Starting /dee2/code/volunteer_pipeline.sh SRR5031045
    current disk space = 160489259008
    free memory = 73952296 
SRR5031045 SRAfilesize
9d79c2ced09f8705ea43fc246f7b0ddf  SRR5031045.sra
SRR5031045.sra file validated
SRR5031045 is single end
SRR5031045 is conventional basespace
SRR5031045 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031045_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	32.34375	33.0	31.0	34.0	31.0	34.0
2	32.5455	34.0	31.0	34.0	31.0	34.0
3	32.62925	34.0	31.0	34.0	31.0	34.0
4	36.2205	37.0	35.0	37.0	35.0	37.0
5	35.96575	37.0	35.0	37.0	35.0	37.0
6	35.84675	37.0	35.0	37.0	35.0	37.0
7	36.0185	37.0	35.0	37.0	35.0	37.0
8	35.84025	37.0	35.0	37.0	35.0	37.0
9	37.632	39.0	37.0	39.0	35.0	39.0
10	37.83325	39.0	37.0	39.0	35.0	39.0
11	37.6805	39.0	37.0	39.0	35.0	39.0
12	37.63675	39.0	37.0	39.0	35.0	39.0
13	37.702	39.0	37.0	39.0	35.0	39.0
14	39.08625	40.0	38.0	41.0	36.0	41.0
15	39.067	40.0	38.0	41.0	36.0	41.0
16	39.022	40.0	38.0	41.0	36.0	41.0
17	38.99975	40.0	38.0	41.0	35.0	41.0
18	39.06775	40.0	39.0	41.0	35.0	41.0
19	38.495	40.0	38.0	41.0	34.0	41.0
20	38.82225	40.0	38.0	41.0	35.0	41.0
21	38.7815	40.0	38.0	41.0	34.0	41.0
22	38.95525	40.0	39.0	41.0	35.0	41.0
23	38.7625	40.0	38.0	41.0	35.0	41.0
24	38.75825	40.0	38.0	41.0	35.0	41.0
25	39.06775	40.0	39.0	41.0	36.0	41.0
26	38.72925	40.0	38.0	41.0	35.0	41.0
27	38.79775	40.0	38.0	41.0	35.0	41.0
28	38.74625	40.0	38.0	41.0	35.0	41.0
29	38.27725	40.0	38.0	41.0	33.0	41.0
30	38.186	40.0	38.0	41.0	33.0	41.0
31	38.51	40.0	38.0	41.0	34.0	41.0
32	38.4225	40.0	38.0	41.0	34.0	41.0
33	38.412	40.0	38.0	41.0	34.0	41.0
34	38.4345	40.0	38.0	41.0	34.0	41.0
35	38.262	40.0	38.0	41.0	34.0	41.0
36	37.899	40.0	37.0	41.0	33.0	41.0
37	37.57325	40.0	37.0	41.0	32.0	41.0
38	36.80175	39.0	36.0	41.0	30.0	41.0
39	37.347	39.0	37.0	41.0	32.0	41.0
40	37.63975	40.0	37.0	41.0	33.0	41.0
41	37.6885	40.0	37.0	41.0	32.0	41.0
42	37.95025	40.0	38.0	41.0	33.0	41.0
43	38.22925	40.0	38.0	41.0	34.0	41.0
44	37.8895	40.0	37.0	41.0	33.0	41.0
45	37.85825	40.0	38.0	41.0	33.0	41.0
46	37.75775	40.0	37.0	41.0	33.0	41.0
47	37.10225	40.0	36.0	41.0	31.0	41.0
48	36.93225	40.0	36.0	41.0	31.0	41.0
49	37.10625	40.0	36.0	41.0	31.0	41.0
50	36.5465	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
14	1.0
15	2.0
16	0.0
17	0.0
18	1.0
19	2.0
20	7.0
21	2.0
22	5.0
23	2.0
24	10.0
25	3.0
26	20.0
27	18.0
28	22.0
29	26.0
30	41.0
31	55.0
32	89.0
33	119.0
34	167.0
35	176.0
36	283.0
37	436.0
38	757.0
39	1756.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.95	23.400000000000002	48.65	17.0
2	23.640010027575833	28.052143394334422	19.4785660566558	28.829280521433944
3	25.224999999999998	16.975	22.400000000000002	35.4
4	35.125	28.475	15.35	21.05
5	21.7	37.4	27.400000000000002	13.5
6	27.85	15.625	39.800000000000004	16.725
7	17.75	21.075	20.525	40.65
8	21.05	28.849999999999998	19.975	30.125
9	24.6	31.25	26.875	17.275
10	22.725	19.925	29.849999999999998	27.500000000000004
11	34.35	11.875	17.8	35.975
12	17.349999999999998	20.549999999999997	31.825	30.275000000000002
13	27.975	18.175	34.675	19.175
14	29.95	31.324999999999996	20.200000000000003	18.525
15	38.4	23.45	25.6	12.55
16	19.35	19.1	24.349999999999998	37.2
17	27.725	22.95	34.825	14.499999999999998
18	26.900000000000002	17.275	30.975	24.85
19	36.825	15.174999999999999	31.974999999999998	16.025
20	45.425	15.950000000000001	25.75	12.875
21	23.849999999999998	23.075000000000003	24.025	29.049999999999997
22	31.1	14.325	43.725	10.85
23	25.474999999999998	13.975000000000001	43.55	17.0
24	49.075	15.525	25.924999999999997	9.475
25	48.525	24.099999999999998	16.5	10.875
26	28.7	43.25	14.85	13.200000000000001
27	16.075	45.125	23.400000000000002	15.4
28	12.375	25.0	45.675	16.950000000000003
29	14.6	13.775	53.349999999999994	18.275
30	10.549999999999999	6.950000000000001	35.475	47.025
31	14.85	5.625	46.2	33.324999999999996
32	27.650000000000002	7.199999999999999	21.625	43.525000000000006
33	51.05	10.625	14.875	23.45
34	59.199999999999996	7.5	17.724999999999998	15.575
35	64.9	7.449999999999999	18.825	8.825
36	42.375	9.4	34.699999999999996	13.525
37	44.95	12.8	19.7	22.55
38	23.175	19.950000000000003	13.025	43.85
39	16.775000000000002	23.175	12.475	47.575
40	16.75	45.4	12.6	25.25
41	23.7	46.125	10.7	19.475
42	46.025	30.099999999999998	12.825000000000001	11.05
43	50.849999999999994	28.4	9.025	11.725
44	33.050000000000004	44.675	7.575	14.7
45	22.15	48.125	13.125	16.6
46	15.45	26.075	17.325	41.15
47	10.8	16.425	38.2	34.575
48	12.575	12.4	21.475	53.55
49	15.425	17.825	14.799999999999999	51.949999999999996
50	17.675	35.699999999999996	13.625000000000002	33.0
>>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	1.0
12	2.0
13	1.0
14	0.0
15	0.5
16	1.0
17	0.5
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	0.5
28	1.0
29	2.0
30	3.0
31	5.5
32	8.0
33	11.0
34	14.0
35	18.5
36	23.0
37	32.5
38	42.0
39	47.5
40	53.0
41	50.0
42	47.0
43	92.0
44	137.0
45	166.0
46	195.0
47	302.0
48	409.0
49	489.5
50	570.0
51	721.0
52	872.0
53	618.0
54	364.0
55	481.0
56	598.0
57	427.0
58	256.0
59	164.5
60	73.0
61	57.5
62	42.0
63	100.0
64	158.0
