Starting /dee2/code/volunteer_pipeline.sh SRR5031048
    current disk space = 160488046592
    free memory = 73934064 
SRR5031048 SRAfilesize
21af27372eb4e7ecc27c1d88a7e61700  SRR5031048.sra
SRR5031048.sra file validated
SRR5031048 is single end
SRR5031048 is conventional basespace
SRR5031048 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031048_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.219	33.0	31.0	34.0	30.0	34.0
2	32.4795	34.0	31.0	34.0	31.0	34.0
3	32.44925	34.0	31.0	34.0	30.0	34.0
4	36.148	37.0	35.0	37.0	35.0	37.0
5	35.8795	37.0	35.0	37.0	35.0	37.0
6	35.63025	37.0	35.0	37.0	33.0	37.0
7	35.751	37.0	35.0	37.0	35.0	37.0
8	35.68	37.0	35.0	37.0	33.0	37.0
9	37.358	39.0	37.0	39.0	34.0	39.0
10	37.58125	39.0	37.0	39.0	35.0	39.0
11	37.551	39.0	37.0	39.0	35.0	39.0
12	37.48425	39.0	37.0	39.0	34.0	39.0
13	37.576	39.0	37.0	39.0	35.0	39.0
14	38.89575	40.0	38.0	41.0	35.0	41.0
15	38.7185	40.0	38.0	41.0	34.0	41.0
16	38.74625	40.0	38.0	41.0	35.0	41.0
17	38.748	40.0	38.0	41.0	34.0	41.0
18	38.7995	40.0	38.0	41.0	35.0	41.0
19	38.36575	40.0	38.0	41.0	34.0	41.0
20	38.6215	40.0	38.0	41.0	34.0	41.0
21	38.59075	40.0	38.0	41.0	34.0	41.0
22	38.8215	40.0	38.0	41.0	35.0	41.0
23	38.5795	40.0	38.0	41.0	34.0	41.0
24	38.75775	40.0	38.0	41.0	35.0	41.0
25	38.91725	40.0	39.0	41.0	35.0	41.0
26	38.8305	40.0	38.0	41.0	35.0	41.0
27	38.76875	40.0	38.0	41.0	35.0	41.0
28	38.75875	40.0	38.0	41.0	34.0	41.0
29	38.328	40.0	38.0	41.0	33.0	41.0
30	38.303	40.0	38.0	41.0	34.0	41.0
31	38.43575	40.0	38.0	41.0	34.0	41.0
32	38.176	40.0	38.0	41.0	33.0	41.0
33	37.966	40.0	38.0	41.0	33.0	41.0
34	37.92175	40.0	38.0	41.0	33.0	41.0
35	37.79275	40.0	37.0	41.0	33.0	41.0
36	37.60975	40.0	37.0	41.0	32.0	41.0
37	37.4325	40.0	37.0	41.0	31.0	41.0
38	36.9025	39.0	36.0	41.0	30.0	41.0
39	37.36	39.0	37.0	41.0	31.0	41.0
40	37.6385	40.0	37.0	41.0	33.0	41.0
41	37.6595	40.0	37.0	41.0	33.0	41.0
42	37.894	40.0	37.0	41.0	33.0	41.0
43	38.167	40.0	38.0	41.0	33.0	41.0
44	37.93075	40.0	38.0	41.0	33.0	41.0
45	37.87025	40.0	37.0	41.0	33.0	41.0
46	37.8075	40.0	37.0	41.0	33.0	41.0
47	37.3825	40.0	37.0	41.0	32.0	41.0
48	36.99625	40.0	36.0	41.0	31.0	41.0
49	37.03925	40.0	36.0	41.0	31.0	41.0
50	36.52925	39.0	36.0	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
6	1.0
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	3.0
16	2.0
17	0.0
18	4.0
19	0.0
20	1.0
21	2.0
22	4.0
23	5.0
24	8.0
25	8.0
26	19.0
27	24.0
28	24.0
29	43.0
30	48.0
31	69.0
32	79.0
33	106.0
34	148.0
35	210.0
36	301.0
37	484.0
38	687.0
39	1720.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.3999999999999995	24.925	55.15	12.525
2	27.613806903451728	26.88844422211106	17.83391695847924	27.66383191595798
3	21.725	26.1	20.9	31.275
4	34.175	27.3	13.875000000000002	24.65
5	26.0	37.4	26.674999999999997	9.925
6	35.475	14.85	36.675000000000004	13.0
7	14.374999999999998	24.725	24.125	36.775000000000006
8	30.4	27.250000000000004	15.275	27.075
9	17.9	35.05	33.074999999999996	13.975000000000001
10	19.8	28.575	25.775	25.85
11	35.975	8.35	16.525000000000002	39.15
12	15.1	21.224999999999998	29.95	33.725
13	31.0	16.425	37.0	15.575
14	33.85	27.575	25.174999999999997	13.4
15	37.75	22.875	26.950000000000003	12.425
16	18.375	17.125	26.1	38.4
17	23.125	27.125	36.525	13.225000000000001
18	24.349999999999998	18.55	29.25	27.85
19	31.574999999999996	17.974999999999998	34.225	16.225
20	47.5	13.0	27.200000000000003	12.3
21	21.8	18.575	33.525	26.1
22	28.625	10.95	50.55	9.875
23	25.924999999999997	14.174999999999999	46.675	13.225000000000001
24	54.925000000000004	11.95	26.724999999999998	6.4
25	54.35	24.175	13.725000000000001	7.75
26	28.349999999999998	50.24999999999999	12.2	9.2
27	13.325000000000001	51.4	24.05	11.225
28	9.25	25.025	52.97500000000001	12.75
29	10.525	11.55	58.425000000000004	19.5
30	8.674999999999999	6.0	38.800000000000004	46.525
31	12.125	4.725	47.125	36.025
32	27.450000000000003	4.95	22.825	44.775
33	57.25	6.7250000000000005	12.65	23.375
34	68.65	5.45	13.225000000000001	12.675
35	66.425	5.375	19.775000000000002	8.425
36	43.974999999999994	6.0249999999999995	38.5	11.5
37	47.025	8.375	20.8	23.799999999999997
38	24.575	12.275	11.025	52.125
39	14.075	23.0	8.6	54.325
40	14.924999999999999	51.675000000000004	7.775	25.624999999999996
41	24.775	52.400000000000006	8.225	14.6
42	52.575	30.0	8.25	9.175
43	55.75	28.95	6.4750000000000005	8.825
44	30.2	50.975	6.675000000000001	12.15
45	16.6	53.27499999999999	10.299999999999999	19.825
46	11.075	26.075	18.4	44.45
47	8.4	14.249999999999998	39.574999999999996	37.775
48	9.225	10.25	21.8	58.72500000000001
49	12.4	19.05	12.4	56.15
50	19.825	38.6	11.05	30.525000000000002
>>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	0.5
24	1.0
25	1.5
26	2.0
27	1.5
28	1.0
29	1.5
30	2.0
31	4.0
32	6.0
33	9.5
34	13.0
35	16.0
36	19.0
37	18.0
38	17.0
39	18.5
40	20.0
41	32.0
42	44.0
43	137.0
44	230.0
45	243.0
46	256.0
47	341.0
48	426.0
49	586.0
50	746.0
51	797.0
52	848.0
53	605.5
54	363.0
55	410.0
56	457.0
57	331.5
58	206.0
59	141.0
60	76.0
61	60.5
