Starting /dee2/code/volunteer_pipeline.sh SRR5030906
    current disk space = 160657866752
    free memory = 73951208 
SRR5030906 SRAfilesize
5fca76f45dbc9dedb04b0465f383fab1  SRR5030906.sra
SRR5030906.sra file validated
SRR5030906 is single end
SRR5030906 is conventional basespace
SRR5030906 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030906_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.32175	33.0	31.0	34.0	31.0	34.0
2	32.6805	34.0	31.0	34.0	31.0	34.0
3	32.737	34.0	31.0	34.0	31.0	34.0
4	36.18275	37.0	37.0	37.0	35.0	37.0
5	36.265	37.0	37.0	37.0	35.0	37.0
6	35.90575	37.0	35.0	37.0	35.0	37.0
7	36.06725	37.0	35.0	37.0	35.0	37.0
8	36.14475	37.0	36.0	37.0	35.0	37.0
9	37.86075	39.0	38.0	39.0	35.0	39.0
10	37.9015	39.0	38.0	39.0	35.0	39.0
11	37.80225	39.0	38.0	39.0	35.0	39.0
12	37.84525	39.0	38.0	39.0	35.0	39.0
13	37.82575	39.0	38.0	39.0	35.0	39.0
14	39.2375	41.0	39.0	41.0	36.0	41.0
15	39.17775	41.0	39.0	41.0	36.0	41.0
16	38.95275	40.0	38.0	41.0	35.0	41.0
17	39.2315	41.0	39.0	41.0	36.0	41.0
18	39.25225	41.0	39.0	41.0	36.0	41.0
19	38.99675	40.0	39.0	41.0	36.0	41.0
20	39.186	40.0	39.0	41.0	36.0	41.0
21	39.16325	41.0	39.0	41.0	36.0	41.0
22	39.2695	41.0	39.0	41.0	36.0	41.0
23	39.037	40.0	39.0	41.0	36.0	41.0
24	38.3325	40.0	38.0	41.0	34.0	41.0
25	38.6435	40.0	38.0	41.0	34.0	41.0
26	38.74625	40.0	38.0	41.0	34.0	41.0
27	38.65525	40.0	38.0	41.0	34.0	41.0
28	38.81	40.0	38.0	41.0	35.0	41.0
29	38.908	40.0	38.0	41.0	35.0	41.0
30	38.77275	40.0	38.0	41.0	35.0	41.0
31	38.91625	40.0	38.0	41.0	35.0	41.0
32	39.022	41.0	39.0	41.0	35.0	41.0
33	37.4965	40.0	38.0	41.0	32.0	41.0
34	37.28175	40.0	38.0	41.0	31.0	41.0
35	33.373	38.0	32.0	40.0	15.0	41.0
36	28.868	37.0	15.0	40.0	8.0	41.0
37	29.2305	35.0	22.0	39.0	6.0	40.0
38	32.1985	37.0	30.0	39.0	15.0	41.0
39	31.9365	37.0	30.0	40.0	8.0	41.0
40	32.779	38.0	32.0	40.0	8.0	41.0
41	30.626	37.0	27.0	40.0	2.0	41.0
42	32.089	37.0	31.0	40.0	2.0	41.0
43	30.5735	37.0	27.0	40.0	2.0	41.0
44	31.655	38.0	31.0	40.0	2.0	41.0
45	29.037	36.0	24.0	40.0	2.0	41.0
46	26.984	34.0	13.0	39.0	2.0	41.0
47	27.3635	35.0	15.0	40.0	2.0	41.0
48	28.27075	36.0	21.0	40.0	2.0	41.0
49	26.2215	35.0	2.0	40.0	2.0	41.0
50	23.0955	30.0	2.0	38.0	2.0	40.0
>>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
15	1.0
16	0.0
17	4.0
18	4.0
19	6.0
20	8.0
21	15.0
22	32.0
23	32.0
24	44.0
25	63.0
26	81.0
27	159.0
28	70.0
29	111.0
30	112.0
31	182.0
32	163.0
33	157.0
34	239.0
35	287.0
36	326.0
37	409.0
38	585.0
39	910.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.043096968178402	24.17940365823102	54.698070658982715	13.079428714607868
2	24.125	27.85	22.375	25.650000000000002
3	17.2	18.675	19.6	44.525
4	24.625	37.875	14.575	22.925
5	22.275	37.525	29.175	11.025
6	33.625	15.675	39.800000000000004	10.9
7	14.325	23.225	26.275	36.175000000000004
8	25.05	42.05	13.025	19.875
9	16.225	40.9	31.025000000000002	11.85
10	19.950000000000003	20.424999999999997	26.825	32.800000000000004
11	33.300000000000004	13.5	12.85	40.35
12	16.1	17.825	23.575	42.5
13	20.925	21.625	38.35	19.1
14	37.824999999999996	22.45	25.7	14.025000000000002
15	36.25	20.674999999999997	29.475	13.600000000000001
16	12.475	25.1	21.675	40.75
17	24.425	23.25	38.125	14.2
18	28.875	17.9	29.925	23.3
19	36.8	14.649999999999999	31.175000000000004	17.375
20	49.9	16.650000000000002	22.175	11.275
21	21.15	27.825	23.05	27.975
22	32.125	14.124999999999998	46.300000000000004	7.449999999999999
23	22.6	13.525	50.675000000000004	13.200000000000001
24	49.775000000000006	12.275	30.675	7.2749999999999995
25	57.15	19.650000000000002	13.750000000000002	9.45
26	33.025	46.425	10.65	9.9
27	13.875000000000002	55.2	19.975	10.95
28	8.9	31.525	49.0	10.575
29	8.3	12.174999999999999	62.0	17.525
30	9.1	5.75	42.1	43.05
31	11.55	4.675	46.325	37.45
32	23.65	6.0	26.375	43.974999999999994
33	52.025	6.2	13.925	27.85
34	69.125	5.75	10.549999999999999	14.575
35	65.14999999999999	6.950000000000001	18.6	9.3
36	65.64999999999999	7.85	16.975	9.525
37	40.025	8.85	27.0	24.125
38	28.775000000000002	10.549999999999999	13.950000000000001	46.725
39	15.35	23.3	7.475	53.87499999999999
40	11.875	48.675000000000004	9.45	30.0
41	24.45	53.025	9.35	13.175
42	49.45	34.125	8.475000000000001	7.95
43	55.325	28.249999999999996	8.799999999999999	7.625
44	34.1	47.949999999999996	6.0	11.95
45	15.875	53.77499999999999	8.6	21.75
46	9.45	33.525	23.150000000000002	33.875
47	8.3	14.325	35.099999999999994	42.275
48	8.825	8.9	26.900000000000002	55.375
49	11.1	23.549999999999997	12.174999999999999	53.175
50	26.825	28.575	7.55	37.05
>>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	0.5
10	1.0
11	0.5
12	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	1.0
18	2.0
19	1.0
20	0.0
21	1.0
22	2.0
23	2.0
24	2.0
25	1.5
26	1.0
27	0.5
28	0.0
29	1.0
30	2.0
31	5.5
32	9.0
33	14.5
34	20.0
35	29.0
36	38.0
37	50.5
38	63.0
39	57.0
40	51.0
41	54.5
42	58.0
43	78.5
44	99.0
45	179.0
46	259.0
47	327.0
48	395.0
49	513.5
50	632.0
51	795.0
52	958.0
53	706.5
54	455.0
55	385.0
56	315.0
57	307.5
58	300.0
59	207.0
60	114.0
61	90.5
62	67.0
63	72.0
64	77.0
65	51.5
66	26.0
67	16.5
68	7.0
69	12.0
70	17.0
71	18.5
72	20.0
73	11.5
74	3.0
75	2.0
76	1.0
77	1.0
78	1.0
79	1.5
80	2.0
81	1.5
82	1.0
83	0.5
