Starting /dee2/code/volunteer_pipeline.sh SRR5030875
    current disk space = 160653033472
    free memory = 73955040 
SRR5030875 SRAfilesize
703b47e0a9a2e4d4d7c24810672e200f  SRR5030875.sra
SRR5030875.sra file validated
SRR5030875 is single end
SRR5030875 is conventional basespace
SRR5030875 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030875_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	52
>>END_MODULE
>>Per base sequence quality	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.26175	33.0	31.0	34.0	31.0	34.0
2	32.69725	34.0	31.0	34.0	31.0	34.0
3	32.71675	34.0	31.0	34.0	31.0	34.0
4	36.17375	37.0	35.0	37.0	35.0	37.0
5	36.19025	37.0	37.0	37.0	35.0	37.0
6	35.941	37.0	35.0	37.0	35.0	37.0
7	36.06975	37.0	35.0	37.0	35.0	37.0
8	36.106	37.0	35.0	37.0	35.0	37.0
9	37.859	39.0	38.0	39.0	35.0	39.0
10	37.8845	39.0	38.0	39.0	35.0	39.0
11	37.8745	39.0	38.0	39.0	35.0	39.0
12	37.8575	39.0	38.0	39.0	35.0	39.0
13	37.81375	39.0	38.0	39.0	35.0	39.0
14	39.21225	41.0	39.0	41.0	36.0	41.0
15	39.1305	41.0	39.0	41.0	36.0	41.0
16	39.12	40.0	39.0	41.0	36.0	41.0
17	39.164	40.0	39.0	41.0	36.0	41.0
18	39.1205	41.0	39.0	41.0	35.0	41.0
19	39.01275	40.0	39.0	41.0	35.0	41.0
20	39.1215	40.0	39.0	41.0	36.0	41.0
21	39.1255	40.0	39.0	41.0	36.0	41.0
22	39.1135	40.0	39.0	41.0	36.0	41.0
23	39.002	40.0	39.0	41.0	35.0	41.0
24	38.24975	40.0	38.0	41.0	33.0	41.0
25	38.46275	40.0	38.0	41.0	34.0	41.0
26	38.5275	40.0	38.0	41.0	34.0	41.0
27	38.634	40.0	38.0	41.0	34.0	41.0
28	38.68525	40.0	38.0	41.0	34.0	41.0
29	38.36975	40.0	38.0	41.0	34.0	41.0
30	38.0865	40.0	38.0	41.0	33.0	41.0
31	38.485	40.0	38.0	41.0	34.0	41.0
32	38.71225	40.0	38.0	41.0	35.0	41.0
33	36.91825	40.0	37.0	41.0	30.0	41.0
34	36.49575	39.0	36.0	41.0	30.0	41.0
35	32.706	38.0	31.0	40.0	15.0	41.0
36	29.79225	37.0	22.0	40.0	8.0	41.0
37	30.09925	36.0	25.0	39.0	6.0	41.0
38	32.50175	37.0	30.0	39.0	18.0	41.0
39	32.12975	37.0	31.0	40.0	8.0	41.0
40	32.84225	37.0	32.0	40.0	8.0	41.0
41	30.858	36.0	28.0	40.0	2.0	41.0
42	32.25025	37.0	31.0	40.0	2.0	41.0
43	30.47075	37.0	28.0	40.0	2.0	41.0
44	31.168	37.0	30.0	40.0	2.0	41.0
45	29.30425	36.0	26.0	40.0	2.0	41.0
46	27.095	35.0	13.0	39.0	2.0	41.0
47	27.07	34.0	15.0	39.0	2.0	41.0
48	27.75625	35.0	18.0	39.0	2.0	41.0
49	25.984	34.0	2.0	39.0	2.0	41.0
50	22.2925	29.0	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
11	1.0
12	1.0
13	0.0
14	1.0
15	1.0
16	0.0
17	5.0
18	2.0
19	4.0
20	10.0
21	11.0
22	32.0
23	34.0
24	32.0
25	59.0
26	90.0
27	149.0
28	70.0
29	104.0
30	173.0
31	176.0
32	138.0
33	160.0
34	249.0
35	289.0
36	357.0
37	443.0
38	654.0
39	755.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.866082603254068	26.558197747183982	42.30287859824781	18.272841051314142
2	25.624999999999996	27.35	20.05	26.974999999999998
3	21.475	20.375	21.65	36.5
4	31.5	29.275000000000002	16.5	22.725
5	21.75	37.8	27.0	13.450000000000001
6	29.125	15.950000000000001	38.5	16.425
7	20.025000000000002	19.2	24.099999999999998	36.675000000000004
8	24.8	32.0	16.150000000000002	27.05
9	19.25	34.575	29.9	16.275000000000002
10	23.599999999999998	20.525	28.849999999999998	27.025
11	37.675	15.049999999999999	14.05	33.225
12	17.5	21.175	29.299999999999997	32.025
13	25.95	20.849999999999998	34.275	18.925
14	29.575000000000003	28.175	21.325	20.925
15	32.625	24.45	25.5	17.424999999999997
16	20.45	20.3	22.525000000000002	36.725
17	25.8	24.375	35.0	14.825
18	24.0	18.8	30.375000000000004	26.825
19	34.775	14.325	32.25	18.65
20	40.325	16.275000000000002	28.175	15.225
21	25.95	22.2	25.525	26.325
22	30.475	13.55	42.525	13.450000000000001
23	25.15	14.424999999999999	42.225	18.2
24	48.525	14.274999999999999	25.674999999999997	11.525
25	47.725	22.125	15.875	14.274999999999999
26	29.25	40.175	14.124999999999998	16.45
27	17.325	43.65	20.724999999999998	18.3
28	15.4	26.075	42.225	16.3
29	15.075	15.049999999999999	52.925	16.950000000000003
30	11.625	9.475	34.449999999999996	44.45
31	14.299999999999999	8.425	45.925	31.35
32	28.225	7.074999999999999	23.974999999999998	40.725
33	46.949999999999996	11.975	16.075	25.0
34	55.35	8.125	17.25	19.275000000000002
35	57.074999999999996	9.0	20.175	13.750000000000002
36	59.45	9.9	17.75	12.9
37	38.25	13.25	23.7	24.8
38	27.625	15.8	14.774999999999999	41.8
39	18.45	23.775	12.625	45.15
40	17.474999999999998	43.125	14.325	25.074999999999996
41	25.6	42.35	13.325000000000001	18.725
42	44.725	30.325000000000003	14.899999999999999	10.05
43	44.625	31.25	11.075	13.05
44	32.225	43.675000000000004	9.775	14.325
45	21.224999999999998	45.425	12.475	20.875
46	16.400000000000002	29.5	23.974999999999998	30.125
47	12.375	16.625	34.425	36.575
48	15.0	11.725	22.725	50.55
49	14.499999999999998	22.3	16.6	46.6
50	29.475	22.85	12.525	35.15
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.5
4	1.0
5	0.5
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.5
14	1.0
15	0.5
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	1.5
26	3.0
27	3.0
28	3.0
29	2.0
30	1.0
31	7.0
32	13.0
33	21.0
34	29.0
35	41.0
36	53.0
37	70.0
38	87.0
39	82.0
40	77.0
41	73.0
42	69.0
43	106.0
44	143.0
45	178.0
46	213.0
47	246.5
48	280.0
49	386.0
50	492.0
51	618.0
52	744.0
53	636.5
54	529.0
55	446.0
56	363.0
57	337.0
58	311.0
59	228.0
60	145.0
61	123.5
62	102.0
63	131.0
64	160.0
65	101.5
66	43.0
67	30.0
68	17.0
69	20.5
70	24.0
71	45.5
72	67.0
73	40.0
74	13.0
75	10.0
76	7.0
77	4.5
78	2.0
79	3.0
80	4.0
81	4.0
82	4.0
83	2.0
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	0.125
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	warn
#Total Deduplicated Percentage	51.725
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.61865635572741	41.699999999999996
2	8.844852585790237	9.15
3	2.803286611889802	4.35
4	1.4983083615273078	3.1
5	0.9666505558240696	2.5
6	0.9666505558240696	3.0
7	0.6766553890768487	2.45
8	0.43499275012083133	1.7999999999999998
9	0.5316578057032383	2.475
>10	2.5616239729337846	23.225
>50	0.0	0.0
>100	0.09666505558240696	6.25