62	45.0
63	79.5
64	114.0
65	68.5
66	23.0
67	18.0
68	13.0
69	15.0
70	17.0
71	31.5
72	46.0
73	24.5
74	3.0
75	1.5
76	0.0
77	0.5
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	35.125
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.01779359430604	26.35
2	9.8932384341637	6.950000000000001
3	4.6263345195729535	4.875
4	2.704626334519573	3.8
5	1.1387900355871887	2.0
6	1.0676156583629894	2.25
7	0.7829181494661922	1.925
8	0.3558718861209964	1.0
9	0.3558718861209964	1.125
>10	3.202846975088968	21.05
>50	0.5693950177935944	14.475
>100	0.2846975088967972	14.2
>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	170	4.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	159	3.975	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	123	3.075	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	116	2.9000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	95	2.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	85	2.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	80	2.0	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	72	1.7999999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	67	1.675	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	63	1.575	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	63	1.575	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	54	1.35	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGC	36	0.8999999999999999	RNA PCR Primer, Index 20 (100% over 50bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	32	0.8	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	24	0.6	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	16	0.4	RNA PCR Primer, Index 1 (97% over 35bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	15	0.375	No Hit
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	15	0.375	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	10	0.25	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTC	10	0.25	RNA PCR Primer, Index 20 (100% over 44bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTG	6	0.15	RNA PCR Primer, Index 15 (97% over 36bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTAT	6	0.15	RNA PCR Primer, Index 20 (100% over 48bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	6	0.15	RNA PCR Primer, Index 1 (97% over 35bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGTGGAATTCTCGGGTGC	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TTGCAATGATGTCATCTTACTACTGAAATGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
>>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	1.025	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	1.225	0.0	0.0	0.0
6	0.0	1.225	0.0	0.0	0.0
7	0.0	1.525	0.0	0.0	0.0
8	0.0	1.6	0.0	0.0	0.0
9	0.0	1.65	0.0	0.0	0.0
10	0.0	1.725	0.0	0.0	0.0
11	0.0	1.9	0.0	0.0	0.0
12	0.0	2.2	0.0	0.0	0.0
13	0.0	2.425	0.0	0.0	0.0
14	0.0	2.7	0.0	0.0	0.0
15	0.0	3.075	0.0	0.0	0.0
16	0.0	3.95	0.0	0.0	0.0
17	0.0	4.3	0.0	0.0	0.0
18	0.0	5.125	0.0	0.0	0.0
19	0.0	5.65	0.0	0.0	0.0
20	0.0	6.8	0.0	0.0	0.0
21	0.0	11.575	0.0	0.0	0.0
22	0.0	24.65	0.0	0.0	0.0
23	0.0	57.15	0.0	0.0	0.0
24	0.0	72.0	0.0	0.0	0.0
25	0.0	77.7	0.0	0.0	0.0
26	0.0	79.3	0.0	0.0	0.0
27	0.0	80.0	0.0	0.0	0.0
28	0.0	80.775	0.0	0.0	0.0
29	0.0	81.425	0.0	0.0	0.0
30	0.0	81.9	0.0	0.0	0.0
31	0.0	82.625	0.0	0.0	0.0
32	0.0	83.6	0.0	0.0	0.0
33	0.0	84.825	0.0	0.0	0.0
34	0.0	86.875	0.0	0.0	0.0
35	0.0	87.65	0.0	0.0	0.0
36	0.0	88.525	0.0	0.0	0.0
37	0.0	88.95	0.0	0.0	0.0
38	0.0	89.175	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	40	5.315087E-9	44.000004	2
GGTGAGT	20	6.952051E-4	44.000004	17
ATCCAGG	20	6.952051E-4	44.000004	9
TTGTATA	20	6.952051E-4	44.000004	13
TCGGTGA	20	6.952051E-4	44.000004	15
TCCAGGA	20	6.952051E-4	44.000004	10
GTATAGT	20	6.952051E-4	44.000004	15
ATAGTTT	20	6.952051E-4	44.000004	17
AGTAATC	20	6.952051E-4	44.000004	5
AGGCTTG	20	6.952051E-4	44.000004	18
CGGTGAG	20	6.952051E-4	44.000004	16
TAATCCA	20	6.952051E-4	44.000004	7
GGTAGTA	40	5.315087E-9	44.000004	4
AGGTAGT	40	5.315087E-9	44.000004	3
TGTATAG	20	6.952051E-4	44.000004	14
GTAATCC	20	6.952051E-4	44.000004	6
GTCGGTG	20	6.952051E-4	44.000004	14
CCAGGAT	20	6.952051E-4	44.000004	11
CTCGACT	25	3.6958358E-5	44.0	13
AACGCTG	25	3.6958358E-5	44.0	8
>>END_MODULE
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
Read 155190 spots for SRR5031048.sra
Written 155190 spots for SRR5031048.sra
Read 155184 spots for SRR5031048.sra
Written 155184 spots for SRR5031048.sra
SRR ids: ['SRR5031048.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_7fg_z3e_
SRR5031048.sra spots: 1862214
blocks: [[1, 155184], [155185, 310368], [310369, 465552], [465553, 620736], [620737, 775920], [775921, 931104], [931105, 1086288], [1086289, 1241472], [1241473, 1396656], [1396657, 1551840], [1551841, 1707024], [1707025, 1862214]]
SRR5031048 file size 321690
SRR5031048 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031048 SRR5031048_1.fastq
Input file:	SRR5031048_1.fastq
trimmed:	SRR5031048-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 07:12:59 2020 >> started