65	91.5
66	25.0
67	21.0
68	17.0
69	21.5
70	26.0
71	43.5
72	61.0
73	31.0
74	1.0
75	0.5
76	0.0
77	0.5
78	1.0
79	1.0
80	1.0
81	0.5
82	0.0
83	0.0
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	0.0
2	0.27499999999999997
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	41.0
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.58536585365854	31.4
2	10.0	8.200000000000001
3	4.573170731707317	5.625
4	2.2560975609756095	3.6999999999999997
5	0.853658536585366	1.7500000000000002
6	1.097560975609756	2.7
7	0.4878048780487805	1.4000000000000001
8	0.3658536585365854	1.2
9	0.426829268292683	1.575
>10	2.804878048780488	20.175
>50	0.3658536585365854	11.875
>100	0.1829268292682927	10.4
>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	155	3.875	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	146	3.65	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	115	2.875	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	93	2.325	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	90	2.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	89	2.225	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	50	1.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGC	35	0.8750000000000001	RNA PCR Primer, Index 17 (100% over 50bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	31	0.775	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	30	0.75	RNA PCR Primer, Index 1 (97% over 35bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	24	0.6	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTC	17	0.42500000000000004	RNA PCR Primer, Index 17 (100% over 44bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	14	0.35000000000000003	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	13	0.325	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	12	0.3	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	12	0.3	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	10	0.25	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	9	0.22499999999999998	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	8	0.2	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTAT	7	0.17500000000000002	RNA PCR Primer, Index 17 (100% over 48bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAG	6	0.15	RNA PCR Primer, Index 3 (97% over 37bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTA	5	0.125	RNA PCR Primer, Index 3 (97% over 36bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CACCCAGAAGATTTCATGACCAATGAACACTCTGACCATGGAATTCTCGG	5	0.125	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.975	0.0	0.0	0.0
2	0.0	0.975	0.0	0.0	0.0
3	0.0	1.15	0.0	0.0	0.0
4	0.0	1.175	0.0	0.0	0.0
5	0.0	1.25	0.0	0.0	0.0
6	0.0	1.325	0.0	0.0	0.0
7	0.0	1.85	0.0	0.0	0.0
8	0.0	2.025	0.0	0.0	0.0
9	0.0	2.175	0.0	0.0	0.0
10	0.0	2.35	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	2.9	0.0	0.0	0.0
14	0.0	3.25	0.0	0.0	0.0
15	0.0	3.85	0.0	0.0	0.0
16	0.0	5.15	0.0	0.0	0.0
17	0.0	5.775	0.0	0.0	0.0
18	0.0	7.05	0.0	0.0	0.0
19	0.0	7.4	0.0	0.0	0.0
20	0.0	8.375	0.0	0.0	0.0
21	0.0	14.0	0.0	0.0	0.0
22	0.0	23.625	0.0	0.0	0.0
23	0.0	50.675	0.0	0.0	0.0
24	0.0	62.95	0.0	0.0	0.0
25	0.0	69.2	0.0	0.0	0.0
26	0.0	70.5	0.0	0.0	0.0
27	0.0	71.175	0.0	0.0	0.0
28	0.0	71.9	0.0	0.0	0.0
29	0.0	72.6	0.0	0.0	0.0
30	0.0	73.2	0.0	0.0	0.0
31	0.0	73.975	0.0	0.0	0.0
32	0.0	75.025	0.0	0.0	0.0
33	0.0	76.425	0.0	0.0	0.0
34	0.0	81.075	0.0	0.0	0.0
35	0.0	82.7	0.0	0.0	0.0
36	0.0	83.575	0.0	0.0	0.0
37	0.0	84.475	0.0	0.0	0.0
38	0.0	84.8	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCGACC	30	1.7904422E-6	44.531647	1
GCGACCT	30	1.7904422E-6	44.531647	2
TCGGATC	30	1.7904422E-6	44.531647	1
CGGATCC	30	1.7904422E-6	44.531647	2
ATTGCAC	25	3.4343255E-5	44.531647	2
GAGGTAG	20	6.54202E-4	44.531643	2
TATTGCA	20	6.54202E-4	44.531643	1
ACATTCA	35	9.2630216E-8	44.531643	2
ACCCTGT	20	6.54202E-4	44.531643	2
TGAGGTA	20	6.54202E-4	44.531643	1
TACCCTG	20	6.54202E-4	44.531643	1
AACATTC	35	9.2630216E-8	44.531643	1
AACGCTG	25	3.7082697E-5	43.975002	8
CGCTGAT	25	3.7082697E-5	43.975002	28
TTGCACT	25	3.7082697E-5	43.975002	3
ACGCTGT	25	3.7082697E-5	43.975002	9
CTGAGCT	30	1.9592044E-6	43.975002	11
GCGACCC	25	3.7082697E-5	43.975002	22
TTCAACG	25	3.7082697E-5	43.975002	5
TCGGTGA	25	3.7082697E-5	43.975002	15
>>END_MODULE
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277266 spots for SRR5031045.sra
Written 277266 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
Read 277255 spots for SRR5031045.sra
Written 277255 spots for SRR5031045.sra
SRR ids: ['SRR5031045.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_mxmbcpe9
SRR5031045.sra spots: 3327071
blocks: [[1, 277255], [277256, 554510], [554511, 831765], [831766, 1109020], [1109021, 1386275], [1386276, 1663530], [1663531, 1940785], [1940786, 2218040], [2218041, 2495295], [2495296, 2772550], [2772551, 3049805], [3049806, 3327071]]
SRR5031045 file size 575595
SRR5031045 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031045 SRR5031045_1.fastq
Input file:	SRR5031045_1.fastq
trimmed:	SRR5031045-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 07:13:01 2020 >> started

