Starting /dee2/code/volunteer_pipeline.sh SRR5031037
    current disk space = 160521158656
    free memory = 73965488 
SRR5031037 SRAfilesize
1c53ca5deac6eb3d121eec13667f0211  SRR5031037.sra
SRR5031037.sra file validated
SRR5031037 is single end
SRR5031037 is conventional basespace
SRR5031037 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031037_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	32.284	33.0	31.0	34.0	31.0	34.0
2	32.545	34.0	31.0	34.0	31.0	34.0
3	32.624	34.0	31.0	34.0	31.0	34.0
4	36.1505	37.0	35.0	37.0	35.0	37.0
5	35.89025	37.0	35.0	37.0	35.0	37.0
6	35.885	37.0	35.0	37.0	35.0	37.0
7	35.89575	37.0	35.0	37.0	35.0	37.0
8	35.747	37.0	35.0	37.0	33.0	37.0
9	37.575	39.0	37.0	39.0	35.0	39.0
10	37.75175	39.0	37.0	39.0	35.0	39.0
11	37.641	39.0	37.0	39.0	35.0	39.0
12	37.61	39.0	37.0	39.0	35.0	39.0
13	37.63375	39.0	37.0	39.0	35.0	39.0
14	39.0005	40.0	38.0	41.0	36.0	41.0
15	39.01375	40.0	38.0	41.0	35.0	41.0
16	38.9265	40.0	38.0	41.0	35.0	41.0
17	38.95425	40.0	38.0	41.0	35.0	41.0
18	39.037	40.0	38.0	41.0	35.0	41.0
19	38.6865	40.0	38.0	41.0	34.0	41.0
20	38.8675	40.0	38.0	41.0	35.0	41.0
21	38.78725	40.0	38.0	41.0	35.0	41.0
22	38.9995	40.0	38.0	41.0	35.0	41.0
23	38.745	40.0	38.0	41.0	35.0	41.0
24	38.7065	40.0	38.0	41.0	34.0	41.0
25	38.97225	40.0	39.0	41.0	35.0	41.0
26	38.699	40.0	38.0	41.0	34.0	41.0
27	38.645	40.0	38.0	41.0	34.0	41.0
28	38.5885	40.0	38.0	41.0	34.0	41.0
29	38.06275	40.0	38.0	41.0	33.0	41.0
30	37.97175	40.0	38.0	41.0	32.0	41.0
31	38.34525	40.0	38.0	41.0	33.0	41.0
32	38.3095	40.0	38.0	41.0	33.0	41.0
33	38.193	40.0	38.0	41.0	33.0	41.0
34	38.3665	40.0	38.0	41.0	34.0	41.0
35	38.18125	40.0	38.0	41.0	34.0	41.0
36	37.8215	40.0	37.0	41.0	33.0	41.0
37	37.339	40.0	37.0	41.0	31.0	41.0
38	36.7365	39.0	36.0	41.0	30.0	41.0
39	37.15875	39.0	37.0	41.0	31.0	41.0
40	37.435	40.0	37.0	41.0	32.0	41.0
41	37.60625	40.0	37.0	41.0	32.0	41.0
42	37.7675	40.0	37.0	41.0	33.0	41.0
43	38.02275	40.0	37.0	41.0	33.0	41.0
44	37.64075	40.0	37.0	41.0	33.0	41.0
45	37.67675	40.0	37.0	41.0	33.0	41.0
46	37.64175	40.0	37.0	41.0	33.0	41.0
47	37.1675	40.0	36.0	41.0	31.0	41.0
48	36.7585	39.0	35.0	41.0	31.0	41.0
49	36.97725	40.0	36.0	41.0	31.0	41.0
50	36.35925	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
13	1.0
14	0.0
15	0.0
16	2.0
17	0.0
18	2.0
19	2.0
20	3.0
21	2.0
22	2.0
23	2.0
24	9.0
25	11.0
26	7.0
27	20.0
28	31.0
29	34.0
30	47.0
31	90.0
32	84.0
33	106.0
34	141.0
35	210.0
36	295.0
37	476.0
38	740.0
39	1683.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.525	25.7	46.725	16.05
2	21.6270337922403	28.785982478097623	18.69837296620776	30.888610763454317
3	25.25	17.25	22.5	35.0
4	33.15	27.375	15.725	23.75
5	21.925	34.775	28.325	14.975
6	31.4	15.725	37.35	15.525
7	18.65	21.975	20.4	38.975
8	21.95	28.175	17.575	32.300000000000004
9	25.874999999999996	31.624999999999996	24.9	17.599999999999998
10	24.725	18.425	28.050000000000004	28.799999999999997
11	32.725	12.950000000000001	17.175	37.15
12	16.825000000000003	18.45	31.374999999999996	33.35
13	28.325	17.05	32.574999999999996	22.05
14	29.525000000000002	31.724999999999998	20.45	18.3
15	37.125	21.875	25.8	15.2
16	18.175	19.925	24.3	37.6
17	28.475	20.474999999999998	34.475	16.575
18	25.775	16.35	32.074999999999996	25.8
19	34.4	14.674999999999999	32.824999999999996	18.099999999999998
20	45.625	15.075	24.45	14.85
21	24.224999999999998	21.7	24.55	29.525000000000002
22	29.675	14.475	44.425	11.425
23	26.724999999999998	14.7	42.3	16.275000000000002
24	47.699999999999996	16.5	26.200000000000003	9.6
25	48.775	23.125	16.625	11.475
26	29.425	41.975	14.95	13.65
27	16.150000000000002	44.35	24.925	14.575
28	12.925	24.375	45.375	17.325
29	14.075	13.125	54.400000000000006	18.4
30	11.675	7.7	34.949999999999996	45.675
31	16.575	5.475	43.45	34.5
32	27.525	6.35	23.175	42.95
33	51.24999999999999	9.375	15.375	24.0
34	58.375	8.3	17.75	15.575
35	62.724999999999994	8.525	18.475	10.274999999999999
36	40.175	9.875	35.75	14.2
37	43.3	12.4	20.775	23.525
38	24.25	18.0	13.700000000000001	44.05
39	17.175	23.150000000000002	12.225	47.449999999999996
40	17.224999999999998	44.6	12.7	25.474999999999998
41	24.95	46.050000000000004	11.375	17.625
42	45.324999999999996	29.275000000000002	12.65	12.75
43	50.824999999999996	27.925	9.775	11.475
44	31.35	43.85	9.6	15.2
45	21.125	46.625	14.099999999999998	18.15
46	15.925	24.7	18.325	41.05
47	11.475	15.25	37.375	35.9
48	12.85	14.249999999999998	20.75	52.15
49	16.55	18.6	14.524999999999999	50.324999999999996
50	19.325	36.5	13.750000000000002	30.425
>>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	0.5
22	1.0
23	0.5
24	0.0
25	0.5
26	1.0
27	1.5
28	2.0
29	1.5
30	1.0
31	8.5
32	16.0
33	13.5
34	11.0
35	16.5
36	22.0
37	28.0
38	34.0
39	41.5
40	49.0
41	56.0
42	63.0
43	85.0
44	107.0
45	127.0
46	147.0
47	263.0
48	379.0
49	477.5
50	576.0
51	711.5
52	847.0
53	650.5
54	454.0
55	498.5
56	543.0
57	419.0
58	295.0
59	199.0
60	103.0
61	73.0
62	43.0
63	74.0
64	105.0
65	69.5
66	34.0
67	25.0
68	16.0
69	24.5
70	33.0
71	68.0
72	103.0
73	54.5
74	6.0
75	3.5
76	1.0
77	2.0
78	3.0
79	3.5
80	4.0
81	2.0
82	0.0
83	0.0
84	0.0
85	0.5
86	1.0
87	0.5
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	39.300000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.0	29.475
2	9.732824427480915	7.6499999999999995
3	5.216284987277354	6.15
