Starting /dee2/code/volunteer_pipeline.sh SRR5031035
    current disk space = 160529563648
    free memory = 73933216 
SRR5031035 SRAfilesize
7b7da60ae712535bf4fe441d84966fe5  SRR5031035.sra
SRR5031035.sra file validated
SRR5031035 is single end
SRR5031035 is conventional basespace
SRR5031035 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031035_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3095	33.0	31.0	34.0	30.0	34.0
2	32.5725	34.0	31.0	34.0	31.0	34.0
3	32.6265	34.0	31.0	34.0	31.0	34.0
4	36.212	37.0	35.0	37.0	35.0	37.0
5	35.89325	37.0	35.0	37.0	35.0	37.0
6	35.7925	37.0	35.0	37.0	33.0	37.0
7	35.88975	37.0	35.0	37.0	35.0	37.0
8	35.7575	37.0	35.0	37.0	35.0	37.0
9	37.5155	39.0	37.0	39.0	35.0	39.0
10	37.63225	39.0	37.0	39.0	35.0	39.0
11	37.51525	39.0	37.0	39.0	35.0	39.0
12	37.501	39.0	37.0	39.0	35.0	39.0
13	37.606	39.0	37.0	39.0	35.0	39.0
14	38.887	40.0	38.0	41.0	35.0	41.0
15	38.775	40.0	38.0	41.0	35.0	41.0
16	38.9075	40.0	38.0	41.0	35.0	41.0
17	38.712	40.0	38.0	41.0	34.0	41.0
18	38.80075	40.0	38.0	41.0	34.0	41.0
19	38.463	40.0	38.0	41.0	34.0	41.0
20	38.622	40.0	38.0	41.0	34.0	41.0
21	38.53125	40.0	38.0	41.0	34.0	41.0
22	38.62225	40.0	38.0	41.0	34.0	41.0
23	38.38775	40.0	38.0	41.0	34.0	41.0
24	38.4345	40.0	38.0	41.0	34.0	41.0
25	38.529	40.0	38.0	41.0	34.0	41.0
26	38.141	40.0	38.0	41.0	33.0	41.0
27	38.1915	40.0	38.0	41.0	33.0	41.0
28	38.18875	40.0	38.0	41.0	33.0	41.0
29	37.70825	40.0	37.0	41.0	31.0	41.0
30	37.66225	40.0	37.0	41.0	31.0	41.0
31	38.0	40.0	38.0	41.0	32.0	41.0
32	37.95725	40.0	38.0	41.0	33.0	41.0
33	37.87275	40.0	38.0	41.0	33.0	41.0
34	38.2385	40.0	38.0	41.0	33.0	41.0
35	38.03325	40.0	38.0	41.0	33.0	41.0
36	37.63875	40.0	37.0	41.0	32.0	41.0
37	37.0155	39.0	36.0	41.0	30.0	41.0
38	36.459	39.0	35.0	40.0	30.0	41.0
39	36.928	39.0	36.0	40.0	30.0	41.0
40	37.15825	39.0	36.0	41.0	31.0	41.0
41	37.28075	40.0	36.0	41.0	31.0	41.0
42	37.558	40.0	37.0	41.0	32.0	41.0
43	37.88425	40.0	37.0	41.0	33.0	41.0
44	37.6965	40.0	37.0	41.0	33.0	41.0
45	37.586	40.0	37.0	41.0	33.0	41.0
46	37.49675	40.0	37.0	41.0	33.0	41.0
47	36.89075	40.0	36.0	41.0	30.0	41.0
48	36.5365	39.0	35.0	41.0	30.0	41.0
49	36.67175	39.0	35.0	41.0	31.0	41.0
50	36.293	39.0	35.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
11	1.0
12	0.0
13	0.0
14	1.0
15	0.0
16	1.0
17	5.0
18	1.0
19	2.0
20	1.0
21	9.0
22	4.0
23	7.0
24	6.0
25	11.0
26	11.0
27	19.0
28	37.0
29	50.0
30	51.0
31	69.0
32	98.0
33	135.0
34	171.0
35	222.0
36	288.0
37	443.0
38	770.0
39	1587.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.175	25.2	44.45	19.175
2	25.362681340670335	26.088044022011005	17.63381690845423	30.915457728864432
3	24.175	18.25	21.925	35.65
4	36.15	25.900000000000002	15.2	22.75
5	23.1	36.85	28.000000000000004	12.049999999999999
6	32.05	13.4	35.725	18.825
7	17.224999999999998	21.6	21.775	39.4
8	24.775	26.625	17.4	31.2
9	23.849999999999998	29.575000000000003	26.474999999999998	20.1
10	20.8	23.1	26.05	30.049999999999997
11	35.525	12.174999999999999	16.1	36.199999999999996
12	19.275000000000002	19.75	27.525	33.45
13	29.875	16.3	35.35	18.475
14	28.875	28.9	21.8	20.424999999999997
15	34.849999999999994	24.099999999999998	26.3	14.75
16	20.75	18.25	22.675	38.324999999999996
17	27.474999999999998	22.45	34.175	15.9
18	24.675	17.625	29.625	28.075
19	36.6	14.725	28.975	19.7
20	43.425000000000004	14.149999999999999	28.675	13.750000000000002
21	27.275	21.55	23.849999999999998	27.325
22	31.025000000000002	14.899999999999999	41.55	12.525
23	25.05	13.775	43.4	17.775
24	49.375	14.025000000000002	25.525	11.075
25	48.225	23.175	16.45	12.15
26	27.900000000000002	42.375	15.125	14.6
27	17.5	44.725	20.275000000000002	17.5
28	13.925	24.65	44.375	17.05
29	17.65	12.6	51.6	18.15
30	12.35	7.475	33.575	46.6
31	15.075	5.975	45.975	32.975
32	28.199999999999996	7.1499999999999995	22.275	42.375
33	49.3	11.825	14.7	24.175
34	57.15	8.175	17.7	16.975
35	62.150000000000006	9.65	17.474999999999998	10.725
36	42.05	9.950000000000001	34.575	13.425
37	42.125	15.55	22.125	20.200000000000003
38	24.575	18.425	14.224999999999998	42.775
39	16.900000000000002	20.825	14.025000000000002	48.25
40	16.35	43.85	14.549999999999999	25.25
41	22.1	46.075	11.200000000000001	20.625
42	45.125	27.400000000000002	15.2	12.275
43	50.575	25.35	9.45	14.625
44	34.050000000000004	42.65	9.4	13.900000000000002
45	22.35	46.675	12.975	18.0
46	17.625	25.575	17.424999999999997	39.375
47	11.625	15.575	39.25	33.550000000000004
48	14.85	11.525	21.0	52.625
49	13.15	19.175	14.774999999999999	52.900000000000006
50	16.975	36.95	12.4	33.675
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.5
30	1.0
31	7.0
32	13.0
33	9.5
34	6.0
35	20.0
36	34.0
37	35.0
38	36.0
39	38.5
40	41.0
41	41.0
42	41.0
43	73.5
44	106.0
45	136.5
46	167.0
47	260.0
48	353.0
49	444.5
50	536.0
51	678.0
52	820.0
53	635.5
54	451.0
55	480.5
56	510.0
57	397.5
58	285.0
59	192.0
60	99.0
61	81.0
62	63.0
63	142.5
64	222.0
65	135.5
66	49.0
67	34.5
68	20.0
69	27.0
70	34.0
71	66.0
72	98.0
73	53.0
74	8.0
75	4.5
76	1.0
77	1.0
78	1.0
79	2.5
80	4.0
81	2.5
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	0.0
2	0.05
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	38.975
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.01026298909558	29.625
2	10.13470173187941	7.9
3	4.169339320076972	4.875
