Starting /dee2/code/volunteer_pipeline.sh SRR5030955
    current disk space = 160604323840
    free memory = 73937620 
SRR5030955 SRAfilesize
43dffa10fa97876933aade16e621c755  SRR5030955.sra
SRR5030955.sra file validated
SRR5030955 is single end
SRR5030955 is conventional basespace
SRR5030955 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030955_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	32.392	34.0	31.0	34.0	31.0	34.0
2	32.65425	34.0	31.0	34.0	31.0	34.0
3	32.8525	34.0	31.0	34.0	31.0	34.0
4	36.2865	37.0	37.0	37.0	35.0	37.0
5	36.337	37.0	37.0	37.0	35.0	37.0
6	36.225	37.0	37.0	37.0	35.0	37.0
7	36.194	37.0	36.0	37.0	35.0	37.0
8	36.234	37.0	37.0	37.0	35.0	37.0
9	37.94075	39.0	38.0	39.0	35.0	39.0
10	37.93825	39.0	38.0	39.0	35.0	39.0
11	37.7925	39.0	38.0	39.0	35.0	39.0
12	37.828	39.0	38.0	39.0	35.0	39.0
13	37.795	39.0	38.0	39.0	35.0	39.0
14	39.21275	41.0	39.0	41.0	36.0	41.0
15	39.15925	40.0	39.0	41.0	36.0	41.0
16	39.22875	40.0	39.0	41.0	36.0	41.0
17	39.3445	41.0	39.0	41.0	36.0	41.0
18	39.2665	41.0	39.0	41.0	36.0	41.0
19	38.98475	40.0	39.0	41.0	35.0	41.0
20	39.06675	40.0	39.0	41.0	36.0	41.0
21	39.19475	40.0	39.0	41.0	36.0	41.0
22	39.111	40.0	39.0	41.0	36.0	41.0
23	38.91725	40.0	38.0	41.0	35.0	41.0
24	38.4975	40.0	38.0	41.0	34.0	41.0
25	38.74925	40.0	38.0	41.0	34.0	41.0
26	38.781	40.0	38.0	41.0	35.0	41.0
27	38.844	40.0	38.0	41.0	35.0	41.0
28	38.6305	40.0	38.0	41.0	34.0	41.0
29	37.70825	40.0	38.0	41.0	31.0	41.0
30	38.07975	40.0	38.0	41.0	33.0	41.0
31	38.40075	40.0	38.0	41.0	34.0	41.0
32	38.68425	40.0	38.0	41.0	34.0	41.0
33	38.0015	40.0	38.0	41.0	33.0	41.0
34	38.03875	40.0	38.0	41.0	33.0	41.0
35	37.884	40.0	38.0	41.0	33.0	41.0
36	34.3675	38.0	31.0	40.0	23.0	41.0
37	35.755	38.0	35.0	40.0	30.0	41.0
38	36.9135	39.0	37.0	40.0	31.0	41.0
39	36.91325	39.0	37.0	40.0	31.0	41.0
40	36.921	39.0	37.0	40.0	31.0	41.0
41	37.09025	39.0	37.0	41.0	32.0	41.0
42	37.38025	40.0	37.0	41.0	32.0	41.0
43	37.202	40.0	37.0	41.0	32.0	41.0
44	37.0155	40.0	37.0	41.0	31.0	41.0
45	36.8195	39.0	36.0	41.0	31.0	41.0
46	34.97	38.0	34.0	40.0	26.0	41.0
47	35.70725	39.0	35.0	40.0	28.0	41.0
48	35.96625	39.0	35.0	41.0	30.0	41.0
49	34.98325	38.0	35.0	40.0	27.0	41.0
50	30.20975	34.0	27.0	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
11	1.0
12	1.0
13	0.0
14	0.0
15	3.0
16	1.0
17	1.0
18	0.0
19	2.0
20	1.0
21	3.0
22	10.0
23	12.0
24	9.0
25	19.0
26	25.0
27	17.0
28	38.0
29	30.0
30	51.0
31	68.0
32	83.0
33	116.0
34	159.0
35	235.0
36	294.0
37	545.0
38	999.0
39	1277.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.364776718514802	22.10235825388861	51.5805318615153	14.952333166081285
2	20.875	26.025	19.725	33.375
3	26.474999999999998	16.45	23.45	33.625
4	31.65	29.049999999999997	14.45	24.85
5	19.375	41.85	23.425	15.35
6	28.725	18.6	39.25	13.425
7	18.375	19.975	23.625	38.025
8	23.3	30.2	14.499999999999998	32.0
9	26.3	32.275	27.474999999999998	13.950000000000001
10	23.65	18.75	33.35	24.25
11	29.4	15.45	15.950000000000001	39.2
12	14.099999999999998	19.525000000000002	34.225	32.15
13	28.599999999999998	20.599999999999998	28.125	22.675
14	26.724999999999998	34.5	19.35	19.425
15	36.78419604901225	23.53088272068017	24.90622655663916	14.778694673668417
16	15.8	23.9	21.875	38.425
17	23.549999999999997	20.8	39.65	16.0
18	22.05	17.299999999999997	36.775000000000006	23.875
19	36.375	16.2	29.7	17.724999999999998
20	43.6	17.224999999999998	24.375	14.799999999999999
21	22.650000000000002	19.425	25.825	32.1
22	28.15	14.625	46.975	10.25
23	25.5	14.625	43.8	16.075
24	49.925000000000004	16.675	23.799999999999997	9.6
25	48.575	24.0	15.1	12.325
26	25.85	46.9	15.174999999999999	12.075
27	17.349999999999998	46.375	23.875	12.4
28	13.3	23.974999999999998	47.699999999999996	15.024999999999999
29	10.05	15.45	56.625	17.875
30	10.775	8.725	33.900000000000006	46.6
31	14.825	7.1499999999999995	47.075	30.95
32	26.724999999999998	8.4	20.225	44.65
33	53.849999999999994	9.6	14.274999999999999	22.275
34	58.074999999999996	9.375	17.299999999999997	15.25
35	61.025	9.3	18.275	11.4
36	41.449999999999996	10.825	34.599999999999994	13.125
37	45.475	11.475	19.0	24.05
38	21.725	16.900000000000002	13.675	47.699999999999996
39	16.675	25.2	9.575	48.55
40	16.125	47.475	12.2	24.2
41	24.224999999999998	46.9	10.424999999999999	18.45
42	49.825	29.7	10.549999999999999	9.925
43	48.9	32.6	9.675	8.825
44	26.924999999999997	49.525000000000006	8.975	14.575
45	18.15	50.525	14.000000000000002	17.325
46	11.675	27.825	19.15	41.349999999999994
47	9.325	17.275	38.875	34.525
48	10.575	14.649999999999999	18.875	55.900000000000006
49	14.05	20.5	14.35	51.1
50	19.15	37.675	13.675	29.5
>>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	0.0
14	0.0
15	0.0
16	0.0
17	1.0
18	2.0
19	2.0
20	2.0
21	1.5
22	1.0
23	0.5
24	0.0
25	1.0
26	2.0
27	2.5
28	3.0
29	4.0
30	5.0
31	18.0
32	31.0
33	29.5
34	28.0
35	47.5
36	67.0
37	68.0
38	69.0
39	63.0
40	57.0
41	66.0
42	75.0
43	99.0
44	123.0
45	170.5
46	218.0
47	331.0
48	444.0
49	505.5
50	567.0
51	644.5
52	722.0
53	570.0
54	418.0
55	474.5
56	531.0
57	441.0
58	351.0
59	217.0
60	83.0
61	62.0
62	41.0
63	57.5
64	74.0
65	52.0
66	30.0
67	19.0
68	8.0
69	10.5
70	13.0
71	19.5
72	26.0
73	15.0
74	4.0
75	2.0
76	0.0
77	1.0
78	2.0
79	1.5
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	0.35000000000000003
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	0.025
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	41.875
