Starting /dee2/code/volunteer_pipeline.sh SRR5030850
    current disk space = 160661585920
    free memory = 73936400 
SRR5030850 SRAfilesize
5552d47ed1999204e3d9fa783ca368c5  SRR5030850.sra
SRR5030850.sra file validated
SRR5030850 is single end
SRR5030850 is conventional basespace
SRR5030850 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030850_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	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3975	33.0	31.0	34.0	31.0	34.0
2	32.66475	34.0	31.0	34.0	31.0	34.0
3	32.80825	34.0	31.0	34.0	31.0	34.0
4	36.28775	37.0	37.0	37.0	35.0	37.0
5	36.33	37.0	37.0	37.0	35.0	37.0
6	36.1345	37.0	37.0	37.0	35.0	37.0
7	36.13775	37.0	35.0	37.0	35.0	37.0
8	36.194	37.0	36.0	37.0	35.0	37.0
9	37.982	39.0	38.0	39.0	35.0	39.0
10	37.937	39.0	38.0	39.0	35.0	39.0
11	37.85575	39.0	38.0	39.0	35.0	39.0
12	37.86975	39.0	38.0	39.0	35.0	39.0
13	37.79075	39.0	38.0	39.0	35.0	39.0
14	39.24775	41.0	39.0	41.0	36.0	41.0
15	39.23925	41.0	39.0	41.0	36.0	41.0
16	39.28225	40.0	39.0	41.0	36.0	41.0
17	39.433	41.0	39.0	41.0	36.0	41.0
18	39.384	41.0	39.0	41.0	36.0	41.0
19	39.1855	41.0	39.0	41.0	36.0	41.0
20	39.086	41.0	39.0	41.0	36.0	41.0
21	39.204	40.0	39.0	41.0	36.0	41.0
22	39.2235	41.0	39.0	41.0	36.0	41.0
23	39.0825	41.0	39.0	41.0	35.0	41.0
24	38.877	40.0	39.0	41.0	35.0	41.0
25	39.1305	41.0	39.0	41.0	35.0	41.0
26	39.195	41.0	39.0	41.0	36.0	41.0
27	39.1775	41.0	39.0	41.0	36.0	41.0
28	38.97675	40.0	39.0	41.0	35.0	41.0
29	38.0255	40.0	38.0	41.0	32.0	41.0
30	38.5215	40.0	38.0	41.0	34.0	41.0
31	38.77025	40.0	38.0	41.0	35.0	41.0
32	39.10925	41.0	39.0	41.0	35.0	41.0
33	38.28575	40.0	38.0	41.0	33.0	41.0
34	38.14675	40.0	38.0	41.0	33.0	41.0
35	37.834	39.0	37.0	41.0	33.0	41.0
36	34.111	38.0	30.0	40.0	23.0	41.0
37	35.59025	38.0	34.0	40.0	30.0	41.0
38	36.9355	39.0	37.0	40.0	31.0	41.0
39	36.861	39.0	36.0	40.0	31.0	41.0
40	37.05075	39.0	37.0	40.0	31.0	41.0
41	37.01325	39.0	36.0	40.0	31.0	41.0
42	37.37	40.0	37.0	41.0	33.0	41.0
43	37.121	39.0	36.0	41.0	32.0	41.0
44	36.94025	39.0	36.0	41.0	31.0	41.0
45	36.7335	39.0	36.0	40.0	31.0	41.0
46	34.95275	38.0	34.0	40.0	26.0	41.0
47	35.604	38.0	35.0	40.0	28.0	41.0
48	36.17275	39.0	35.0	40.0	30.0	41.0
49	34.856	38.0	34.0	40.0	27.0	41.0
50	30.514	34.0	28.0	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	0.0
16	0.0
17	1.0
18	1.0
19	3.0
20	1.0
21	6.0
22	7.0
23	10.0
24	12.0
25	14.0
26	16.0
27	26.0
28	26.0
29	34.0
30	43.0
31	61.0
32	99.0
33	111.0
34	150.0
35	192.0
36	333.0
37	551.0
38	1031.0
39	1270.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.734069242348218	25.413948820873056	49.14701455092825	15.704967385850477
2	24.0	26.150000000000002	18.45	31.4
3	26.0	19.775000000000002	21.925	32.300000000000004
4	30.675	28.575	12.8	27.950000000000003
5	19.1	43.375	24.375	13.15
6	34.525	16.25	34.875	14.35
7	16.125	19.375	24.925	39.574999999999996
8	25.424999999999997	29.15	14.6	30.825000000000003
9	22.575	34.449999999999996	27.875	15.1
10	22.95	23.075000000000003	29.25	24.725
11	29.975	13.025	16.775000000000002	40.225
12	15.75	18.775	31.175000000000004	34.300000000000004
13	31.775	19.675	29.575000000000003	18.975
14	29.375	32.625	19.975	18.025
15	33.73343335833959	26.556639159789945	25.85646411602901	13.85346336584146
16	19.0	21.675	21.125	38.2
17	21.525	23.724999999999998	39.324999999999996	15.425
18	23.474999999999998	19.475	30.525000000000002	26.525
19	36.775000000000006	14.424999999999999	29.25	19.55
20	41.575	15.275	29.7	13.450000000000001
21	24.45	19.025	28.025	28.499999999999996
22	29.825000000000003	12.9	46.475	10.8
23	26.950000000000003	13.850000000000001	43.425000000000004	15.775
24	51.15	15.174999999999999	24.75	8.924999999999999
25	48.375	25.25	14.475	11.899999999999999
26	26.85	45.300000000000004	15.525	12.325
27	15.65	46.775	23.7	13.875000000000002
28	12.45	23.65	47.699999999999996	16.2
29	11.75	13.625000000000002	56.125	18.5
30	10.75	7.8	34.075	47.375
31	14.975	6.3	46.925	31.8
32	29.4	6.575	21.375	42.65
33	53.900000000000006	10.075000000000001	13.200000000000001	22.825
34	59.75	7.8	17.974999999999998	14.475
35	63.025	7.575	18.575	10.825
36	42.6	8.75	35.099999999999994	13.55
37	43.625	12.075	19.35	24.95
38	22.375	18.224999999999998	12.25	47.15
39	15.8	24.025	11.475	48.699999999999996
40	17.549999999999997	47.475	11.774999999999999	23.200000000000003
41	25.025	48.65	9.1	17.224999999999998
42	49.45	28.9	11.799999999999999	9.85
43	49.45	30.675	8.525	11.35
44	29.099999999999998	48.949999999999996	8.5	13.450000000000001
45	19.45	49.1	12.975	18.475
46	13.275	26.825	18.6	41.3
47	9.475	15.525	39.574999999999996	35.425000000000004
48	11.525	14.000000000000002	19.625	54.85
49	14.85	20.575	14.424999999999999	50.14999999999999
50	19.8	36.449999999999996	13.625000000000002	30.125
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.5
2	1.0
3	0.5
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	0.5
26	1.0
27	2.5
28	4.0
29	4.0
30	4.0
31	11.5
32	19.0
33	21.0
34	23.0
35	33.5
36	44.0
37	52.5
38	61.0
39	57.5
40	54.0
41	58.0
42	62.0
43	97.0
44	132.0
45	165.0
46	198.0
47	311.0
48	424.0
49	528.5
50	633.0
51	707.0
52	781.0