84	0.0
85	0.0
86	0.0
87	0.5
88	1.0
89	0.5
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.22499999999999998
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	0.0
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	49.125
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.40712468193384	39.5
2	7.684478371501273	7.55
3	3.6641221374045805	5.4
4	1.88295165394402	3.6999999999999997
5	1.1195928753180662	2.75
6	1.0687022900763359	3.15
7	0.5597964376590331	1.925
8	0.5597964376590331	2.1999999999999997
9	0.356234096692112	1.575
>10	2.595419847328244	24.375
>50	0.05089058524173028	1.975
>100	0.05089058524173028	5.8999999999999995
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	236	5.8999999999999995	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	79	1.975	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	30	0.75	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGC	26	0.65	RNA PCR Primer, Index 29 (100% over 50bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	21	0.525	RNA PCR Primer, Index 1 (96% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	15	0.375	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	14	0.35000000000000003	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTC	11	0.27499999999999997	RNA PCR Primer, Index 29 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	11	0.27499999999999997	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	10	0.25	RNA PCR Primer, Index 7 (100% over 35bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	9	0.22499999999999998	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CAGCAGCACACTGTGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	8	0.2	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	7	0.17500000000000002	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	7	0.17500000000000002	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	7	0.17500000000000002	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	7	0.17500000000000002	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACAGAAATATTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGTGGAATTCTCGGGTGC	6	0.15	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	6	0.15	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	5	0.125	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
ACGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACCCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 24bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCAA	5	0.125	RNA PCR Primer, Index 1 (96% over 26bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GAGCAATGATGACCCCAACATGCCATCTGAGTGGCTTTGCTGAAATCCAG	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	0.7	0.0	0.0	0.0
2	0.0	0.7	0.0	0.0	0.0
3	0.0	0.75	0.0	0.0	0.0
4	0.0	0.775	0.0	0.0	0.0
5	0.0	0.825	0.0	0.0	0.0
6	0.0	0.9	0.0	0.0	0.0
7	0.0	1.275	0.0	0.0	0.0
8	0.0	1.35	0.0	0.0	0.0
9	0.0	1.35	0.0	0.0	0.0
10	0.0	1.45	0.0	0.0	0.0
11	0.0	1.55	0.0	0.0	0.0
12	0.0	1.65	0.0	0.0	0.0
13	0.0	1.75	0.0	0.0	0.0
14	0.0	1.875	0.0	0.0	0.0
15	0.0	2.0	0.0	0.0	0.0
16	0.0	2.525	0.0	0.0	0.0
17	0.0	2.825	0.0	0.0	0.0
18	0.0	3.75	0.0	0.0	0.0
19	0.0	4.075	0.0	0.0	0.0
20	0.0	5.025	0.0	0.0	0.0
21	0.0	8.4	0.0	0.0	0.0
22	0.0	18.55	0.0	0.0	0.0
23	0.0	49.325	0.0	0.0	0.0
24	0.0	68.4	0.0	0.0	0.0
25	0.0	74.375	0.0	0.0	0.0
26	0.0	75.15	0.0	0.0	0.0
27	0.0	75.5	0.0	0.0	0.0
28	0.0	75.85	0.0	0.0	0.0
29	0.0	76.075	0.0	0.0	0.0
30	0.0	76.375	0.0	0.0	0.0
31	0.0	76.9	0.0	0.0	0.0
32	0.0	77.975	0.0	0.0	0.0
33	0.0	78.975	0.0	0.0	0.0
34	0.0	80.525	0.0	0.0	0.0
35	0.0	81.55	0.0	0.0	0.0
36	0.0	82.175	0.0	0.0	0.0
37	0.0	82.8	0.0	0.0	0.0
38	0.0	83.2	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	45	2.728484E-10	44.000004	8
GGTTGTA	20	6.952051E-4	44.000004	11
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
ACGCTGT	45	2.728484E-10	44.000004	9
AATCCAG	20	6.952051E-4	44.000004	8
ATCCAGG	20	6.952051E-4	44.000004	9
AGTAGGT	20	6.952051E-4	44.000004	7
TTCAAGT	20	6.952051E-4	44.000004	1
TTCAACG	45	2.728484E-10	44.000004	5
CGGGGCC	20	6.952051E-4	44.000004	32
AGGATAG	20	6.952051E-4	44.000004	13
TCGGTGA	40	5.315087E-9	44.000004	15
ATAGGCT	20	6.952051E-4	44.000004	16
CATTCAA	45	2.728484E-10	44.000004	3
TCAACGC	45	2.728484E-10	44.000004	6
TCCAGGA	20	6.952051E-4	44.000004	10
ACATCCT	20	6.952051E-4	44.000004	6
ACATTCA	45	2.728484E-10	44.000004	2
GGATAGG	20	6.952051E-4	44.000004	14
>>END_MODULE
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412000 spots for SRR5030906.sra
Written 412000 spots for SRR5030906.sra
Read 412003 spots for SRR5030906.sra
Written 412003 spots for SRR5030906.sra
SRR ids: ['SRR5030906.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_vu2ubmub
SRR5030906.sra spots: 4944003
blocks: [[1, 412000], [412001, 824000], [824001, 1236000], [1236001, 1648000], [1648001, 2060000], [2060001, 2472000], [2472001, 2884000], [2884001, 3296000], [3296001, 3708000], [3708001, 4120000], [4120001, 4532000], [4532001, 4944003]]
SRR5030906 file size 855835
SRR5030906 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030906 SRR5030906_1.fastq
Input file:	SRR5030906_1.fastq
trimmed:	SRR5030906-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 06:41:28 2020 >> started