Wed Mar  4 07:13:00 2020 >> done (1.421s)
1862214 reads processed; of these:
    149 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
1862060 (99.99%) reads available; of these:
  95835 ( 5.15%) trimmed reads available after processing
1766225 (94.85%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     42	  0.00%
 19	     50	  0.00%
 20	    110	  0.01%
 21	    137	  0.01%
 22	    240	  0.01%
 23	    264	  0.01%
 24	    238	  0.01%
 25	    358	  0.02%
 26	    313	  0.02%
 27	    424	  0.02%
 28	    488	  0.03%
 29	    737	  0.04%
 30	    550	  0.03%
 31	    630	  0.03%
 32	    667	  0.04%
 33	    734	  0.04%
 34	    908	  0.05%
 35	   1635	  0.09%
 36	   1486	  0.08%
 37	   1584	  0.09%
 38	   1593	  0.09%
 39	   1770	  0.10%
 40	   2230	  0.12%
 41	   1999	  0.11%
 42	   2637	  0.14%
 43	   3881	  0.21%
 44	   5668	  0.30%
 45	   6939	  0.37%
 46	   9431	  0.51%
 47	  12079	  0.65%
 48	  18133	  0.97%
 49	  17880	  0.96%
 50	1766225	 94.85%
1862060 reads passed initial QC


