Starting /dee2/code/volunteer_pipeline.sh SRR5031010
    current disk space = 160541310976
    free memory = 73947208 
SRR5031010 SRAfilesize
346d25733bc0a3f1ba7451dc1530f5c5  SRR5031010.sra
SRR5031010.sra file validated
SRR5031010 is single end
SRR5031010 is conventional basespace
SRR5031010 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031010_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	32.18275	33.0	31.0	34.0	30.0	34.0
2	32.45475	34.0	31.0	34.0	31.0	34.0
3	32.481	34.0	31.0	34.0	31.0	34.0
4	36.088	37.0	35.0	37.0	35.0	37.0
5	35.9615	37.0	35.0	37.0	35.0	37.0
6	35.77525	37.0	35.0	37.0	33.0	37.0
7	35.664	37.0	35.0	37.0	33.0	37.0
8	35.89325	37.0	35.0	37.0	35.0	37.0
9	37.47525	39.0	37.0	39.0	35.0	39.0
10	37.4685	39.0	37.0	39.0	35.0	39.0
11	37.0115	39.0	37.0	39.0	33.0	39.0
12	37.4845	39.0	37.0	39.0	34.0	39.0
13	37.494	39.0	37.0	39.0	34.0	39.0
14	38.91875	40.0	38.0	41.0	35.0	41.0
15	38.86275	40.0	38.0	41.0	35.0	41.0
16	38.9195	40.0	38.0	41.0	35.0	41.0
17	38.97275	40.0	38.0	41.0	35.0	41.0
18	38.87475	40.0	38.0	41.0	35.0	41.0
19	38.7025	40.0	38.0	41.0	34.0	41.0
20	38.72525	40.0	38.0	41.0	34.0	41.0
21	38.84	40.0	38.0	41.0	34.0	41.0
22	38.85775	40.0	38.0	41.0	34.0	41.0
23	38.565	40.0	38.0	41.0	34.0	41.0
24	38.798	40.0	38.0	41.0	34.0	41.0
25	38.9235	40.0	38.0	41.0	35.0	41.0
26	38.7735	40.0	38.0	41.0	34.0	41.0
27	38.8555	40.0	38.0	41.0	35.0	41.0
28	38.59975	40.0	38.0	41.0	34.0	41.0
29	38.29175	40.0	38.0	41.0	33.0	41.0
30	38.198	40.0	38.0	41.0	33.0	41.0
31	38.36875	40.0	38.0	41.0	33.0	41.0
32	38.305	40.0	38.0	41.0	33.0	41.0
33	37.87825	40.0	38.0	41.0	33.0	41.0
34	38.06975	40.0	38.0	41.0	33.0	41.0
35	37.9065	40.0	37.0	41.0	33.0	41.0
36	37.78475	40.0	37.0	41.0	33.0	41.0
37	37.03625	39.0	36.0	41.0	31.0	41.0
38	37.1075	39.0	36.0	41.0	31.0	41.0
39	37.653	40.0	37.0	41.0	33.0	41.0
40	37.74975	40.0	37.0	41.0	33.0	41.0
41	38.0005	40.0	37.0	41.0	33.0	41.0
42	37.7225	40.0	37.0	41.0	33.0	41.0
43	37.75125	40.0	37.0	41.0	33.0	41.0
44	37.6585	40.0	37.0	41.0	33.0	41.0
45	37.6015	40.0	37.0	41.0	33.0	41.0
46	37.3625	40.0	37.0	41.0	33.0	41.0
47	36.72425	40.0	36.0	41.0	31.0	41.0
48	36.5935	39.0	35.0	41.0	30.0	41.0
49	36.576	39.0	35.0	41.0	31.0	41.0
50	35.93525	38.0	34.0	41.0	30.0	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
15	2.0
16	1.0
17	2.0
18	1.0
19	1.0
20	0.0
21	7.0
22	4.0
23	6.0
24	7.0
25	12.0
26	20.0
27	20.0
28	26.0
29	43.0
30	41.0
31	55.0
32	114.0
33	114.0
34	161.0
35	189.0
36	295.0
37	471.0
38	768.0
39	1640.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.325	24.75	47.075	17.849999999999998
2	26.015037593984964	25.46365914786967	20.075187969924812	28.446115288220554
3	22.125	20.075000000000003	23.125	34.675
4	31.5	28.125	16.55	23.825
5	24.525	36.125	26.224999999999998	13.125
6	33.575	15.4	33.425	17.599999999999998
7	17.025000000000002	23.724999999999998	22.375	36.875
8	24.625	26.700000000000003	18.7	29.975
9	21.099999999999998	30.599999999999998	30.15	18.15
10	23.05	23.150000000000002	26.575	27.224999999999998
11	32.95	12.125	18.5	36.425000000000004
12	18.7	19.25	28.925	33.125
13	28.325	18.675	33.675	19.325
14	29.225	29.125	21.725	19.925
15	35.125	24.4	26.400000000000002	14.075
16	20.424999999999997	21.125	24.5	33.95
17	27.3	23.75	35.225	13.725000000000001
18	23.799999999999997	19.175	28.275	28.749999999999996
19	36.199999999999996	15.25	29.25	19.3
20	42.449999999999996	16.025	26.924999999999997	14.6
21	25.575	19.975	26.55	27.900000000000002
22	28.1	13.350000000000001	45.975	12.575
23	28.15	13.700000000000001	40.5	17.65
24	49.925000000000004	15.125	25.924999999999997	9.025
25	47.425	24.325	16.900000000000002	11.35
26	28.95	42.975	14.325	13.750000000000002
27	17.125	43.8	24.224999999999998	14.85
28	12.825000000000001	24.3	45.6	17.275
29	15.15	12.65	51.87500000000001	20.325
30	12.075	8.35	35.375	44.2
31	15.5	6.9750000000000005	44.25	33.275
32	29.225	7.3999999999999995	21.4	41.975
33	49.725	11.075	16.2	23.0
34	56.775	9.65	16.525000000000002	17.05
35	60.925	8.3	20.075000000000003	10.7
36	42.175000000000004	8.95	34.675	14.2
37	41.875	12.675	21.3	24.15
38	23.95	17.375	13.825000000000001	44.85
39	17.599999999999998	22.625	12.9	46.875
40	15.975	44.725	13.450000000000001	25.85
41	25.424999999999997	45.725	9.975000000000001	18.875
42	46.275	28.325	13.775	11.625
43	48.725	27.725	9.925	13.625000000000002
44	33.050000000000004	43.824999999999996	9.375	13.750000000000002
45	21.0	46.625	13.0	19.375
46	15.675	25.650000000000002	18.275	40.400000000000006
47	11.225	16.2	37.275000000000006	35.3
48	13.100000000000001	13.075000000000001	20.175	53.65
49	13.65	19.15	15.875	51.324999999999996
50	19.55	34.65	12.725	33.074999999999996
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.5
4	1.0
5	0.5
6	0.0
7	0.0
8	0.0
9	0.5
10	1.0
11	0.5
12	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	0.5
26	1.0
27	0.5
28	0.0
29	2.5
30	5.0
31	10.5
32	16.0
33	18.0
34	20.0
35	24.5
36	29.0
37	29.5
38	30.0
39	37.0
40	44.0
41	52.5
42	61.0
43	89.5
44	118.0
45	148.5
46	179.0
47	288.5
48	398.0
49	494.0
50	590.0
51	700.0
52	810.0
53	621.5
54	433.0
55	460.0
56	487.0
57	387.0
58	287.0
59	202.0
60	117.0
61	91.5
62	66.0
63	103.5
64	141.0
65	87.5
