Starting /dee2/code/volunteer_pipeline.sh SRR5031016
    current disk space = 160553795584
    free memory = 73928316 
SRR5031016 SRAfilesize
fe1412a70ce4f17a0123c98504e42477  SRR5031016.sra
SRR5031016.sra file validated
SRR5031016 is single end
SRR5031016 is conventional basespace
SRR5031016 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031016_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	32.34825	33.0	31.0	34.0	31.0	34.0
2	32.59575	34.0	31.0	34.0	31.0	34.0
3	32.624	34.0	31.0	34.0	31.0	34.0
4	36.21325	37.0	35.0	37.0	35.0	37.0
5	36.10025	37.0	35.0	37.0	35.0	37.0
6	35.9615	37.0	35.0	37.0	35.0	37.0
7	35.846	37.0	35.0	37.0	35.0	37.0
8	35.938	37.0	35.0	37.0	35.0	37.0
9	37.62675	39.0	37.0	39.0	35.0	39.0
10	37.561	39.0	37.0	39.0	35.0	39.0
11	37.25475	39.0	37.0	39.0	33.0	39.0
12	37.55325	39.0	37.0	39.0	35.0	39.0
13	37.55875	39.0	37.0	39.0	35.0	39.0
14	38.9265	40.0	38.0	41.0	35.0	41.0
15	38.79325	40.0	38.0	41.0	34.0	41.0
16	38.92775	40.0	38.0	41.0	35.0	41.0
17	38.992	40.0	38.0	41.0	35.0	41.0
18	38.89625	40.0	38.0	41.0	35.0	41.0
19	38.69525	40.0	38.0	41.0	34.0	41.0
20	38.63375	40.0	38.0	41.0	34.0	41.0
21	38.80875	40.0	38.0	41.0	34.0	41.0
22	38.834	40.0	38.0	41.0	35.0	41.0
23	38.414	40.0	38.0	41.0	34.0	41.0
24	38.497	40.0	38.0	41.0	34.0	41.0
25	38.4885	40.0	38.0	41.0	34.0	41.0
26	38.38625	40.0	38.0	41.0	34.0	41.0
27	38.61275	40.0	38.0	41.0	34.0	41.0
28	38.433	40.0	38.0	41.0	34.0	41.0
29	38.0195	40.0	38.0	41.0	32.0	41.0
30	37.85225	40.0	38.0	41.0	32.0	41.0
31	38.301	40.0	38.0	41.0	34.0	41.0
32	38.4675	40.0	38.0	41.0	34.0	41.0
33	38.19425	40.0	38.0	41.0	33.0	41.0
34	38.08	40.0	38.0	41.0	33.0	41.0
35	37.94	40.0	38.0	41.0	33.0	41.0
36	37.76475	40.0	37.0	41.0	32.0	41.0
37	37.264	40.0	37.0	41.0	31.0	41.0
38	37.09425	39.0	37.0	41.0	31.0	41.0
39	37.62575	40.0	37.0	41.0	32.0	41.0
40	37.636	40.0	37.0	41.0	33.0	41.0
41	37.86825	40.0	37.0	41.0	33.0	41.0
42	37.7725	40.0	37.0	41.0	33.0	41.0
43	37.71425	40.0	37.0	41.0	33.0	41.0
44	37.798	40.0	37.0	41.0	33.0	41.0
45	37.71525	40.0	37.0	41.0	33.0	41.0
46	37.46375	40.0	37.0	41.0	33.0	41.0
47	36.862	40.0	36.0	41.0	30.0	41.0
48	36.6685	40.0	36.0	41.0	30.0	41.0
49	36.71425	40.0	36.0	41.0	30.0	41.0
50	36.149	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
16	1.0
17	0.0
18	1.0
19	1.0
20	3.0
21	6.0
22	1.0
23	11.0
24	12.0
25	9.0
26	15.0
27	20.0
28	34.0
29	33.0
30	62.0
31	73.0
32	93.0
33	88.0
34	171.0
35	220.0
36	282.0
37	403.0
38	746.0
39	1715.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.9750000000000005	26.8	51.0	14.224999999999998
2	23.63408521303258	27.61904761904762	17.593984962406015	31.152882205513784
3	25.05	20.65	23.9	30.4
4	33.35	28.499999999999996	14.2	23.95
5	21.375	41.575	26.700000000000003	10.35
6	34.0	15.875	35.425000000000004	14.7
7	14.674999999999999	21.375	23.799999999999997	40.150000000000006
8	24.2	28.65	14.7	32.45
9	21.349999999999998	33.925	28.549999999999997	16.175
10	20.200000000000003	22.400000000000002	29.95	27.450000000000003
11	31.374999999999996	9.775	17.65	41.199999999999996
