Starting /dee2/code/volunteer_pipeline.sh SRR5031038
    current disk space = 160517505024
    free memory = 1054438104 
SRR5031038 SRAfilesize
cf4033ef5a67a2ea35bd68a05dff4f2a  SRR5031038.sra
SRR5031038.sra file validated
SRR5031038 is single end
SRR5031038 is conventional basespace
SRR5031038 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031038_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	32.3335	33.0	31.0	34.0	31.0	34.0
2	32.58675	34.0	31.0	34.0	31.0	34.0
3	32.63875	34.0	31.0	34.0	31.0	34.0
4	36.18125	37.0	35.0	37.0	35.0	37.0
5	35.91575	37.0	35.0	37.0	35.0	37.0
6	35.8925	37.0	35.0	37.0	35.0	37.0
7	35.94275	37.0	35.0	37.0	35.0	37.0
8	35.7635	37.0	35.0	37.0	33.0	37.0
9	37.4595	39.0	37.0	39.0	34.0	39.0
10	37.64775	39.0	37.0	39.0	35.0	39.0
11	37.58275	39.0	37.0	39.0	35.0	39.0
12	37.60625	39.0	37.0	39.0	35.0	39.0
13	37.576	39.0	37.0	39.0	35.0	39.0
14	38.89625	40.0	38.0	41.0	35.0	41.0
15	38.89175	40.0	38.0	41.0	35.0	41.0
16	38.986	40.0	38.0	41.0	35.0	41.0
17	38.906	40.0	38.0	41.0	35.0	41.0
18	39.02525	40.0	38.0	41.0	35.0	41.0
19	38.77625	40.0	38.0	41.0	34.0	41.0
20	38.827	40.0	38.0	41.0	35.0	41.0
21	38.678	40.0	38.0	41.0	34.0	41.0
22	38.8355	40.0	38.0	41.0	35.0	41.0
23	38.6115	40.0	38.0	41.0	34.0	41.0
24	38.772	40.0	38.0	41.0	35.0	41.0
25	39.05825	41.0	39.0	41.0	35.0	41.0
26	38.64675	40.0	38.0	41.0	34.0	41.0
27	38.62025	40.0	38.0	41.0	34.0	41.0
28	38.69	40.0	38.0	41.0	34.0	41.0
29	38.09425	40.0	38.0	41.0	33.0	41.0
30	37.8725	40.0	37.0	41.0	32.0	41.0
31	38.18575	40.0	38.0	41.0	33.0	41.0
32	38.261	40.0	38.0	41.0	33.0	41.0
33	38.1455	40.0	38.0	41.0	33.0	41.0
34	38.44475	40.0	38.0	41.0	34.0	41.0
35	38.175	40.0	38.0	41.0	33.0	41.0
36	37.9285	40.0	37.0	41.0	33.0	41.0
37	37.47925	40.0	37.0	41.0	31.0	41.0
38	36.72075	39.0	36.0	41.0	30.0	41.0
39	37.08975	39.0	36.0	41.0	31.0	41.0
40	37.37925	39.0	37.0	41.0	32.0	41.0
41	37.564	40.0	37.0	41.0	32.0	41.0
42	37.84175	40.0	37.0	41.0	33.0	41.0
43	38.08675	40.0	38.0	41.0	33.0	41.0
44	37.76425	40.0	37.0	41.0	33.0	41.0
45	37.66075	40.0	37.0	41.0	33.0	41.0
46	37.5715	40.0	37.0	41.0	33.0	41.0
47	36.90925	40.0	35.0	41.0	30.0	41.0
48	36.6855	39.0	35.0	41.0	30.0	41.0
49	36.92625	40.0	35.0	41.0	31.0	41.0
50	36.307	39.0	35.0	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
11	1.0
12	0.0
13	1.0
14	0.0
15	1.0
16	1.0
17	0.0
18	2.0
19	1.0
20	4.0
21	5.0
22	5.0
23	9.0
24	7.0
25	6.0
26	11.0
27	21.0
28	30.0
29	48.0
30	39.0
31	69.0
32	97.0
33	117.0
34	165.0
35	200.0
36	266.0
37	452.0
38	696.0
39	1746.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.4	23.225	47.449999999999996	18.925
2	24.58072590738423	25.306633291614517	19.749687108886107	30.36295369211515
3	23.724999999999998	19.125	21.45	35.699999999999996
4	35.699999999999996	25.3	15.15	23.849999999999998
5	23.849999999999998	37.425000000000004	25.7	13.025
6	33.550000000000004	14.099999999999998	33.074999999999996	19.275000000000002
7	16.85	22.95	22.6	37.6
8	24.85	25.874999999999996	18.4	30.875000000000004
9	22.400000000000002	30.85	27.1	19.650000000000002
10	20.75	23.150000000000002	27.200000000000003	28.9
11	32.800000000000004	12.375	16.45	38.375
12	17.95	20.075000000000003	28.825	33.15
13	29.45	17.675	34.050000000000004	18.825