66	34.0
67	27.0
68	20.0
69	24.5
70	29.0
71	49.0
72	69.0
73	38.5
74	8.0
75	4.5
76	1.0
77	1.5
78	2.0
79	1.5
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	0.25
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	40.325
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.8753874767514	31.0
2	9.733415995040298	7.85
3	3.47179169249845	4.2
4	2.3558586484810915	3.8
5	1.6738995660260385	3.375
6	0.9919404835709857	2.4
7	0.4339739615623063	1.225
8	0.49597024178549287	1.6
9	0.5579665220086795	2.025
>10	2.8518288902665843	22.75
>50	0.3719776813391197	11.05
>100	0.18598884066955984	8.725
>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	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	114	2.85	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	103	2.5749999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	100	2.5	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	94	2.35	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	83	2.075	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	55	1.375	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	54	1.35	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	47	1.175	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
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	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	29	0.7250000000000001	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	24	0.6	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	21	0.525	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	21	0.525	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGC	21	0.525	RNA PCR Primer, Index 30 (100% over 50bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTC	15	0.375	RNA PCR Primer, Index 30 (100% over 44bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	13	0.325	RNA PCR Primer, Index 1 (100% over 31bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	13	0.325	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	12	0.3	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACC	6	0.15	RNA PCR Primer, Index 29 (97% over 37bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	5	0.125	RNA PCR Primer, Index 7 (100% over 35bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATGGAAT	5	0.125	No Hit
CTAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	5	0.125	No Hit
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTGGAATT	5	0.125	No Hit
CTGCGTTCGCGCTCTCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAC	5	0.125	RNA PCR Primer, Index 30 (100% over 36bp)
TGAGAACTGAATTCCATAGGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>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	0.525	0.0	0.0	0.0
2	0.0	0.55	0.0	0.0	0.0
3	0.0	0.65	0.0	0.0	0.0
4	0.0	0.675	0.0	0.0	0.0
5	0.0	0.775	0.0	0.0	0.0
6	0.0	0.9	0.0	0.0	0.0
7	0.0	1.45	0.0	0.0	0.0
8	0.0	1.625	0.0	0.0	0.0
9	0.0	1.925	0.0	0.0	0.0
10	0.0	2.025	0.0	0.0	0.0
11	0.0	2.275	0.0	0.0	0.0
12	0.0	2.5	0.0	0.0	0.0
13	0.0	2.95	0.0	0.0	0.0
14	0.0	3.375	0.0	0.0	0.0
15	0.0	3.725	0.0	0.0	0.0
16	0.0	5.25	0.0	0.0	0.0
17	0.0	5.775	0.0	0.0	0.0
18	0.0	6.95	0.0	0.0	0.0
19	0.0	7.425	0.0	0.0	0.0
20	0.0	8.575	0.0	0.0	0.0
21	0.0	13.075	0.0	0.0	0.0
22	0.0	23.975	0.0	0.0	0.0
23	0.0	49.925	0.0	0.0	0.0
24	0.0	62.0	0.0	0.0	0.0
25	0.0	67.85	0.0	0.0	0.0
26	0.0	68.85	0.0	0.0	0.0
27	0.0	69.775	0.0	0.0	0.0
28	0.0	70.475	0.0	0.0	0.0
29	0.0	71.05	0.0	0.0	0.0
30	0.0	71.775	0.0	0.0	0.0
31	0.0	72.95	0.0	0.0	0.0
32	0.0	73.85	0.0	0.0	0.0
33	0.0	75.25	0.0	0.0	0.0
34	0.0	79.15	0.0	0.0	0.0
35	0.0	80.275	0.0	0.0	0.0
36	0.0	81.25	0.0	0.0	0.0
37	0.0	82.4	0.0	0.0	0.0
38	0.0	83.05	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCTGAT	20	6.952051E-4	44.000004	28
CCGCTGA	20	6.952051E-4	44.000004	27
GTGAGTT	20	6.952051E-4	44.000004	18
GAGTTGG	20	6.952051E-4	44.000004	20
GCTGATG	20	6.952051E-4	44.000004	29
AGTTGGA	20	6.952051E-4	44.000004	21
TGAGTTG	20	6.952051E-4	44.000004	19
GCCCTAG	25	3.6958358E-5	44.0	11
CGCGACC	30	1.9515464E-6	44.0	1
AACGCTG	30	1.9515464E-6	44.0	8
ATCCTAG	25	3.6958358E-5	44.0	5
ACTAATC	25	3.6958358E-5	44.0	1
AATCCTA	25	3.6958358E-5	44.0	4
GGTGAGT	25	3.6958358E-5	44.0	17
ACGCTGT	30	1.9515464E-6	44.0	9
AGCTTGG	35	1.02281774E-7	44.0	14
TCCTAGC	25	3.6958358E-5	44.0	6
GCGACCT	30	1.9515464E-6	44.0	2
GCGACCC	30	1.9515464E-6	44.0	22
TTCAACG	30	1.9515464E-6	44.0	5
>>END_MODULE
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197119 spots for SRR5031010.sra
Written 197119 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
Read 197112 spots for SRR5031010.sra
Written 197112 spots for SRR5031010.sra
SRR ids: ['SRR5031010.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ghtruklo
SRR5031010.sra spots: 2365351
blocks: [[1, 197112], [197113, 394224], [394225, 591336], [591337, 788448], [788449, 985560], [985561, 1182672], [1182673, 1379784], [1379785, 1576896], [1576897, 1774008], [1774009, 1971120], [1971121, 2168232], [2168233, 2365351]]
SRR5031010 file size 408897
SRR5031010 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031010 SRR5031010_1.fastq
Input file:	SRR5031010_1.fastq
trimmed:	SRR5031010-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 07:05:29 2020 >> started