Wed Mar  4 07:13:03 2020 >> done (1.905s)
3327071 reads processed; of these:
    268 ( 0.01%) short reads filtered out after trimming by size control
     17 ( 0.00%) empty reads filtered out after trimming by size control
3326786 (99.99%) reads available; of these:
 175295 ( 5.27%) trimmed reads available after processing
3151491 (94.73%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     79	  0.00%
 19	     89	  0.00%
 20	    216	  0.01%
 21	    250	  0.01%
 22	    378	  0.01%
 23	    482	  0.01%
 24	    557	  0.02%
 25	    751	  0.02%
 26	    550	  0.02%
 27	    778	  0.02%
 28	    899	  0.03%
 29	   1293	  0.04%
 30	    905	  0.03%
 31	   1097	  0.03%
 32	   1175	  0.04%
 33	   1497	  0.04%
 34	   1683	  0.05%
 35	   3396	  0.10%
 36	   2860	  0.09%
 37	   3281	  0.10%
 38	   3140	  0.09%
 39	   3274	  0.10%
 40	   3729	  0.11%
 41	   3668	  0.11%
 42	   4778	  0.14%
 43	   7216	  0.22%
 44	   9782	  0.29%
 45	  12575	  0.38%
 46	  18887	  0.57%
 47	  21381	  0.64%
 48	  30760	  0.92%
 49	  33889	  1.02%
 50	3151491	 94.73%
3326786 reads passed initial QC