4	2.2264631043257	3.5000000000000004
5	1.9720101781170483	3.875
6	1.0178117048346056	2.4
7	0.38167938931297707	1.05
8	0.5725190839694656	1.7999999999999998
9	0.2544529262086514	0.8999999999999999
>10	3.11704834605598	23.075000000000003
>50	0.19083969465648853	5.45
>100	0.3180661577608142	14.674999999999999
>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	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	121	3.025	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	116	2.9000000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	107	2.675	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	89	2.225	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	65	1.625	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	45	1.125	No Hit
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	43	1.075	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	43	1.075	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	36	0.8999999999999999	RNA PCR Primer, Index 7 (97% over 35bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGC	26	0.65	RNA PCR Primer, Index 9 (100% over 50bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	21	0.525	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	17	0.42500000000000004	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	17	0.42500000000000004	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	15	0.375	No Hit
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	13	0.325	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	12	0.3	RNA PCR Primer, Index 9 (100% over 44bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	12	0.3	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	12	0.3	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 31bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	10	0.25	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	10	0.25	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTGCC	8	0.2	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	8	0.2	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	8	0.2	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	6	0.15	RNA PCR Primer, Index 6 (100% over 34bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAT	6	0.15	RNA PCR Primer, Index 9 (100% over 36bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGGCAGTGTAGTTAGCTGATTGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	5	0.125	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AAGGGATTCTGATGTTGGTCACACTCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TGACCAATGAACACTCTGACCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGAATTGTGGCTGGACATCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	5	0.125	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGAGGAGCTCACAGTCTAGTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.675	0.0	0.0	0.0
2	0.0	0.675	0.0	0.0	0.0
3	0.0	0.7	0.0	0.0	0.0
4	0.0	0.7	0.0	0.0	0.0
5	0.0	0.725	0.0	0.0	0.0
6	0.0	0.8	0.0	0.0	0.0
7	0.0	1.225	0.0	0.0	0.0
8	0.0	1.425	0.0	0.0	0.0
9	0.0	1.55	0.0	0.0	0.0
10	0.0	1.725	0.0	0.0	0.0
11	0.0	1.85	0.0	0.0	0.0
12	0.0	2.15	0.0	0.0	0.0
13	0.0	2.3	0.0	0.0	0.0
14	0.0	2.7	0.0	0.0	0.0
15	0.0	3.175	0.0	0.0	0.0
16	0.0	4.575	0.0	0.0	0.0
17	0.0	5.375	0.0	0.0	0.0
18	0.0	6.55	0.0	0.0	0.0
19	0.0	7.15	0.0	0.0	0.0
20	0.0	7.9	0.0	0.0	0.0
21	0.0	13.5	0.0	0.0	0.0
22	0.0	23.075	0.0	0.0	0.0
23	0.0	49.725	0.0	0.0	0.0
24	0.0	62.125	0.0	0.0	0.0
25	0.0	67.65	0.0	0.0	0.0
26	0.0	69.05	0.0	0.0	0.0
27	0.0	69.95	0.0	0.0	0.0
28	0.0	70.35	0.0	0.0	0.0
29	0.0	71.15	0.0	0.0	0.0
30	0.0	71.825	0.0	0.0	0.0
31	0.0	72.95	0.0	0.0	0.0
32	0.0	74.25	0.0	0.0	0.0
33	0.0	76.0	0.0	0.0	0.0
34	0.0	79.425	0.0	0.0	0.0
35	0.0	80.85	0.0	0.0	0.0
36	0.0	82.075	0.0	0.0	0.0
37	0.0	83.075	0.0	0.0	0.0
38	0.0	83.875	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCGGATC	40	4.7512003E-9	44.531643	1
CGGATCC	40	4.7512003E-9	44.531643	2
ACATTCA	40	4.7512003E-9	44.531643	2
AACATTC	40	4.7512003E-9	44.531643	1
CTTGGTG	25	3.7082697E-5	43.975002	16
GCTTGGT	25	3.7082697E-5	43.975002	15
AACGCTG	35	1.0274016E-7	43.975	8
ACGCTGT	35	1.0274016E-7	43.975	9
TTCAACG	35	1.0274016E-7	43.975	5
GGATCCG	40	5.342372E-9	43.975	3
CCGTCTG	40	5.342372E-9	43.975	7
CATTCAA	40	5.342372E-9	43.975	3
TCAACGC	35	1.0274016E-7	43.975	6
GCTGTCG	40	5.342372E-9	43.975	11
GATCCGT	40	5.342372E-9	43.975	4
TCCGTCT	40	5.342372E-9	43.975	6
ATCCGTC	40	5.342372E-9	43.975	5
TGAGCTT	40	5.342372E-9	43.975	12
ATTCAAC	40	5.342372E-9	43.975	4
CGTCTGA	40	5.342372E-9	43.975	8
>>END_MODULE
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
Read 240575 spots for SRR5031037.sra
Written 240575 spots for SRR5031037.sra
Read 240571 spots for SRR5031037.sra
Written 240571 spots for SRR5031037.sra
SRR ids: ['SRR5031037.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_k7y1zw6t
SRR5031037.sra spots: 2886856
blocks: [[1, 240571], [240572, 481142], [481143, 721713], [721714, 962284], [962285, 1202855], [1202856, 1443426], [1443427, 1683997], [1683998, 1924568], [1924569, 2165139], [2165140, 2405710], [2405711, 2646281], [2646282, 2886856]]
SRR5031037 file size 499293
SRR5031037 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031037 SRR5031037_1.fastq
Input file:	SRR5031037_1.fastq
trimmed:	SRR5031037-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 07:11:15 2020 >> started