Wed Mar  4 07:05:30 2020 >> done (1.212s)
2365351 reads processed; of these:
    199 ( 0.01%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
2365148 (99.99%) reads available; of these:
 156922 ( 6.63%) trimmed reads available after processing
2208226 (93.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     48	  0.00%
 19	     93	  0.00%
 20	    134	  0.01%
 21	    175	  0.01%
 22	    293	  0.01%
 23	    391	  0.02%
 24	    401	  0.02%
 25	    554	  0.02%
 26	    465	  0.02%
 27	    548	  0.02%
 28	    670	  0.03%
 29	   1060	  0.04%
 30	    710	  0.03%
 31	    806	  0.03%
 32	    903	  0.04%
 33	   1003	  0.04%
 34	   1181	  0.05%
 35	   2076	  0.09%
 36	   2008	  0.08%
 37	   2416	  0.10%
 38	   2484	  0.11%
 39	   2875	  0.12%
 40	   3258	  0.14%
 41	   3381	  0.14%
 42	   4323	  0.18%
 43	   6026	  0.25%
 44	   8651	  0.37%
 45	  11294	  0.48%
 46	  16146	  0.68%
 47	  18862	  0.80%
 48	  29169	  1.23%
 49	  34518	  1.46%
 50	2208226	 93.37%
2365148 reads passed initial QC