12	15.375	17.424999999999997	31.674999999999997	35.525
13	32.125	18.525	31.2	18.15
14	32.95	31.45	19.3	16.3
15	35.975	24.099999999999998	26.950000000000003	12.975
16	18.825	20.175	23.325000000000003	37.675
17	25.074999999999996	21.3	39.300000000000004	14.325
18	25.650000000000002	18.375	27.900000000000002	28.075
19	36.525	13.5	32.025	17.95
20	44.35	15.225	26.650000000000002	13.775
21	21.7	20.1	28.349999999999998	29.849999999999998
22	28.95	12.15	48.625	10.274999999999999
23	27.125	12.825000000000001	45.300000000000004	14.75
24	51.2	13.775	27.1	7.925
25	50.125	23.9	16.45	9.525
26	28.575	47.199999999999996	13.350000000000001	10.875
27	16.175	48.1	23.425	12.3
28	11.225	25.55	49.325	13.900000000000002
29	11.375	13.8	56.35	18.475
30	9.85	7.000000000000001	38.275	44.875
31	13.450000000000001	4.2	47.175	35.175
32	27.3	5.625	22.675	44.4
33	54.05	7.9750000000000005	14.124999999999998	23.849999999999998
34	61.650000000000006	6.625	15.975	15.75
35	65.725	5.65	18.85	9.775
36	44.824999999999996	7.249999999999999	35.125	12.8
37	45.875	10.625	19.975	23.525
38	24.05	15.975	12.275	47.699999999999996
39	16.0	23.674999999999997	10.424999999999999	49.9
40	14.95	48.35	10.299999999999999	26.400000000000002
41	24.5	48.9	8.55	18.05
42	48.225	30.2	10.5	11.075
43	51.800000000000004	31.1	7.199999999999999	9.9
44	31.95	49.025	6.325	12.7
45	19.650000000000002	49.9	11.525	18.925
46	12.475	26.875	18.9	41.75
47	7.9750000000000005	16.475	38.25	37.3
48	9.8	12.575	20.525	57.099999999999994
49	11.325000000000001	19.075	14.149999999999999	55.45
50	17.7	36.6	12.1	33.6
>>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	0.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	1.0
28	2.0
29	3.0
30	4.0
31	10.5
32	17.0
33	17.5
34	18.0
35	14.5
36	11.0
37	21.5
38	32.0
39	40.5
40	49.0
41	45.5
42	42.0
43	76.5
44	111.0
45	152.5
46	194.0
47	329.0
48	464.0
49	576.5
50	689.0
51	765.0
52	841.0
53	633.5
54	426.0
55	450.0
56	474.0
57	366.5
58	259.0
59	159.5
60	60.0
61	52.5
62	45.0
63	74.5
64	104.0
65	71.0
66	38.0
67	24.0
68	10.0
69	18.5
70	27.0
71	50.5
72	74.0
73	38.5
74	3.0
75	2.0
76	1.0
77	0.5
78	0.0
79	0.5
80	1.0
81	1.0
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	0.25
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	36.675000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.4601226993865	27.675
2	9.475119291070211	6.950000000000001
3	4.430811179277437	4.875
4	2.3858214042263124	3.5000000000000004
5	1.3633265167007498	2.5
6	1.499659168370825	3.3000000000000003
7	0.5453306066803	1.4000000000000001
8	0.5453306066803	1.6
9	0.34083162917518744	1.125
>10	3.3401499659168374	24.025
>50	0.34083162917518744	9.9
>100	0.27266530334015	13.15