criterion=sequence-density
sequence-density=84.92
sequence-density-rank=1
fanout-score=21.32
fanout-score-rank=1
prefix-density=86.79
prefix-fanout=20.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC


criterion=fanout-score
sequence-density=84.92
sequence-density-rank=1
fanout-score=21.32
fanout-score-rank=1
prefix-density=86.79
prefix-fanout=20.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC -o SRR5031045 -
Input file:	STDIN
trimmed:	SRR5031045-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC
-- 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 07:13:20 2020 >> started

Wed Mar  4 07:13:25 2020 >> done (5.155s)
3248509 reads processed; of these:
 184395 ( 5.68%) short reads filtered out after trimming by size control
  26600 ( 0.82%) empty reads filtered out after trimming by size control
3037514 (93.50%) reads available; of these:
2873152 (94.59%) trimmed reads available after processing
 164362 ( 5.41%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17813	  0.59%
 19	  30070	  0.99%
 20	 171618	  5.65%
 21	 335454	 11.04%
 22	 907955	 29.89%
 23	 399769	 13.16%
 24	 189455	  6.24%
 25	  53485	  1.76%
 26	  26963	  0.89%
 27	  24894	  0.82%
 28	  25821	  0.85%
 29	  20397	  0.67%
 30	  33503	  1.10%
 31	  46810	  1.54%
 32	  49009	  1.61%
 33	 170511	  5.61%
 34	  49984	  1.65%
 35	  36031	  1.19%
 36	  41974	  1.38%
 37	  19818	  0.65%
 38	  22064	  0.73%
 39	  19060	  0.63%
 40	  27088	  0.89%
 41	  31167	  1.03%
 42	  33944	  1.12%
 43	  23451	  0.77%
 44	  20092	  0.66%
 45	  27837	  0.92%
 46	  19691	  0.65%
 47	  16194	  0.53%
 48	   1574	  0.05%
 49	   2226	  0.07%
 50	 141792	  4.67%


criterion=sequence-density
sequence-density=2.90
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCT


criterion=fanout-score
sequence-density=0.48
sequence-density-rank=34
fanout-score=17.77
fanout-score-rank=1
prefix-density=8.58
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:13:47
                             Started mapping on |	Mar 04 07:13:47
                                    Finished on |	Mar 04 07:14:13
       Mapping speed, Million of reads per hour |	431.42

                          Number of input reads |	3115791
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1637362
                        Uniquely mapped reads % |	52.55%
                          Average mapped length |	24.66
                       Number of splices: Total |	2462
            Number of splices: Annotated (sjdb) |	625
                       Number of splices: GT/AG |	2326
                       Number of splices: GC/AG |	32
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	104
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.75
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	980952
             % of reads mapped to multiple loci |	31.48%
        Number of reads mapped to too many loci |	89865
             % of reads mapped to too many loci |	2.88%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.25%
                     % of reads unmapped: other |	0.83%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	497477	497477	497477
N_multimapping	980952	980952	980952
N_noFeature	78093	99505	1080358
N_ambiguous	909658	417978	12397
UnstrandedReadsAssigned:649611 PositiveStrandReadsAssigned:1119879 NegativeStrandReadsAssigned:544607
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031045 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: SRR5031045-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,115,791 reads, 795,162 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 615 rounds

 109283 SRR5031045.ke.tsv
  52636 SRR5031045.se.tsv
 161919 total
==> SRR5031045.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

==> SRR5031045.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031045 completed mapping pipeline successfully