>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	147	3.675	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	103	2.5749999999999997	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	26	0.65	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	23	0.575	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	23	0.575	RNA PCR Primer, Index 1 (100% over 30bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	21	0.525	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	19	0.475	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	19	0.475	RNA PCR Primer, Index 1 (96% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	18	0.44999999999999996	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	18	0.44999999999999996	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	17	0.42500000000000004	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	16	0.4	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTC	16	0.4	RNA PCR Primer, Index 3 (100% over 44bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTT	16	0.4	RNA PCR Primer, Index 1 (97% over 35bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	15	0.375	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	15	0.375	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	15	0.375	RNA PCR Primer, Index 1 (96% over 27bp)
ACGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	14	0.35000000000000003	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGC	13	0.325	RNA PCR Primer, Index 3 (100% over 50bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	12	0.3	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	11	0.27499999999999997	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	11	0.27499999999999997	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	11	0.27499999999999997	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	11	0.27499999999999997	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	11	0.27499999999999997	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	10	0.25	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	10	0.25	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	10	0.25	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	9	0.22499999999999998	No Hit
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	9	0.22499999999999998	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	9	0.22499999999999998	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	9	0.22499999999999998	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	8	0.2	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GAGCAATGATGACCCCAACATGCCATCTGAGTGGCTTTGCTGAAATCCAG	8	0.2	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	7	0.17500000000000002	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	7	0.17500000000000002	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	7	0.17500000000000002	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	7	0.17500000000000002	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	7	0.17500000000000002	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	7	0.17500000000000002	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TACCATGATGATAACATAGTTCAGCAGACTTAACTCTGATGAACAATCAT	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	6	0.15	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	6	0.15	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
GCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACACT	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGAAGAAAGGT	5	0.125	No Hit
AGCTACATTGTCTGCTGGGTTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGC	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	0.35	0.0	0.0	0.0
2	0.0	0.35	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.4	0.0	0.0	0.0
5	0.0	0.475	0.0	0.0	0.0
6	0.0	0.475	0.0	0.0	0.0
7	0.0	0.95	0.0	0.0	0.0
8	0.0	1.075	0.0	0.0	0.0
9	0.0	1.125	0.0	0.0	0.0
10	0.0	1.225	0.0	0.0	0.0
11	0.0	1.35	0.0	0.0	0.0
12	0.0	1.6	0.0	0.0	0.0
13	0.0	1.775	0.0	0.0	0.0
14	0.0	2.05	0.0	0.0	0.0
15	0.0	2.325	0.0	0.0	0.0
16	0.0	3.025	0.0	0.0	0.0
17	0.0	3.525	0.0	0.0	0.0
18	0.0	4.6	0.0	0.0	0.0
19	0.0	5.025	0.0	0.0	0.0
20	0.0	5.725	0.0	0.0	0.0
21	0.0	9.525	0.0	0.0	0.0
22	0.0	17.475	0.0	0.0	0.0
23	0.0	42.275	0.0	0.0	0.0
24	0.0	54.8	0.0	0.0	0.0
25	0.0	60.525	0.0	0.0	0.0
26	0.0	61.75	0.0	0.0	0.0
27	0.0	62.575	0.0	0.0	0.0
28	0.0	63.2	0.0	0.0	0.0
29	0.0	63.45	0.0	0.0	0.0
30	0.0	63.85	0.0	0.0	0.0
31	0.0	64.4	0.0	0.0	0.0
32	0.0	65.675	0.0	0.0	0.0
33	0.0	66.425	0.0	0.0	0.0
34	0.0	70.375	0.0	0.0	0.0
35	0.0	71.225	0.0	0.0	0.0
36	0.0	72.275	0.0	0.0	0.0
37	0.0	73.225	0.0	0.0	0.0
38	0.0	73.6	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGATGAT	20	6.952051E-4	44.000004	6
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
AATCCAG	20	6.952051E-4	44.000004	8
TAAACAT	20	6.952051E-4	44.000004	3
ATCCAGG	20	6.952051E-4	44.000004	9
AAACATC	20	6.952051E-4	44.000004	4
TTCAAGT	20	6.952051E-4	44.000004	1
AGGATAG	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
AGTGGAA	20	6.952051E-4	44.000004	21
CATTCAA	40	5.315087E-9	44.000004	3
TCCAGGA	20	6.952051E-4	44.000004	10
ACATCCT	20	6.952051E-4	44.000004	6
ACATTCA	40	5.315087E-9	44.000004	2
GGATAGG	20	6.952051E-4	44.000004	14
AACTCCG	20	6.952051E-4	44.000004	44
AGTAATC	20	6.952051E-4	44.000004	5
TAATCCA	20	6.952051E-4	44.000004	7
GGCCAAG	40	5.315087E-9	44.000004	36
>>END_MODULE
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193490 spots for SRR5030875.sra
Written 193490 spots for SRR5030875.sra
Read 193496 spots for SRR5030875.sra
Written 193496 spots for SRR5030875.sra
SRR ids: ['SRR5030875.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_cgw7ie27
SRR5030875.sra spots: 2321886
blocks: [[1, 193490], [193491, 386980], [386981, 580470], [580471, 773960], [773961, 967450], [967451, 1160940], [1160941, 1354430], [1354431, 1547920], [1547921, 1741410], [1741411, 1934900], [1934901, 2128390], [2128391, 2321886]]
SRR5030875 file size 401355
SRR5030875 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030875 SRR5030875_1.fastq
Input file:	SRR5030875_1.fastq
trimmed:	SRR5030875-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 06:34:04 2020 >> started