4	2.245028864656831	3.5000000000000004
5	1.603592046183451	3.125
6	1.0262989095574084	2.4
7	0.4490057729313663	1.225
8	0.3207184092366902	1.0
9	0.5131494547787042	1.7999999999999998
>10	3.0147530468248878	24.099999999999998
>50	0.2565747273893521	8.225
>100	0.2565747273893521	12.225
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	140	3.5000000000000004	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	122	3.05	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	108	2.7	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	98	2.45	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	78	1.95	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGC	39	0.975	RNA PCR Primer, Index 7 (100% over 50bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	36	0.8999999999999999	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 33bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	34	0.8500000000000001	RNA PCR Primer, Index 7 (100% over 35bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	24	0.6	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	23	0.575	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTC	21	0.525	RNA PCR Primer, Index 7 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	19	0.475	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	18	0.44999999999999996	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	18	0.44999999999999996	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	17	0.42500000000000004	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	15	0.375	RNA PCR Primer, Index 1 (100% over 31bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	14	0.35000000000000003	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	10	0.25	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	9	0.22499999999999998	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG	8	0.2	RNA PCR Primer, Index 7 (100% over 36bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	8	0.2	No Hit
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	7	0.17500000000000002	RNA PCR Primer, Index 2 (100% over 34bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCTC	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTTGGAATTCTC	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
TATTGCACTCGTCCCGGCCTCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	5	0.125	No Hit
GAATGTTGCTCGGTGAACCCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG	5	0.125	RNA PCR Primer, Index 7 (100% over 36bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAATCAGACTATAGGCAATAATCACACTATAAATGGAATTCTCGGGTGCC	5	0.125	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGAT	5	0.125	RNA PCR Primer, Index 7 (100% over 38bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	1.075	0.0	0.0	0.0
2	0.0	1.1	0.0	0.0	0.0
3	0.0	1.175	0.0	0.0	0.0
4	0.0	1.175	0.0	0.0	0.0
5	0.0	1.2	0.0	0.0	0.0
6	0.0	1.275	0.0	0.0	0.0
7	0.0	1.875	0.0	0.0	0.0
8	0.0	1.975	0.0	0.0	0.0
9	0.0	2.125	0.0	0.0	0.0
10	0.0	2.375	0.0	0.0	0.0
11	0.0	2.575	0.0	0.0	0.0
12	0.0	2.775	0.0	0.0	0.0
13	0.0	3.15	0.0	0.0	0.0
14	0.0	3.375	0.0	0.0	0.0
15	0.0	4.075	0.0	0.0	0.0
16	0.0	5.45	0.0	0.0	0.0
17	0.0	6.15	0.0	0.0	0.0
18	0.0	7.475	0.0	0.0	0.0
19	0.0	8.1	0.0	0.0	0.0
20	0.0	9.25	0.0	0.0	0.0
21	0.0	13.275	0.0	0.0	0.0
22	0.0	22.225	0.0	0.0	0.0
23	0.0	48.65	0.0	0.0	0.0
24	0.0	60.825	0.0	0.0	0.0
25	0.0	66.275	0.0	0.0	0.0
26	0.0	67.75	0.0	0.0	0.0
27	0.0	68.45	0.0	0.0	0.0
28	0.0	69.175	0.0	0.0	0.0
29	0.0	69.925	0.0	0.0	0.0
30	0.0	70.375	0.0	0.0	0.0
31	0.0	71.5	0.0	0.0	0.0
32	0.0	73.275	0.0	0.0	0.0
33	0.0	74.8	0.0	0.0	0.0
34	0.0	80.075	0.0	0.0	0.0
35	0.0	81.425	0.0	0.0	0.0
36	0.0	82.4	0.0	0.0	0.0
37	0.0	83.575	0.0	0.0	0.0
38	0.0	84.25	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	20	6.952051E-4	44.000004	8
ACGCTGT	20	6.952051E-4	44.000004	9
AATCCAG	20	6.952051E-4	44.000004	8
ATCCAGG	20	6.952051E-4	44.000004	9
TTCAACG	20	6.952051E-4	44.000004	5
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
TCCAGGA	20	6.952051E-4	44.000004	10
ACATTCA	20	6.952051E-4	44.000004	2
ATCAGAC	20	6.952051E-4	44.000004	12
AGACGTG	20	6.952051E-4	44.000004	15
GCTGTCG	20	6.952051E-4	44.000004	11
GACGTGG	20	6.952051E-4	44.000004	16
TCAGACG	20	6.952051E-4	44.000004	13
TAATCCA	20	6.952051E-4	44.000004	7
CAGACGT	20	6.952051E-4	44.000004	14
CTGTCGG	20	6.952051E-4	44.000004	12
CAGGATA	20	6.952051E-4	44.000004	12
GTAATCC	20	6.952051E-4	44.000004	6
ATTCAAC	20	6.952051E-4	44.000004	4
>>END_MODULE
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225153 spots for SRR5031035.sra
Written 225153 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
Read 225152 spots for SRR5031035.sra
Written 225152 spots for SRR5031035.sra
SRR ids: ['SRR5031035.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_c5iplpw9
SRR5031035.sra spots: 2701825
blocks: [[1, 225152], [225153, 450304], [450305, 675456], [675457, 900608], [900609, 1125760], [1125761, 1350912], [1350913, 1576064], [1576065, 1801216], [1801217, 2026368], [2026369, 2251520], [2251521, 2476672], [2476673, 2701825]]
SRR5031035 file size 467220
SRR5031035 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031035 SRR5031035_1.fastq
Input file:	SRR5031035_1.fastq
trimmed:	SRR5031035-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 07:10:56 2020 >> started