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.58208955223881	31.65
2	10.029850746268657	8.4
3	3.940298507462687	4.95
4	2.8656716417910446	4.8
5	1.1343283582089554	2.375
6	1.2537313432835822	3.15
7	0.7761194029850746	2.275
8	1.0149253731343284	3.4000000000000004
9	0.3582089552238806	1.35
>10	2.626865671641791	21.075
>50	0.23880597014925373	7.199999999999999
>100	0.1791044776119403	9.375
>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
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	166	4.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	106	2.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	103	2.5749999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	78	1.95	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	72	1.7999999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	70	1.7500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	31	0.775	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCC	29	0.7250000000000001	RNA PCR Primer, Index 5 (97% over 35bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTC	23	0.575	RNA PCR Primer, Index 36 (100% over 44bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	21	0.525	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	20	0.5	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	19	0.475	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	16	0.4	No Hit
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	13	0.325	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	11	0.27499999999999997	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGC	10	0.25	RNA PCR Primer, Index 36 (100% over 50bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	9	0.22499999999999998	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	9	0.22499999999999998	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	8	0.2	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	8	0.2	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	8	0.2	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	8	0.2	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	8	0.2	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	7	0.17500000000000002	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	7	0.17500000000000002	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	7	0.17500000000000002	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	7	0.17500000000000002	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCAGCATCAGTGATTTTGTTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	6	0.15	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGATCCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAGCCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	5	0.125	No Hit
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	5	0.125	No Hit
TCGTACCGTGAGTAATAATGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CCTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCT	5	0.125	No Hit
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	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	0.25	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.35	0.0	0.0	0.0
4	0.0	0.375	0.0	0.0	0.0
5	0.0	0.425	0.0	0.0	0.0
6	0.0	0.45	0.0	0.0	0.0
7	0.0	1.15	0.0	0.0	0.0
8	0.0	1.325	0.0	0.0	0.0
9	0.0	1.35	0.0	0.0	0.0
10	0.0	1.475	0.0	0.0	0.0
11	0.0	1.775	0.0	0.0	0.0
12	0.0	1.975	0.0	0.0	0.0
13	0.0	2.2	0.0	0.0	0.0
14	0.0	2.375	0.0	0.0	0.0
15	0.0	2.925	0.0	0.0	0.0
16	0.0	4.3	0.0	0.0	0.0
17	0.0	4.95	0.0	0.0	0.0
18	0.0	6.0	0.0	0.0	0.0
19	0.0	6.425	0.0	0.0	0.0
20	0.0	7.075	0.0	0.0	0.0
21	0.0	12.525	0.0	0.0	0.0
22	0.0	22.925	0.0	0.0	0.0
23	0.0	52.1	0.0	0.0	0.0
24	0.0	62.4	0.0	0.0	0.0
25	0.0	68.225	0.0	0.0	0.0
26	0.0	69.8	0.0	0.0	0.0
27	0.0	70.3	0.0	0.0	0.0
28	0.0	70.825	0.0	0.0	0.0
29	0.0	71.275	0.0	0.0	0.0
30	0.0	71.55	0.0	0.0	0.0
31	0.0	72.425	0.0	0.0	0.0
32	0.0	73.375	0.0	0.0	0.0
33	0.0	74.25	0.0	0.0	0.0
34	0.0	75.95	0.0	0.0	0.0
35	0.0	76.925	0.0	0.0	0.0
36	0.0	77.45	0.0	0.0	0.0
37	0.0	78.175	0.0	0.0	0.0
38	0.0	78.75	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	20	6.952051E-4	44.000004	2
TTGCACT	20	6.952051E-4	44.000004	3
CTGAGCT	80	0.0	44.000004	11
CCCGGCC	20	6.952051E-4	44.000004	13
GAGCTTG	80	0.0	44.000004	13
GGATCCG	80	0.0	44.000004	3
CCGTCTG	80	0.0	44.000004	7
TCGGATC	80	0.0	44.000004	1
CGGATCC	80	0.0	44.000004	2
TATTGCA	20	6.952051E-4	44.000004	1
CTTGGTG	20	6.952051E-4	44.000004	16
GTCCCGG	20	6.952051E-4	44.000004	11
ATTGCAC	20	6.952051E-4	44.000004	2
GATCCGT	80	0.0	44.000004	4
GGCTTGG	45	2.728484E-10	44.000004	19
GGCCAAG	20	6.952051E-4	44.000004	36
GGTAGTA	20	6.952051E-4	44.000004	4
TGAGGTA	20	6.952051E-4	44.000004	1
TTGGTGG	20	6.952051E-4	44.000004	17
TCCGTCT	80	0.0	44.000004	6
>>END_MODULE
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
Read 298313 spots for SRR5030955.sra
Written 298313 spots for SRR5030955.sra
SRR ids: ['SRR5030955.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_xy83o28n
SRR5030955.sra spots: 3579756
blocks: [[1, 298313], [298314, 596626], [596627, 894939], [894940, 1193252], [1193253, 1491565], [1491566, 1789878], [1789879, 2088191], [2088192, 2386504], [2386505, 2684817], [2684818, 2983130], [2983131, 3281443], [3281444, 3579756]]
SRR5030955 file size 619378
SRR5030955 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030955 SRR5030955_1.fastq
Input file:	SRR5030955_1.fastq
trimmed:	SRR5030955-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 06:53:01 2020 >> started