14	28.599999999999998	29.375	22.025	20.0
15	35.099999999999994	24.2	25.324999999999996	15.375
16	21.925	19.25	22.225	36.6
17	26.05	23.400000000000002	35.3	15.25
18	22.900000000000002	16.400000000000002	30.325000000000003	30.375000000000004
19	37.9	14.725	28.4	18.975
20	42.5	14.674999999999999	28.325	14.499999999999998
21	27.1	18.725	25.2	28.975
22	29.325000000000003	14.549999999999999	44.275	11.85
23	26.174999999999997	13.200000000000001	42.65	17.974999999999998
24	51.37500000000001	14.75	23.925	9.950000000000001
25	48.475	24.3	16.05	11.175
26	27.6	43.35	14.299999999999999	14.75
27	16.45	45.074999999999996	22.675	15.8
28	12.925	23.875	45.574999999999996	17.625
29	15.5	13.200000000000001	53.25	18.05
30	11.200000000000001	7.324999999999999	34.050000000000004	47.425
31	15.1	5.55	46.949999999999996	32.4
32	28.675	6.550000000000001	21.825	42.95
33	51.075	11.700000000000001	15.174999999999999	22.05
34	57.49999999999999	7.675	18.625	16.2
35	63.375	8.125	18.025	10.475
36	42.35	8.375	35.699999999999996	13.575000000000001
37	44.2	12.725	20.575	22.5
38	23.925	17.549999999999997	15.1	43.425000000000004
39	17.424999999999997	21.7	13.450000000000001	47.425
40	16.325	44.95	15.0	23.724999999999998
41	23.925	46.275	9.65	20.150000000000002
42	46.625	28.275	14.875	10.225
43	50.425	27.1	9.075	13.4
44	33.550000000000004	43.95	9.225	13.275
45	20.7	47.199999999999996	14.224999999999998	17.875
46	17.05	25.8	16.975	40.175
47	10.299999999999999	16.275000000000002	39.95	33.475
48	14.325	11.799999999999999	20.225	53.65
49	13.450000000000001	17.675	17.349999999999998	51.525
50	17.849999999999998	36.425000000000004	13.425	32.300000000000004
>>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	0.5
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	1.0
30	2.0
31	8.0
32	14.0
33	9.5
34	5.0
35	15.0
36	25.0
37	26.5
38	28.0
39	33.5
40	39.0
41	40.0
42	41.0
43	73.0
44	105.0
45	145.5
46	186.0
47	302.5
48	419.0
49	491.0
50	563.0
51	681.0
52	799.0
53	632.5
54	466.0
55	491.0
56	516.0
57	388.5
58	261.0
59	170.5
60	80.0
61	71.5
62	63.0
63	136.0
64	209.0
65	121.0
66	33.0
67	24.5
68	16.0
69	21.5
70	27.0
71	55.5
72	84.0
73	45.5
74	7.0
75	4.5
76	2.0
77	3.5
78	5.0
79	3.5
80	2.0
81	2.0
82	2.0
83	1.0
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	0.125
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	37.7
#Duplication Level	Percentage of deduplicated	Percentage of total
1	73.87267904509284	27.85
2	9.946949602122016	7.5
3	5.039787798408488	5.7
4	3.116710875331565	4.7
5	1.6578249336870028	3.125
6	1.3262599469496021	3.0
7	0.6631299734748011	1.7500000000000002
8	0.4641909814323607	1.4000000000000001
9	0.3978779840848806	1.35
>10	2.9840848806366047	23.025000000000002
>50	0.2652519893899204	7.7
>100	0.2652519893899204	12.9