Wed Mar  4 07:10:58 2020 >> done (1.655s)
2701825 reads processed; of these:
    371 ( 0.01%) short reads filtered out after trimming by size control
     14 ( 0.00%) empty reads filtered out after trimming by size control
2701440 (99.99%) reads available; of these:
 138144 ( 5.11%) trimmed reads available after processing
2563296 (94.89%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    119	  0.00%
 19	    113	  0.00%
 20	    225	  0.01%
 21	    289	  0.01%
 22	    449	  0.02%
 23	    488	  0.02%
 24	    584	  0.02%
 25	    717	  0.03%
 26	    527	  0.02%
 27	    685	  0.03%
 28	    704	  0.03%
 29	   1145	  0.04%
 30	    740	  0.03%
 31	    882	  0.03%
 32	   1124	  0.04%
 33	   1151	  0.04%
 34	   1267	  0.05%
 35	   2536	  0.09%
 36	   2462	  0.09%
 37	   2694	  0.10%
 38	   2635	  0.10%
 39	   2871	  0.11%
 40	   3284	  0.12%
 41	   3192	  0.12%
 42	   4109	  0.15%
 43	   5868	  0.22%
 44	   7714	  0.29%
 45	  10012	  0.37%
 46	  14574	  0.54%
 47	  16668	  0.62%
 48	  23704	  0.88%
 49	  24612	  0.91%
 50	2563296	 94.89%
2701440 reads passed initial QC


