999999996
47	5.7	11.75	43.35	39.2
48	6.175	10.125	21.725	61.975
49	10.025	17.2	10.2	62.575
50	17.375	43.4	9.375	29.849999999999998
>>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	0.0
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	1.0
28	2.0
29	1.5
30	1.0
31	2.0
32	3.0
33	3.0
34	3.0
35	7.5
36	12.0
37	12.5
38	13.0
39	21.0
40	29.0
41	32.5
42	36.0
43	69.5
44	103.0
45	175.5
46	248.0
47	468.0
48	688.0
49	650.0
50	612.0
51	833.0
52	1054.0
53	695.0
54	336.0
55	339.0
56	342.0
57	326.5
58	311.0
59	188.0
60	65.0
61	48.5
62	32.0
63	42.0
64	52.0
65	32.0
66	12.0
67	10.5
68	9.0
69	10.0
70	11.0
71	17.0
72	23.0
73	12.0
74	1.0
75	1.0
76	1.0
77	0.5
78	0.0
79	0.5
80	1.0
81	0.5
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	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.05
2	0.0
3	0.0
4	0.0
5	0.05
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	32.800000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.6859756097561	24.825
2	8.307926829268293	5.45
3	4.2682926829268295	4.2
4	2.5152439024390247	3.3000000000000003
5	1.9817073170731707	3.25
6	0.6859756097560976	1.35
7	0.5335365853658537	1.225
8	0.7621951219512195	2.0
9	0.5335365853658537	1.575
>10	4.192073170731708	27.925
>50	0.22865853658536583	4.45
>100	0.3048780487804878	20.45
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	320	8.0	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	186	4.65	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	165	4.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	147	3.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	55	1.375	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	47	1.175	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	45	1.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	33	0.8250000000000001	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	24	0.6	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	21	0.525	RNA PCR Primer, Index 2 (100% over 35bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	14	0.35000000000000003	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	13	0.325	RNA PCR Primer, Index 1 (100% over 33bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGGAATATCTC	12	0.3	RNA PCR Primer, Index 37 (100% over 44bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	7	0.17500000000000002	RNA PCR Primer, Index 2 (100% over 34bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	7	0.17500000000000002	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGGAATATCTCGTATGC	7	0.17500000000000002	RNA PCR Primer, Index 37 (100% over 50bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACAGAAATATTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTATAAAGCAATGAGACTGATTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCA	5	0.125	RNA PCR Primer, Index 1 (96% over 26bp)
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.225	0.0	0.0	0.0
2	0.0	0.225	0.0	0.0	0.0
3	0.0	0.225	0.0	0.0	0.0
4	0.0	0.25	0.0	0.0	0.0
5	0.0	0.25	0.0	0.0	0.0
6	0.0	0.325	0.0	0.0	0.0
7	0.0	0.675	0.0	0.0	0.0
8	0.0	0.85	0.0	0.0	0.0
9	0.0	0.9	0.0	0.0	0.0
10	0.0	0.95	0.0	0.0	0.0
11	0.0	1.05	0.0	0.0	0.0
12	0.0	1.15	0.0	0.0	0.0
13	0.0	1.575	0.0	0.0	0.0
14	0.0	1.7	0.0	0.0	0.0
15	0.0	1.925	0.0	0.0	0.0
16	0.0	2.775	0.0	0.0	0.0
17	0.0	3.525	0.0	0.0	0.0
18	0.0	4.1	0.0	0.0	0.0
19	0.0	4.65	0.0	0.0	0.0
20	0.0	5.65	0.0	0.0	0.0
21	0.0	11.175	0.0	0.0	0.0
22	0.0	23.8	0.0	0.0	0.0
23	0.0	61.9	0.0	0.0	0.0
24	0.0	78.9	0.0	0.0	0.0
25	0.0	84.35	0.0	0.0	0.0
26	0.0	85.225	0.0	0.0	0.0
27	0.0	85.8	0.0	0.0	0.0
28	0.0	86.175	0.0	0.0	0.0
29	0.0	86.825	0.0	0.0	0.0
30	0.0	87.25	0.0	0.0	0.0
31	0.0	87.775	0.0	0.0	0.0
32	0.0	88.375	0.0	0.0	0.0
33	0.0	89.2	0.0	0.0	0.0
34	0.0	90.525	0.0	0.0	0.0
35	0.0	91.425	0.0	0.0	0.0
36	0.0	91.725	0.0	0.0	0.0
37	0.0	92.175	0.0	0.0	0.0
38	0.0	92.6	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	65	0.0	44.000004	2
GAGTGGA	20	6.952051E-4	44.000004	20
AGTGGAA	20	6.952051E-4	44.000004	21
GTGAGTT	20	6.952051E-4	44.000004	18
GAGTTGG	20	6.952051E-4	44.000004	20
TGAGGTA	65	0.0	44.000004	1
TGAGTTG	20	6.952051E-4	44.000004	19
TGTAAAC	20	6.952051E-4	44.000004	1
GTAGATT	25	3.6958358E-5	44.0	8
AACGCTG	35	1.02281774E-7	44.0	8
GGTTGTA	35	1.02281774E-7	44.0	11
GGTGAGT	35	1.02281774E-7	44.0	17
AAGTAAT	30	1.9515464E-6	44.0	4
TCAAGTA	30	1.9515464E-6	44.0	2
ACGCTGT	35	1.02281774E-7	44.0	9
AATCCAG	30	1.9515464E-6	44.0	8
ATCCAGG	30	1.9515464E-6	44.0	9
TTGTATA	50	1.4551915E-11	44.0	13
AGTAGGT	30	1.9515464E-6	44.0	7
TTCAAGT	30	1.9515464E-6	44.0	1
>>END_MODULE
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225750 spots for SRR5030970.sra
Written 225750 spots for SRR5030970.sra
Read 225758 spots for SRR5030970.sra
Written 225758 spots for SRR5030970.sra
SRR ids: ['SRR5030970.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ctx8dbnq
SRR5030970.sra spots: 2709008
blocks: [[1, 225750], [225751, 451500], [451501, 677250], [677251, 903000], [903001, 1128750], [1128751, 1354500], [1354501, 1580250], [1580251, 1806000], [1806001, 2031750], [2031751, 2257500], [2257501, 2483250], [2483251, 2709008]]
SRR5030970 file size 468460
SRR5030970 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030970 SRR5030970_1.fastq
Input file:	SRR5030970_1.fastq
trimmed:	SRR5030970-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 06:56:26 2020 >> started