Wed Mar  4 06:34:06 2020 >> done (2.053s)
2321886 reads processed; of these:
    149 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
2321728 (99.99%) reads available; of these:
 277141 (11.94%) trimmed reads available after processing
2044587 (88.06%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     37	  0.00%
 19	     51	  0.00%
 20	    125	  0.01%
 21	    136	  0.01%
 22	    218	  0.01%
 23	    315	  0.01%
 24	    334	  0.01%
 25	    489	  0.02%
 26	    368	  0.02%
 27	    459	  0.02%
 28	    668	  0.03%
 29	    987	  0.04%
 30	    729	  0.03%
 31	   1074	  0.05%
 32	   2858	  0.12%
 33	   7574	  0.33%
 34	  17372	  0.75%
 35	   4155	  0.18%
 36	   4504	  0.19%
 37	   2694	  0.12%
 38	   5220	  0.22%
 39	   5363	  0.23%
 40	   9149	  0.39%
 41	   5524	  0.24%
 42	  14552	  0.63%
 43	   6684	  0.29%
 44	  25788	  1.11%
 45	  17595	  0.76%
 46	  16520	  0.71%
 47	  17915	  0.77%
 48	  46971	  2.02%
 49	  60713	  2.61%
 50	2044587	 88.06%
2321728 reads passed initial QC