criterion=sequence-density
sequence-density=82.98
sequence-density-rank=1
fanout-score=21.67
fanout-score-rank=1
prefix-density=85.20
prefix-fanout=21.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC


criterion=fanout-score
sequence-density=82.98
sequence-density-rank=1
fanout-score=21.67
fanout-score-rank=1
prefix-density=85.20
prefix-fanout=21.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC -o SRR5031010 -
Input file:	STDIN
trimmed:	SRR5031010-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC
-- 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 07:05:43 2020 >> started

Wed Mar  4 07:05:46 2020 >> done (2.403s)
2308157 reads processed; of these:
 153622 ( 6.66%) short reads filtered out after trimming by size control
  18927 ( 0.82%) empty reads filtered out after trimming by size control
2135608 (92.52%) reads available; of these:
1998150 (93.56%) trimmed reads available after processing
 137458 ( 6.44%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12990	  0.61%
 19	  24763	  1.16%
 20	 103248	  4.83%
 21	 235600	 11.03%
 22	 626519	 29.34%
 23	 285515	 13.37%
 24	 123536	  5.78%
 25	  33698	  1.58%
 26	  19278	  0.90%
 27	  16503	  0.77%
 28	  18255	  0.85%
 29	  14532	  0.68%
 30	  22562	  1.06%
 31	  26667	  1.25%
 32	  34948	  1.64%
 33	  95093	  4.45%
 34	  31871	  1.49%
 35	  23873	  1.12%
 36	  27745	  1.30%
 37	  15968	  0.75%
 38	  16439	  0.77%
 39	  15841	  0.74%
 40	  24644	  1.15%
 41	  30408	  1.42%
 42	  34648	  1.62%
 43	  24776	  1.16%
 44	  19041	  0.89%
 45	  23029	  1.08%
 46	  18106	  0.85%
 47	  14185	  0.66%
 48	   1615	  0.08%
 49	   3076	  0.14%
 50	 116636	  5.46%


criterion=sequence-density
sequence-density=6.05
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.48
sequence-density-rank=29
fanout-score=12.86
fanout-score-rank=1
prefix-density=6.17
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:06:06
                             Started mapping on |	Mar 04 07:06:06
                                    Finished on |	Mar 04 07:06:29
       Mapping speed, Million of reads per hour |	343.19

                          Number of input reads |	2192599
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1124509
                        Uniquely mapped reads % |	51.29%
                          Average mapped length |	25.81
                       Number of splices: Total |	1391
            Number of splices: Annotated (sjdb) |	450
                       Number of splices: GT/AG |	1309
                       Number of splices: GC/AG |	23
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	58
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	725180
             % of reads mapped to multiple loci |	33.07%
        Number of reads mapped to too many loci |	68379
             % of reads mapped to too many loci |	3.12%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.85%
                     % of reads unmapped: other |	0.67%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	342910	342910	342910
N_multimapping	725180	725180	725180
N_noFeature	57976	75166	818204
N_ambiguous	602844	352577	12653
UnstrandedReadsAssigned:463689 PositiveStrandReadsAssigned:696766 NegativeStrandReadsAssigned:293652
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031010 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: SRR5031010-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,192,599 reads, 518,279 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,117 rounds

 109283 SRR5031010.ke.tsv
  52636 SRR5031010.se.tsv
 161919 total
==> SRR5031010.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

==> SRR5031010.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	1
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031010 completed mapping pipeline successfully