>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	147	3.675	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	130	3.25	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	108	2.7	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	84	2.1	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	84	2.1	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	39	0.975	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	39	0.975	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	29	0.7250000000000001	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	29	0.7250000000000001	RNA PCR Primer, Index 7 (97% over 35bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	25	0.625	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	23	0.575	RNA PCR Primer, Index 1 (100% over 33bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTC	21	0.525	RNA PCR Primer, Index 10 (100% over 44bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	21	0.525	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGC	18	0.44999999999999996	RNA PCR Primer, Index 10 (100% over 50bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	13	0.325	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	11	0.27499999999999997	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	10	0.25	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	9	0.22499999999999998	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	8	0.2	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTGGAATTCTC	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	5	0.125	RNA PCR Primer, Index 7 (97% over 35bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	5	0.125	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	5	0.125	No Hit
ATCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAG	5	0.125	RNA PCR Primer, Index 7 (97% over 36bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.475	0.0	0.0	0.0
2	0.0	0.475	0.0	0.0	0.0
3	0.0	0.6	0.0	0.0	0.0
4	0.0	0.6	0.0	0.0	0.0
5	0.0	0.65	0.0	0.0	0.0
6	0.0	0.75	0.0	0.0	0.0
7	0.0	1.3	0.0	0.0	0.0
8	0.0	1.475	0.0	0.0	0.0
9	0.0	1.625	0.0	0.0	0.0
10	0.0	1.775	0.0	0.0	0.0
11	0.0	1.925	0.0	0.0	0.0
12	0.0	2.125	0.0	0.0	0.0
13	0.0	2.325	0.0	0.0	0.0
14	0.0	2.625	0.0	0.0	0.0
15	0.0	2.925	0.0	0.0	0.0
16	0.0	4.05	0.0	0.0	0.0
17	0.0	4.55	0.0	0.0	0.0
18	0.0	5.625	0.0	0.0	0.0
19	0.0	6.125	0.0	0.0	0.0
20	0.0	7.125	0.0	0.0	0.0
21	0.0	11.875	0.0	0.0	0.0
22	0.0	21.6	0.0	0.0	0.0
23	0.0	49.2	0.0	0.0	0.0
24	0.0	61.1	0.0	0.0	0.0
25	0.0	67.475	0.0	0.0	0.0
26	0.0	68.8	0.0	0.0	0.0
27	0.0	69.625	0.0	0.0	0.0
28	0.0	70.35	0.0	0.0	0.0
29	0.0	71.375	0.0	0.0	0.0
30	0.0	72.05	0.0	0.0	0.0
31	0.0	72.75	0.0	0.0	0.0
32	0.0	74.5	0.0	0.0	0.0
33	0.0	75.625	0.0	0.0	0.0
34	0.0	80.75	0.0	0.0	0.0
35	0.0	81.825	0.0	0.0	0.0
36	0.0	83.075	0.0	0.0	0.0
37	0.0	84.175	0.0	0.0	0.0
38	0.0	84.825	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TAGAACC	20	6.952051E-4	44.000004	7
GTAGAAC	20	6.952051E-4	44.000004	6
AACCGAC	20	6.952051E-4	44.000004	10
GAGCTTG	45	2.728484E-10	44.000004	13
GGATCCG	45	2.728484E-10	44.000004	3
CCGTCTG	45	2.728484E-10	44.000004	7
TCGGATC	45	2.728484E-10	44.000004	1
CGTAGAA	20	6.952051E-4	44.000004	5
CGGATCC	45	2.728484E-10	44.000004	2
CTTGGTG	20	6.952051E-4	44.000004	16
AGAACCG	20	6.952051E-4	44.000004	8
ACCGACC	20	6.952051E-4	44.000004	11
CACCCGT	20	6.952051E-4	44.000004	1
GAACCGA	20	6.952051E-4	44.000004	9
GATCCGT	45	2.728484E-10	44.000004	4
GCTTGGT	20	6.952051E-4	44.000004	15
ACCTTGC	20	6.952051E-4	44.000004	15
TTGGTGG	20	6.952051E-4	44.000004	17
TCCGTCT	45	2.728484E-10	44.000004	6
ATCCGTC	45	2.728484E-10	44.000004	5
>>END_MODULE
Read 71303 spots for SRR5031038.sra
Written 71303 spots for SRR5031038.sra