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	118	2.9499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	116	2.9000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	88	2.1999999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	85	2.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	73	1.825	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	55	1.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	49	1.225	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	45	1.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCC	35	0.8750000000000001	RNA PCR Primer, Index 5 (97% over 35bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	32	0.8	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGC	21	0.525	RNA PCR Primer, Index 36 (100% over 50bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	20	0.5	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	11	0.27499999999999997	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	10	0.25	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	8	0.2	RNA PCR Primer, Index 2 (100% over 34bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTC	8	0.2	RNA PCR Primer, Index 36 (100% over 44bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	6	0.15	RNA PCR Primer, Index 2 (100% over 34bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCTC	5	0.125	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
AAGCTGCCAGTTGAAGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	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	0.6	0.0	0.0	0.0
2	0.0	0.6	0.0	0.0	0.0
3	0.0	0.675	0.0	0.0	0.0
4	0.0	0.7	0.0	0.0	0.0
5	0.0	0.75	0.0	0.0	0.0
6	0.0	0.75	0.0	0.0	0.0
7	0.0	1.075	0.0	0.0	0.0
8	0.0	1.175	0.0	0.0	0.0
9	0.0	1.25	0.0	0.0	0.0
10	0.0	1.35	0.0	0.0	0.0
11	0.0	1.625	0.0	0.0	0.0
12	0.0	1.8	0.0	0.0	0.0
13	0.0	1.925	0.0	0.0	0.0
14	0.0	2.1	0.0	0.0	0.0
15	0.0	2.375	0.0	0.0	0.0
16	0.0	3.75	0.0	0.0	0.0
17	0.0	4.75	0.0	0.0	0.0
18	0.0	5.65	0.0	0.0	0.0
19	0.0	6.05	0.0	0.0	0.0
20	0.0	6.95	0.0	0.0	0.0
21	0.0	11.85	0.0	0.0	0.0
22	0.0	24.1	0.0	0.0	0.0
23	0.0	53.725	0.0	0.0	0.0
24	0.0	67.4	0.0	0.0	0.0
25	0.0	74.0	0.0	0.0	0.0
26	0.0	75.925	0.0	0.0	0.0
27	0.0	76.775	0.0	0.0	0.0
28	0.0	77.2	0.0	0.0	0.0
29	0.0	77.875	0.0	0.0	0.0
30	0.0	78.125	0.0	0.0	0.0
31	0.0	78.75	0.0	0.0	0.0
32	0.0	79.45	0.0	0.0	0.0
33	0.0	80.55	0.0	0.0	0.0
34	0.0	83.675	0.0	0.0	0.0
35	0.0	84.5	0.0	0.0	0.0
36	0.0	85.2	0.0	0.0	0.0
37	0.0	86.125	0.0	0.0	0.0
38	0.0	86.575	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
AACGCTG	20	6.952051E-4	44.000004	8
GAGGTAG	20	6.952051E-4	44.000004	2
GGTGAGT	20	6.952051E-4	44.000004	17
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
ACGCTGT	20	6.952051E-4	44.000004	9
AACCGGT	20	6.952051E-4	44.000004	9
AATCCAG	20	6.952051E-4	44.000004	8
ATCCAGG	20	6.952051E-4	44.000004	9
TTCAAGT	20	6.952051E-4	44.000004	1
TTCAACG	20	6.952051E-4	44.000004	5
AGGATAG	20	6.952051E-4	44.000004	13
TCGGTGA	20	6.952051E-4	44.000004	15
ATAGGCT	20	6.952051E-4	44.000004	16
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
TCCAGGA	20	6.952051E-4	44.000004	10
GGATAGG	20	6.952051E-4	44.000004	14
>>END_MODULE
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289056 spots for SRR5031016.sra
Written 289056 spots for SRR5031016.sra
Read 289062 spots for SRR5031016.sra
Written 289062 spots for SRR5031016.sra
SRR ids: ['SRR5031016.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_gqzjoihw
SRR5031016.sra spots: 3468678