criterion=sequence-density
sequence-density=82.51
sequence-density-rank=1
fanout-score=21.81
fanout-score-rank=1
prefix-density=84.35
prefix-fanout=21.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC


criterion=fanout-score
sequence-density=82.51
sequence-density-rank=1
fanout-score=21.81
fanout-score-rank=1
prefix-density=84.35
prefix-fanout=21.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC -o SRR5031035 -
Input file:	STDIN
trimmed:	SRR5031035-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC
-- 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 07:11:13 2020 >> started

Wed Mar  4 07:11:17 2020 >> done (3.466s)
2636345 reads processed; of these:
 169726 ( 6.44%) short reads filtered out after trimming by size control
  28265 ( 1.07%) empty reads filtered out after trimming by size control
2438354 (92.49%) reads available; of these:
2266863 (92.97%) trimmed reads available after processing
 171491 ( 7.03%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14287	  0.59%
 19	  28432	  1.17%
 20	 115844	  4.75%
 21	 241520	  9.91%
 22	 670672	 27.51%
 23	 329682	 13.52%
 24	 146261	  6.00%
 25	  44693	  1.83%
 26	  24753	  1.02%
 27	  19711	  0.81%
 28	  24880	  1.02%
 29	  19872	  0.81%
 30	  28075	  1.15%
 31	  45268	  1.86%
 32	  33961	  1.39%
 33	 138981	  5.70%
 34	  37153	  1.52%
 35	  29562	  1.21%
 36	  33580	  1.38%
 37	  17873	  0.73%
 38	  19737	  0.81%
 39	  17816	  0.73%
 40	  25859	  1.06%
 41	  32799	  1.35%
 42	  36086	  1.48%
 43	  25733	  1.06%
 44	  18667	  0.77%
 45	  28263	  1.16%
 46	  22784	  0.93%
 47	  17096	  0.70%
 48	   1816	  0.07%
 49	   2088	  0.09%
 50	 144550	  5.93%


criterion=sequence-density
sequence-density=7.14
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=0.39
sequence-density-rank=30
fanout-score=25.47
fanout-score-rank=1
prefix-density=9.80
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:11:38
                             Started mapping on |	Mar 04 07:11:38
                                    Finished on |	Mar 04 07:12:03
       Mapping speed, Million of reads per hour |	360.50

                          Number of input reads |	2503449
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1235969
                        Uniquely mapped reads % |	49.37%
                          Average mapped length |	25.54
                       Number of splices: Total |	2204
            Number of splices: Annotated (sjdb) |	404
                       Number of splices: GT/AG |	2101
                       Number of splices: GC/AG |	27
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	74
                      Mismatch rate per base, % |	0.27%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.79
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	802821
             % of reads mapped to multiple loci |	32.07%
        Number of reads mapped to too many loci |	67614
             % of reads mapped to too many loci |	2.70%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	15.09%
                     % of reads unmapped: other |	0.77%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	464659	464659	464659
N_multimapping	802821	802821	802821
N_noFeature	96019	115856	846311
N_ambiguous	675651	343448	20537
UnstrandedReadsAssigned:464299 PositiveStrandReadsAssigned:776665 NegativeStrandReadsAssigned:369121
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031035 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: SRR5031035-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,503,449 reads, 586,071 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,142 rounds

 109283 SRR5031035.ke.tsv
  52636 SRR5031035.se.tsv
 161919 total
==> SRR5031035.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

==> SRR5031035.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031035 completed mapping pipeline successfully