Wed Mar  4 07:11:17 2020 >> done (1.677s)
2886856 reads processed; of these:
    256 ( 0.01%) short reads filtered out after trimming by size control
     11 ( 0.00%) empty reads filtered out after trimming by size control
2886589 (99.99%) reads available; of these:
 145488 ( 5.04%) trimmed reads available after processing
2741101 (94.96%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     66	  0.00%
 19	     79	  0.00%
 20	    210	  0.01%
 21	    220	  0.01%
 22	    388	  0.01%
 23	    461	  0.02%
 24	    487	  0.02%
 25	    670	  0.02%
 26	    556	  0.02%
 27	    672	  0.02%
 28	    766	  0.03%
 29	   1208	  0.04%
 30	    775	  0.03%
 31	    890	  0.03%
 32	    895	  0.03%
 33	   1291	  0.04%
 34	   1540	  0.05%
 35	   3201	  0.11%
 36	   2645	  0.09%
 37	   2998	  0.10%
 38	   2750	  0.10%
 39	   2968	  0.10%
 40	   3169	  0.11%
 41	   3287	  0.11%
 42	   4137	  0.14%
 43	   6133	  0.21%
 44	   8027	  0.28%
 45	  10123	  0.35%
 46	  14550	  0.50%
 47	  17779	  0.62%
 48	  25469	  0.88%
 49	  27078	  0.94%
 50	2741101	 94.96%
2886589 reads passed initial QC