Wed Mar  4 06:53:03 2020 >> done (1.966s)
3579756 reads processed; of these:
    157 ( 0.00%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
3579589 (100.00%) reads available; of these:
 215920 ( 6.03%) trimmed reads available after processing
3363669 (93.97%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     57	  0.00%
 19	     73	  0.00%
 20	    165	  0.00%
 21	    218	  0.01%
 22	    395	  0.01%
 23	    429	  0.01%
 24	    502	  0.01%
 25	    628	  0.02%
 26	    492	  0.01%
 27	    655	  0.02%
 28	    901	  0.03%
 29	   1342	  0.04%
 30	    895	  0.03%
 31	   1171	  0.03%
 32	   1160	  0.03%
 33	   1456	  0.04%
 34	   2613	  0.07%
 35	   2861	  0.08%
 36	   2168	  0.06%
 37	   2630	  0.07%
 38	   2812	  0.08%
 39	   3210	  0.09%
 40	   3435	  0.10%
 41	   3812	  0.11%
 42	   4956	  0.14%
 43	   6401	  0.18%
 44	  11148	  0.31%
 45	  14901	  0.42%
 46	  14626	  0.41%
 47	  21994	  0.61%
 48	  42533	  1.19%
 49	  65281	  1.82%
 50	3363669	 93.97%
3579589 reads passed initial QC