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Read 71328 spots for SRR5031038.sra
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SRR ids: ['SRR5031038.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_mga8upgr
SRR5031038.sra spots: 3422569
blocks: [[1, 71303], [71304, 142606], [142607, 213909], [213910, 285212], [285213, 356515], [356516, 427818], [427819, 499121], [499122, 570424], [570425, 641727], [641728, 713030], [713031, 784333], [784334, 855636], [855637, 926939], [926940, 998242], [998243, 1069545], [1069546, 1140848], [1140849, 1212151], [1212152, 1283454], [1283455, 1354757], [1354758, 1426060], [1426061, 1497363], [1497364, 1568666], [1568667, 1639969], [1639970, 1711272], [1711273, 1782575], [1782576, 1853878], [1853879, 1925181], [1925182, 1996484], [1996485, 2067787], [2067788, 2139090], [2139091, 2210393], [2210394, 2281696], [2281697, 2352999], [2353000, 2424302], [2424303, 2495605], [2495606, 2566908], [2566909, 2638211], [2638212, 2709514], [2709515, 2780817], [2780818, 2852120], [2852121, 2923423], [2923424, 2994726], [2994727, 3066029], [3066030, 3137332], [3137333, 3208635], [3208636, 3279938], [3279939, 3351241], [3351242, 3422569]]
SRR5031038 file size 592145
SRR5031038 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5031038 SRR5031038_1.fastq
Input file:	SRR5031038_1.fastq
trimmed:	SRR5031038-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):	32
Wed Mar  4 07:11:23 2020 >> started

Wed Mar  4 07:11:25 2020 >> done (2.247s)
3422569 reads processed; of these:
    339 ( 0.01%) short reads filtered out after trimming by size control
     14 ( 0.00%) empty reads filtered out after trimming by size control
3422216 (99.99%) reads available; of these:
 172241 ( 5.03%) trimmed reads available after processing
3249975 (94.97%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    123	  0.00%
 19	    121	  0.00%
 20	    244	  0.01%
 21	    276	  0.01%
 22	    506	  0.01%
 23	    563	  0.02%
 24	    636	  0.02%
 25	    779	  0.02%
 26	    644	  0.02%
 27	    836	  0.02%
 28	    871	  0.03%
 29	   1390	  0.04%
 30	    855	  0.02%
 31	   1031	  0.03%
 32	   1165	  0.03%
 33	   1456	  0.04%
 34	   1727	  0.05%
 35	   3209	  0.09%
 36	   3013	  0.09%
 37	   3421	  0.10%
 38	   3250	  0.09%
 39	   3325	  0.10%
 40	   3606	  0.11%
 41	   3758	  0.11%
 42	   4747	  0.14%
 43	   7402	  0.22%
 44	   9990	  0.29%
 45	  12347	  0.36%
 46	  17940	  0.52%
 47	  20962	  0.61%
 48	  30162	  0.88%
 49	  31886	  0.93%
 50	3249975	 94.97%
3422216 reads passed initial QC


criterion=sequence-density
sequence-density=84.32
sequence-density-rank=1
fanout-score=22.09
fanout-score-rank=1
prefix-density=86.73
prefix-fanout=21.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC


criterion=fanout-score
sequence-density=84.32
sequence-density-rank=1
fanout-score=22.09
fanout-score-rank=1
prefix-density=86.73
prefix-fanout=21.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC -o SRR5031038 -
Input file:	STDIN
trimmed:	SRR5031038-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC
-- 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):	32
Wed Mar  4 07:11:43 2020 >> started

Wed Mar  4 07:11:48 2020 >> done (5.113s)
3341693 reads processed; of these:
 187463 ( 5.61%) short reads filtered out after trimming by size control
  17772 ( 0.53%) empty reads filtered out after trimming by size control
3136458 (93.86%) reads available; of these:
2954069 (94.18%) trimmed reads available after processing
 182389 ( 5.82%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17812	  0.57%
 19	  33449	  1.07%
 20	 161569	  5.15%
 21	 338834	 10.80%
 22	 919868	 29.33%
 23	 411804	 13.13%
 24	 184204	  5.87%
 25	  53564	  1.71%
 26	  28804	  0.92%
 27	  24802	  0.79%
 28	  27824	  0.89%
 29	  22092	  0.70%
 30	  36028	  1.15%
 31	  55896	  1.78%
 32	  42203	  1.35%
 33	 165462	  5.28%
 34	  47873	  1.53%
 35	  38255	  1.22%
 36	  46143	  1.47%
 37	  21904	  0.70%
 38	  23983	  0.76%
 39	  22142	  0.71%
 40	  33274	  1.06%
 41	  40452	  1.29%
 42	  45409	  1.45%
 43	  31264	  1.00%
 44	  23634	  0.75%
 45	  32475	  1.04%
 46	  24839	  0.79%
 47	  19035	  0.61%
 48	   1699	  0.05%
 49	   2471	  0.08%
 50	 157391	  5.02%


criterion=sequence-density
sequence-density=6.07
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.40
sequence-density-rank=34
fanout-score=25.23
fanout-score-rank=1
prefix-density=10.14
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 07:12:28
                             Started mapping on |	Mar 04 07:12:28
                                    Finished on |	Mar 04 07:12:58
       Mapping speed, Million of reads per hour |	386.04

                          Number of input reads |	3216981
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1651634
                        Uniquely mapped reads % |	51.34%
                          Average mapped length |	25.24
                       Number of splices: Total |	2385
            Number of splices: Annotated (sjdb) |	379
                       Number of splices: GT/AG |	2248
                       Number of splices: GC/AG |	19
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	117
                      Mismatch rate per base, % |	0.24%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.81
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1036832
             % of reads mapped to multiple loci |	32.23%
        Number of reads mapped to too many loci |	84698
             % of reads mapped to too many loci |	2.63%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.16%
                     % of reads unmapped: other |	0.64%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	528515	528515	528515
N_multimapping	1036832	1036832	1036832
N_noFeature	113397	137257	1131851
N_ambiguous	911897	468575	21574
UnstrandedReadsAssigned:626340 PositiveStrandReadsAssigned:1045802 NegativeStrandReadsAssigned:498209
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031038 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: SRR5031038-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,216,981 reads, 778,582 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,166 rounds

 109283 SRR5031038.ke.tsv
  52636 SRR5031038.se.tsv
 161919 total
==> SRR5031038.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

==> SRR5031038.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031038 completed mapping pipeline successfully