Wed Mar  4 06:41:31 2020 >> done (2.809s)
4944003 reads processed; of these:
    267 ( 0.01%) short reads filtered out after trimming by size control
     11 ( 0.00%) empty reads filtered out after trimming by size control
4943725 (99.99%) reads available; of these:
 568365 (11.50%) trimmed reads available after processing
4375360 (88.50%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     70	  0.00%
 19	     79	  0.00%
 20	    162	  0.00%
 21	    248	  0.01%
 22	    468	  0.01%
 23	    583	  0.01%
 24	    552	  0.01%
 25	    648	  0.01%
 26	    607	  0.01%
 27	    764	  0.02%
 28	   1039	  0.02%
 29	   2355	  0.05%
 30	   1182	  0.02%
 31	   1648	  0.03%
 32	   4160	  0.08%
 33	  13705	  0.28%
 34	  43590	  0.88%
 35	   9599	  0.19%
 36	  11100	  0.22%
 37	   5230	  0.11%
 38	  10740	  0.22%
 39	   9070	  0.18%
 40	  21499	  0.43%
 41	  11213	  0.23%
 42	  33153	  0.67%
 43	  12813	  0.26%
 44	  66531	  1.35%
 45	  32072	  0.65%
 46	  26342	  0.53%
 47	  30653	  0.62%
 48	 113288	  2.29%
 49	 103202	  2.09%
 50	4375360	 88.50%
4943725 reads passed initial QC