criterion=sequence-density
sequence-density=78.91
sequence-density-rank=1
fanout-score=19.30
fanout-score-rank=1
prefix-density=81.11
prefix-fanout=18.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC


criterion=fanout-score
sequence-density=78.91
sequence-density-rank=1
fanout-score=19.30
fanout-score-rank=1
prefix-density=81.11
prefix-fanout=18.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC -o SRR5030955 -
Input file:	STDIN
trimmed:	SRR5030955-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC
-- 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 06:53:21 2020 >> started

Wed Mar  4 06:53:27 2020 >> done (5.373s)
3488967 reads processed; of these:
 197246 ( 5.65%) short reads filtered out after trimming by size control
  11463 ( 0.33%) empty reads filtered out after trimming by size control
3280258 (94.02%) reads available; of these:
2868045 (87.43%) trimmed reads available after processing
 412213 (12.57%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17712	  0.54%
 19	  27478	  0.84%
 20	 188372	  5.74%
 21	 368792	 11.24%
 22	 982341	 29.95%
 23	 392311	 11.96%
 24	 199207	  6.07%
 25	  59386	  1.81%
 26	  27295	  0.83%
 27	  20614	  0.63%
 28	  22812	  0.70%
 29	  17322	  0.53%
 30	  24040	  0.73%
 31	  33481	  1.02%
 32	  33271	  1.01%
 33	  73381	  2.24%
 34	  36638	  1.12%
 35	  29312	  0.89%
 36	  32060	  0.98%
 37	  20102	  0.61%
 38	  21893	  0.67%
 39	  22650	  0.69%
 40	  34635	  1.06%
 41	  37177	  1.13%
 42	  41171	  1.26%
 43	  30521	  0.93%
 44	  26348	  0.80%
 45	  35393	  1.08%
 46	  24669	  0.75%
 47	  18419	  0.56%
 48	   4532	  0.14%
 49	  14974	  0.46%
 50	 361949	 11.03%


criterion=sequence-density
sequence-density=5.30
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.55
sequence-density-rank=23
fanout-score=19.50
fanout-score-rank=1
prefix-density=10.77
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 06:54:05
                             Started mapping on |	Mar 04 06:54:06
                                    Finished on |	Mar 04 06:54:30
       Mapping speed, Million of reads per hour |	505.63

                          Number of input reads |	3370880
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2097706
                        Uniquely mapped reads % |	62.23%
                          Average mapped length |	27.66
                       Number of splices: Total |	1692
            Number of splices: Annotated (sjdb) |	406
                       Number of splices: GT/AG |	1533
                       Number of splices: GC/AG |	26
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	133
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.57
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.06
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	912443
             % of reads mapped to multiple loci |	27.07%
        Number of reads mapped to too many loci |	73280
             % of reads mapped to too many loci |	2.17%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.63%
                     % of reads unmapped: other |	0.90%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	360731	360731	360731
N_multimapping	912443	912443	912443
N_noFeature	77414	102653	1403188
N_ambiguous	1168334	555921	18802
UnstrandedReadsAssigned:851958 PositiveStrandReadsAssigned:1439132 NegativeStrandReadsAssigned:675716
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030955 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: SRR5030955-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,370,880 reads, 953,014 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,169 rounds

 109283 SRR5030955.ke.tsv
  52636 SRR5030955.se.tsv
 161919 total
==> SRR5030955.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

==> SRR5030955.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	1
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030955 completed mapping pipeline successfully