criterion=sequence-density
sequence-density=84.21
sequence-density-rank=1
fanout-score=21.77
fanout-score-rank=1
prefix-density=86.66
prefix-fanout=21.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC


criterion=fanout-score
sequence-density=84.21
sequence-density-rank=1
fanout-score=21.77
fanout-score-rank=1
prefix-density=86.66
prefix-fanout=21.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC -o SRR5031037 -
Input file:	STDIN
trimmed:	SRR5031037-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 07:11:32 2020 >> started

Wed Mar  4 07:11:35 2020 >> done (3.094s)
2818669 reads processed; of these:
 160528 ( 5.70%) short reads filtered out after trimming by size control
  14730 ( 0.52%) empty reads filtered out after trimming by size control
2643411 (93.78%) reads available; of these:
2486098 (94.05%) trimmed reads available after processing
 157313 ( 5.95%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15557	  0.59%
 19	  26974	  1.02%
 20	 150789	  5.70%
 21	 283279	 10.72%
 22	 782723	 29.61%
 23	 347703	 13.15%
 24	 166006	  6.28%
 25	  47783	  1.81%
 26	  25242	  0.95%
 27	  20908	  0.79%
 28	  23440	  0.89%
 29	  18891	  0.71%
 30	  31288	  1.18%
 31	  42684	  1.61%
 32	  42673	  1.61%
 33	 101761	  3.85%
 34	  40736	  1.54%
 35	  31844	  1.20%
 36	  34819	  1.32%
 37	  19019	  0.72%
 38	  21240	  0.80%
 39	  18686	  0.71%
 40	  27846	  1.05%
 41	  32158	  1.22%
 42	  35914	  1.36%
 43	  25018	  0.95%
 44	  19275	  0.73%
 45	  30824	  1.17%
 46	  21963	  0.83%
 47	  15812	  0.60%
 48	   1319	  0.05%
 49	   2159	  0.08%
 50	 137078	  5.19%


criterion=sequence-density
sequence-density=7.79
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.48
sequence-density-rank=34
fanout-score=18.44
fanout-score-rank=1
prefix-density=8.85
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:11:56
                             Started mapping on |	Mar 04 07:11:56
                                    Finished on |	Mar 04 07:12:20
       Mapping speed, Million of reads per hour |	406.70

                          Number of input reads |	2711331
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1468483
                        Uniquely mapped reads % |	54.16%
                          Average mapped length |	25.12
                       Number of splices: Total |	2328
            Number of splices: Annotated (sjdb) |	524
                       Number of splices: GT/AG |	2234
                       Number of splices: GC/AG |	30
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	63
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	841499
             % of reads mapped to multiple loci |	31.04%
        Number of reads mapped to too many loci |	68263
             % of reads mapped to too many loci |	2.52%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.31%
                     % of reads unmapped: other |	0.97%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	401349	401349	401349
N_multimapping	841499	841499	841499
N_noFeature	75418	96373	976376
N_ambiguous	802262	371929	12086
UnstrandedReadsAssigned:590803 PositiveStrandReadsAssigned:1000181 NegativeStrandReadsAssigned:480021
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031037 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: SRR5031037-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,711,331 reads, 679,063 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,145 rounds

 109283 SRR5031037.ke.tsv
  52636 SRR5031037.se.tsv
 161919 total
==> SRR5031037.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

==> SRR5031037.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031037 completed mapping pipeline successfully