53	601.5
54	422.0
55	459.5
56	497.0
57	366.5
58	236.0
59	161.0
60	86.0
61	60.5
62	35.0
63	87.0
64	139.0
65	84.0
66	29.0
67	23.5
68	18.0
69	22.5
70	27.0
71	40.5
72	54.0
73	30.0
74	6.0
75	3.5
76	1.0
77	2.5
78	4.0
79	3.0
80	2.0
81	2.5
82	3.0
83	1.5
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	39.074999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.30390275111965	29.425
2	9.980806142034549	7.8
3	4.286628278950736	5.025
4	2.4312220089571337	3.8
5	1.2156110044785668	2.375
6	1.599488163787588	3.75
7	0.7037747920665387	1.925
8	0.5758157389635317	1.7999999999999998
9	0.4478566858605247	1.575
>10	2.8790786948176583	21.275
>50	0.3198976327575176	9.35
>100	0.2559181062060141	11.899999999999999
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	155	3.875	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	106	2.65	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	103	2.5749999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	100	2.5	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	83	2.075	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	69	1.725	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	49	1.225	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	28	0.7000000000000001	RNA PCR Primer, Index 9 (100% over 44bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	26	0.65	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	25	0.625	RNA PCR Primer, Index 7 (97% over 35bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	21	0.525	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	15	0.375	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGC	14	0.35000000000000003	RNA PCR Primer, Index 9 (100% over 50bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	13	0.325	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	12	0.3	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	12	0.3	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	10	0.25	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	10	0.25	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	10	0.25	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 33bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	9	0.22499999999999998	No Hit
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	6	0.15	RNA PCR Primer, Index 1 (100% over 32bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	6	0.15	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCTACAGTGCACGTGTCTCCAGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTTGGAATTCTC	5	0.125	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	5	0.125	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	5	0.125	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.475	0.0	0.0	0.0
2	0.0	0.475	0.0	0.0	0.0
3	0.0	0.55	0.0	0.0	0.0
4	0.0	0.55	0.0	0.0	0.0
5	0.0	0.6	0.0	0.0	0.0
6	0.0	0.6	0.0	0.0	0.0
7	0.0	1.4	0.0	0.0	0.0
8	0.0	1.5	0.0	0.0	0.0
9	0.0	1.575	0.0	0.0	0.0
10	0.0	1.775	0.0	0.0	0.0
11	0.0	1.925	0.0	0.0	0.0
12	0.0	2.125	0.0	0.0	0.0
13	0.0	2.325	0.0	0.0	0.0
14	0.0	2.6	0.0	0.0	0.0
15	0.0	3.05	0.0	0.0	0.0
16	0.0	4.25	0.0	0.0	0.0
17	0.0	4.675	0.0	0.0	0.0
18	0.0	5.7	0.0	0.0	0.0
19	0.0	6.425	0.0	0.0	0.0
20	0.0	7.6	0.0	0.0	0.0
21	0.0	13.525	0.0	0.0	0.0
22	0.0	24.5	0.0	0.0	0.0
23	0.0	53.375	0.0	0.0	0.0
24	0.0	65.2	0.0	0.0	0.0
25	0.0	70.425	0.0	0.0	0.0
26	0.0	71.925	0.0	0.0	0.0
27	0.0	72.675	0.0	0.0	0.0
28	0.0	73.075	0.0	0.0	0.0
29	0.0	73.45	0.0	0.0	0.0
30	0.0	73.8	0.0	0.0	0.0
31	0.0	74.7	0.0	0.0	0.0
32	0.0	75.6	0.0	0.0	0.0
33	0.0	76.425	0.0	0.0	0.0
34	0.0	79.75	0.0	0.0	0.0
35	0.0	80.45	0.0	0.0	0.0
36	0.0	81.05	0.0	0.0	0.0
37	0.0	81.55	0.0	0.0	0.0
38	0.0	81.9	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACTGTTG	20	6.952051E-4	44.000004	18
GTTGAAG	20	6.952051E-4	44.000004	10
CAGTTGA	20	6.952051E-4	44.000004	8
CTGAGCT	40	5.315087E-9	44.000004	11
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	40	5.315087E-9	44.000004	1
CGGATCC	40	5.315087E-9	44.000004	2
GAAGAAC	20	6.952051E-4	44.000004	13
CTTGGCT	20	6.952051E-4	44.000004	16
CGTGGAA	20	6.952051E-4	44.000004	21
GCTGCCA	20	6.952051E-4	44.000004	3
GAACTGT	20	6.952051E-4	44.000004	16
GATCCGT	40	5.315087E-9	44.000004	4
TGAAGAA	20	6.952051E-4	44.000004	12
AGTTGAA	20	6.952051E-4	44.000004	9
TCCGTCT	40	5.315087E-9	44.000004	6
>>END_MODULE
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Read 302335 spots for SRR5030850.sra
Written 302335 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
Read 302334 spots for SRR5030850.sra
Written 302334 spots for SRR5030850.sra
SRR ids: ['SRR5030850.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_bntuk8su
SRR5030850.sra spots: 3628009
blocks: [[1, 302334], [302335, 604668], [604669, 907002], [907003, 1209336], [1209337, 1511670], [1511671, 1814004], [1814005, 2116338], [2116339, 2418672], [2418673, 2721006], [2721007, 3023340], [3023341, 3325674], [3325675, 3628009]]
SRR5030850 file size 627738
SRR5030850 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030850 SRR5030850_1.fastq
Input file:	SRR5030850_1.fastq
trimmed:	SRR5030850-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 06:28:18 2020 >> started