criterion=sequence-density
sequence-density=71.99
sequence-density-rank=1
fanout-score=21.50
fanout-score-rank=3
prefix-density=74.95
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC


criterion=fanout-score
sequence-density=1.37
sequence-density-rank=7
fanout-score=520.62
fanout-score-rank=1
prefix-density=74.04
prefix-fanout=9.6
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC -o SRR5030875 -
Input file:	STDIN
trimmed:	SRR5030875-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC
-- 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 06:34:22 2020 >> started

Wed Mar  4 06:34:26 2020 >> done (3.211s)
2257236 reads processed; of these:
  98385 ( 4.36%) short reads filtered out after trimming by size control
   9339 ( 0.41%) empty reads filtered out after trimming by size control
2149512 (95.23%) reads available; of these:
1737776 (80.85%) trimmed reads available after processing
 411736 (19.15%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11598	  0.54%
 19	  18388	  0.86%
 20	  84905	  3.95%
 21	 198672	  9.24%
 22	 537953	 25.03%
 23	 279333	 13.00%
 24	 116414	  5.42%
 25	  31313	  1.46%
 26	  16463	  0.77%
 27	  14000	  0.65%
 28	  14896	  0.69%
 29	  11951	  0.56%
 30	  17898	  0.83%
 31	  25409	  1.18%
 32	  22009	  1.02%
 33	  96766	  4.50%
 34	  25606	  1.19%
 35	  19282	  0.90%
 36	  26593	  1.24%
 37	  11811	  0.55%
 38	  13865	  0.65%
 39	  13986	  0.65%
 40	  19752	  0.92%
 41	  23854	  1.11%
 42	  30072	  1.40%
 43	  21009	  0.98%
 44	  19782	  0.92%
 45	  24515	  1.14%
 46	  20334	  0.95%
 47	  16852	  0.78%
 48	   6577	  0.31%
 49	  11883	  0.55%
 50	 345771	 16.09%


criterion=sequence-density
sequence-density=6.81
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.55
sequence-density-rank=26
fanout-score=11.01
fanout-score-rank=1
prefix-density=6.09
prefix-fanout=1.0
sequence=TGAGCTTGGCTATT
                                 Started job on |	Mar 04 06:35:16
                             Started mapping on |	Mar 04 06:35:16
                                    Finished on |	Mar 04 06:35:43
       Mapping speed, Million of reads per hour |	295.20

                          Number of input reads |	2214004
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1140994
                        Uniquely mapped reads % |	51.54%
                          Average mapped length |	29.45
                       Number of splices: Total |	1374
            Number of splices: Annotated (sjdb) |	197
                       Number of splices: GT/AG |	1272
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	86
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.35
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	670911
             % of reads mapped to multiple loci |	30.30%
        Number of reads mapped to too many loci |	56515
             % of reads mapped to too many loci |	2.55%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	15.04%
                     % of reads unmapped: other |	0.57%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	402099	402099	402099
N_multimapping	670911	670911	670911
N_noFeature	61204	75803	849569
N_ambiguous	619930	369889	12097
UnstrandedReadsAssigned:459860 PositiveStrandReadsAssigned:695302 NegativeStrandReadsAssigned:279328
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030875 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: SRR5030875-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,214,004 reads, 502,944 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,101 rounds

 109283 SRR5030875.ke.tsv
  52636 SRR5030875.se.tsv
 161919 total
==> SRR5030875.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

==> SRR5030875.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030875 completed mapping pipeline successfully