criterion=sequence-density
sequence-density=82.36
sequence-density-rank=1
fanout-score=18.03
fanout-score-rank=3
prefix-density=84.81
prefix-fanout=17.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC


criterion=fanout-score
sequence-density=1.30
sequence-density-rank=12
fanout-score=563.46
fanout-score-rank=1
prefix-density=84.08
prefix-fanout=8.7
sequence=GGAATTCTCGGTGCCAAGGA
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC -o SRR5030906 -
Input file:	STDIN
trimmed:	SRR5030906-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC
-- 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 06:41:55 2020 >> started

Wed Mar  4 06:42:01 2020 >> done (6.527s)
4824599 reads processed; of these:
 160711 ( 3.33%) short reads filtered out after trimming by size control
  22218 ( 0.46%) empty reads filtered out after trimming by size control
4641670 (96.21%) reads available; of these:
4131915 (89.02%) trimmed reads available after processing
 509755 (10.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  22781	  0.49%
 19	  44512	  0.96%
 20	 181659	  3.91%
 21	 511818	 11.03%
 22	1545198	 33.29%
 23	 854264	 18.40%
 24	 284804	  6.14%
 25	  47984	  1.03%
 26	  23238	  0.50%
 27	  22021	  0.47%
 28	  24363	  0.52%
 29	  20116	  0.43%
 30	  35217	  0.76%
 31	  49507	  1.07%
 32	  43695	  0.94%
 33	  83971	  1.81%
 34	  40259	  0.87%
 35	  27446	  0.59%
 36	  38015	  0.82%
 37	  17871	  0.39%
 38	  21711	  0.47%
 39	  19862	  0.43%
 40	  29079	  0.63%
 41	  35000	  0.75%
 42	  45697	  0.98%
 43	  30114	  0.65%
 44	  31231	  0.67%
 45	  30029	  0.65%
 46	  24486	  0.53%
 47	  18983	  0.41%
 48	   9064	  0.20%
 49	  15417	  0.33%
 50	 412258	  8.88%


criterion=sequence-density
sequence-density=5.23
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=21
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.46
sequence-density-rank=30
fanout-score=10.04
fanout-score-rank=1
prefix-density=0.82
prefix-fanout=5.6
sequence=GGAATTCTCGGGGCCCAGG
                                 Started job on |	Mar 04 06:42:50
                             Started mapping on |	Mar 04 06:42:51
                                    Finished on |	Mar 04 06:43:41
       Mapping speed, Million of reads per hour |	342.78

                          Number of input reads |	4760796
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2287669
                        Uniquely mapped reads % |	48.05%
                          Average mapped length |	26.89
                       Number of splices: Total |	2350
            Number of splices: Annotated (sjdb) |	280
                       Number of splices: GT/AG |	2135
                       Number of splices: GC/AG |	35
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	179
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.30
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.06
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1974776
             % of reads mapped to multiple loci |	41.48%
        Number of reads mapped to too many loci |	88993
             % of reads mapped to too many loci |	1.87%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.05%
                     % of reads unmapped: other |	0.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	498351	498351	498351
N_multimapping	1974776	1974776	1974776
N_noFeature	111099	129944	1803012
N_ambiguous	1210656	796966	16504
UnstrandedReadsAssigned:965914 PositiveStrandReadsAssigned:1360759 NegativeStrandReadsAssigned:468153
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030906 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: SRR5030906-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,760,796 reads, 895,858 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 853 rounds

 109283 SRR5030906.ke.tsv
  52636 SRR5030906.se.tsv
 161919 total
==> SRR5030906.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

==> SRR5030906.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	3
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030906 completed mapping pipeline successfully