Wed Mar  4 06:28:20 2020 >> done (1.947s)
3628009 reads processed; of these:
    165 ( 0.00%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
3627839 (100.00%) reads available; of these:
 208940 ( 5.76%) trimmed reads available after processing
3418899 (94.24%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     59	  0.00%
 19	     67	  0.00%
 20	    158	  0.00%
 21	    176	  0.00%
 22	    353	  0.01%
 23	    392	  0.01%
 24	    473	  0.01%
 25	    602	  0.02%
 26	    464	  0.01%
 27	    640	  0.02%
 28	    859	  0.02%
 29	   1119	  0.03%
 30	    895	  0.02%
 31	   1204	  0.03%
 32	   1280	  0.04%
 33	   1706	  0.05%
 34	   3612	  0.10%
 35	   3676	  0.10%
 36	   2799	  0.08%
 37	   2847	  0.08%
 38	   3157	  0.09%
 39	   3442	  0.09%
 40	   3632	  0.10%
 41	   4145	  0.11%
 42	   5180	  0.14%
 43	   7214	  0.20%
 44	  12649	  0.35%
 45	  15767	  0.43%
 46	  14744	  0.41%
 47	  19425	  0.54%
 48	  40274	  1.11%
 49	  55930	  1.54%
 50	3418899	 94.24%
3627839 reads passed initial QC