Wed Mar  4 06:56:28 2020 >> done (1.936s)
2709008 reads processed; of these:
    151 ( 0.01%) short reads filtered out after trimming by size control
      0 ( 0.00%) empty reads filtered out after trimming by size control
2708857 (99.99%) reads available; of these:
 171559 ( 6.33%) trimmed reads available after processing
2537298 (93.67%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     49	  0.00%
 19	     75	  0.00%
 20	    131	  0.00%
 21	    192	  0.01%
 22	    305	  0.01%
 23	    308	  0.01%
 24	    324	  0.01%
 25	    445	  0.02%
 26	    423	  0.02%
 27	    464	  0.02%
 28	    674	  0.02%
 29	   1031	  0.04%
 30	    595	  0.02%
 31	    619	  0.02%
 32	    689	  0.03%
 33	    948	  0.03%
 34	   1296	  0.05%
 35	   2227	  0.08%
 36	   1748	  0.06%
 37	   1956	  0.07%
 38	   1976	  0.07%
 39	   2378	  0.09%
 40	   2781	  0.10%
 41	   2906	  0.11%
 42	   4094	  0.15%
 43	   5574	  0.21%
 44	   8810	  0.33%
 45	  11547	  0.43%
 46	  15817	  0.58%
 47	  19441	  0.72%
 48	  35591	  1.31%
 49	  46145	  1.70%
 50	2537298	 93.67%
2708857 reads passed initial QC


criterion=sequence-density
sequence-density=92.91
sequence-density-rank=1
fanout-score=17.32
fanout-score-rank=1
prefix-density=94.34
prefix-fanout=17.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGGAATATCTCGTATGCC


criterion=fanout-score
sequence-density=92.91
sequence-density-rank=1
fanout-score=17.32
fanout-score-rank=1
prefix-density=94.34
prefix-fanout=17.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGGAATATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGGAATATCTCGTATGCC -o SRR5030970 -
Input file:	STDIN
trimmed:	SRR5030970-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGGAATATCTCGTATGCC
-- 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 06:56:44 2020 >> started

Wed Mar  4 06:56:48 2020 >> done (3.534s)
2650602 reads processed; of these:
 118381 ( 4.47%) short reads filtered out after trimming by size control
   6260 ( 0.24%) empty reads filtered out after trimming by size control
2525961 (95.30%) reads available; of these:
2483385 (98.31%) trimmed reads available after processing
  42576 ( 1.69%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13645	  0.54%
 19	  31743	  1.26%
 20	 141868	  5.62%
 21	 331744	 13.13%
 22	 999219	 39.56%
 23	 467639	 18.51%
 24	 162208	  6.42%
 25	  27079	  1.07%
 26	  13256	  0.52%
 27	  12281	  0.49%
 28	  13721	  0.54%
 29	  10175	  0.40%
 30	  18233	  0.72%
 31	  19392	  0.77%
 32	  23402	  0.93%
 33	  45139	  1.79%
 34	  19699	  0.78%
 35	  12574	  0.50%
 36	  14180	  0.56%
 37	   9066	  0.36%
 38	   9978	  0.40%
 39	   8977	  0.36%
 40	  12457	  0.49%
 41	  16530	  0.65%
 42	  16460	  0.65%
 43	  11839	  0.47%
 44	   9378	  0.37%
 45	   9855	  0.39%
 46	   7171	  0.28%
 47	   5036	  0.20%
 48	    699	  0.03%
 49	   1027	  0.04%
 50	  30291	  1.20%


criterion=sequence-density
sequence-density=6.80
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.45
sequence-density-rank=26
fanout-score=16.71
fanout-score-rank=1
prefix-density=7.47
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 06:57:37
                             Started mapping on |	Mar 04 06:57:38
                                    Finished on |	Mar 04 06:58:08
       Mapping speed, Million of reads per hour |	310.11

                          Number of input reads |	2584216
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1280112
                        Uniquely mapped reads % |	49.54%
                          Average mapped length |	23.24
                       Number of splices: Total |	1171
            Number of splices: Annotated (sjdb) |	116
                       Number of splices: GT/AG |	1091
                       Number of splices: GC/AG |	12
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	67
                      Mismatch rate per base, % |	0.11%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.73
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1106413
             % of reads mapped to multiple loci |	42.81%
        Number of reads mapped to too many loci |	34274
             % of reads mapped to too many loci |	1.33%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.75%
                     % of reads unmapped: other |	0.57%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	197691	197691	197691
N_multimapping	1106413	1106413	1106413
N_noFeature	43642	53073	955740
N_ambiguous	702001	421534	7291
UnstrandedReadsAssigned:534469 PositiveStrandReadsAssigned:805505 NegativeStrandReadsAssigned:317081
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030970 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: SRR5030970-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,584,216 reads, 542,019 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,103 rounds

 109283 SRR5030970.ke.tsv
  52636 SRR5030970.se.tsv
 161919 total
==> SRR5030970.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

==> SRR5030970.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030970 completed mapping pipeline successfully