criterion=sequence-density
sequence-density=88.52
sequence-density-rank=1
fanout-score=20.90
fanout-score-rank=1
prefix-density=89.76
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC


criterion=fanout-score
sequence-density=88.52
sequence-density-rank=1
fanout-score=20.90
fanout-score-rank=1
prefix-density=89.76
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC -o SRR5031048 -
Input file:	STDIN
trimmed:	SRR5031048-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC
-- 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 07:13:12 2020 >> started

Wed Mar  4 07:13:15 2020 >> done (2.935s)
1820216 reads processed; of these:
  76686 ( 4.21%) short reads filtered out after trimming by size control
  19127 ( 1.05%) empty reads filtered out after trimming by size control
1724403 (94.74%) reads available; of these:
1657559 (96.12%) trimmed reads available after processing
  66844 ( 3.88%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   9250	  0.54%
 19	  19336	  1.12%
 20	  92947	  5.39%
 21	 247852	 14.37%
 22	 595227	 34.52%
 23	 270171	 15.67%
 24	 114458	  6.64%
 25	  27298	  1.58%
 26	  14171	  0.82%
 27	  11831	  0.69%
 28	  12314	  0.71%
 29	  10767	  0.62%
 30	  13200	  0.77%
 31	  16095	  0.93%
 32	  18528	  1.07%
 33	  48789	  2.83%
 34	  15154	  0.88%
 35	  11277	  0.65%
 36	  14197	  0.82%
 37	   6692	  0.39%
 38	   8443	  0.49%
 39	   6907	  0.40%
 40	  10528	  0.61%
 41	  13127	  0.76%
 42	  15546	  0.90%
 43	  10683	  0.62%
 44	   8028	  0.47%
 45	  10301	  0.60%
 46	   7139	  0.41%
 47	   6479	  0.38%
 48	    688	  0.04%
 49	    784	  0.05%
 50	  56196	  3.26%


criterion=sequence-density
sequence-density=4.52
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AAGCTGCCAGTTGAAGAACTGTTGGAATTCT


criterion=fanout-score
sequence-density=0.03
sequence-density-rank=36
fanout-score=306.80
fanout-score-rank=1
prefix-density=5.78
prefix-fanout=1.4
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:13:36
                             Started mapping on |	Mar 04 07:13:37
                                    Finished on |	Mar 04 07:14:02
       Mapping speed, Million of reads per hour |	254.34

                          Number of input reads |	1766247
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	867669
                        Uniquely mapped reads % |	49.13%
                          Average mapped length |	23.88
                       Number of splices: Total |	1052
            Number of splices: Annotated (sjdb) |	189
                       Number of splices: GT/AG |	960
                       Number of splices: GC/AG |	15
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	76
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.73
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.09
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	699888
             % of reads mapped to multiple loci |	39.63%
        Number of reads mapped to too many loci |	26292
             % of reads mapped to too many loci |	1.49%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.26%
                     % of reads unmapped: other |	0.51%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	198690	198690	198690
N_multimapping	699888	699888	699888
N_noFeature	41088	49236	610426
N_ambiguous	485564	258693	6248
UnstrandedReadsAssigned:341017 PositiveStrandReadsAssigned:559740 NegativeStrandReadsAssigned:250995
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031048 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: SRR5031048-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,766,247 reads, 426,874 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,043 rounds

 109283 SRR5031048.ke.tsv
  52636 SRR5031048.se.tsv
 161919 total
==> SRR5031048.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

==> SRR5031048.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031048 completed mapping pipeline successfully