criterion=sequence-density
sequence-density=80.52
sequence-density-rank=1
fanout-score=19.07
fanout-score-rank=1
prefix-density=82.27
prefix-fanout=18.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC


criterion=fanout-score
sequence-density=80.52
sequence-density-rank=1
fanout-score=19.07
fanout-score-rank=1
prefix-density=82.27
prefix-fanout=18.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC -o SRR5030850 -
Input file:	STDIN
trimmed:	SRR5030850-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC
-- 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 06:28:36 2020 >> started

Wed Mar  4 06:28:42 2020 >> done (5.403s)
3538263 reads processed; of these:
 207828 ( 5.87%) short reads filtered out after trimming by size control
  13414 ( 0.38%) empty reads filtered out after trimming by size control
3317021 (93.75%) reads available; of these:
2933011 (88.42%) trimmed reads available after processing
 384010 (11.58%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  19444	  0.59%
 19	  36146	  1.09%
 20	 201064	  6.06%
 21	 407217	 12.28%
 22	 988046	 29.79%
 23	 419611	 12.65%
 24	 205051	  6.18%
 25	  52198	  1.57%
 26	  26478	  0.80%
 27	  20177	  0.61%
 28	  20772	  0.63%
 29	  16189	  0.49%
 30	  23864	  0.72%
 31	  26592	  0.80%
 32	  29044	  0.88%
 33	 116715	  3.52%
 34	  25635	  0.77%
 35	  17853	  0.54%
 36	  18941	  0.57%
 37	  14957	  0.45%
 38	  15662	  0.47%
 39	  17389	  0.52%
 40	  26928	  0.81%
 41	  34641	  1.04%
 42	  40796	  1.23%
 43	  30208	  0.91%
 44	  25053	  0.76%
 45	  33579	  1.01%
 46	  26296	  0.79%
 47	  22111	  0.67%
 48	   3783	  0.11%
 49	  12386	  0.37%
 50	 342195	 10.32%


criterion=sequence-density
sequence-density=5.61
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=39
fanout-score=67.74
fanout-score-rank=1
prefix-density=1.29
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:29:04
                             Started mapping on |	Mar 04 06:29:05
                                    Finished on |	Mar 04 06:29:30
       Mapping speed, Million of reads per hour |	490.55

                          Number of input reads |	3406597
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1923703
                        Uniquely mapped reads % |	56.47%
                          Average mapped length |	26.77
                       Number of splices: Total |	1601
            Number of splices: Annotated (sjdb) |	233
                       Number of splices: GT/AG |	1491
                       Number of splices: GC/AG |	22
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	88
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.60
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.15
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1007101
             % of reads mapped to multiple loci |	29.56%
        Number of reads mapped to too many loci |	69418
             % of reads mapped to too many loci |	2.04%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.41%
                     % of reads unmapped: other |	0.52%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	475793	475793	475793
N_multimapping	1007101	1007101	1007101
N_noFeature	75047	96202	1335157
N_ambiguous	1086282	574974	22137
UnstrandedReadsAssigned:762374 PositiveStrandReadsAssigned:1252527 NegativeStrandReadsAssigned:566409
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=21 echo kmer=19
SRR5030850 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: SRR5030850-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,406,597 reads, 906,431 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,087 rounds

 109283 SRR5030850.ke.tsv
  52636 SRR5030850.se.tsv
 161919 total
==> SRR5030850.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

==> SRR5030850.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030850 completed mapping pipeline successfully