blocks: [[1, 289056], [289057, 578112], [578113, 867168], [867169, 1156224], [1156225, 1445280], [1445281, 1734336], [1734337, 2023392], [2023393, 2312448], [2312449, 2601504], [2601505, 2890560], [2890561, 3179616], [3179617, 3468678]]
SRR5031016 file size 600133
SRR5031016 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031016 SRR5031016_1.fastq
Input file:	SRR5031016_1.fastq
trimmed:	SRR5031016-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 07:06:54 2020 >> started

Wed Mar  4 07:06:56 2020 >> done (2.213s)
3468678 reads processed; of these:
    287 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3468385 (99.99%) reads available; of these:
 206916 ( 5.97%) trimmed reads available after processing
3261469 (94.03%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    103	  0.00%
 19	    123	  0.00%
 20	    212	  0.01%
 21	    316	  0.01%
 22	    600	  0.02%
 23	    629	  0.02%
 24	    609	  0.02%
 25	    790	  0.02%
 26	    687	  0.02%
 27	    836	  0.02%
 28	   1047	  0.03%
 29	   1619	  0.05%
 30	   1083	  0.03%
 31	   1174	  0.03%
 32	   1274	  0.04%
 33	   1602	  0.05%
 34	   1893	  0.05%
 35	   3165	  0.09%
 36	   2811	  0.08%
 37	   3566	  0.10%
 38	   3309	  0.10%
 39	   3587	  0.10%
 40	   4174	  0.12%
 41	   4279	  0.12%
 42	   5567	  0.16%
 43	   7697	  0.22%
 44	  10751	  0.31%
 45	  13745	  0.40%
 46	  20418	  0.59%
 47	  25295	  0.73%
 48	  37991	  1.10%
 49	  45964	  1.33%
 50	3261469	 94.03%
3468385 reads passed initial QC


criterion=sequence-density
sequence-density=87.15
sequence-density-rank=1
fanout-score=20.36
fanout-score-rank=1
prefix-density=88.71
prefix-fanout=20.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC


criterion=fanout-score
sequence-density=87.15
sequence-density-rank=1
fanout-score=20.36
fanout-score-rank=1
prefix-density=88.71
prefix-fanout=20.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC -o SRR5031016 -
Input file:	STDIN
trimmed:	SRR5031016-trimmed.fastq

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

Wed Mar  4 07:07:18 2020 >> done (5.152s)
3389558 reads processed; of these:
 186534 ( 5.50%) short reads filtered out after trimming by size control
  19207 ( 0.57%) empty reads filtered out after trimming by size control
3183817 (93.93%) reads available; of these:
3041185 (95.52%) trimmed reads available after processing
 142632 ( 4.48%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16204	  0.51%
 19	  35366	  1.11%
 20	 188221	  5.91%
 21	 420708	 13.21%
 22	1016632	 31.93%
 23	 466855	 14.66%
 24	 225983	  7.10%
 25	  58626	  1.84%
 26	  28723	  0.90%
 27	  21496	  0.68%
 28	  22085	  0.69%
 29	  17145	  0.54%
 30	  25505	  0.80%
 31	  30994	  0.97%
 32	  34182	  1.07%
 33	  98738	  3.10%
 34	  34108	  1.07%
 35	  26137	  0.82%
 36	  32224	  1.01%
 37	  16995	  0.53%
 38	  17467	  0.55%
 39	  17222	  0.54%
 40	  26481	  0.83%
 41	  34320	  1.08%
 42	  40985	  1.29%
 43	  28795	  0.90%
 44	  22259	  0.70%
 45	  28619	  0.90%
 46	  20859	  0.66%
 47	  14680	  0.46%
 48	   1934	  0.06%
 49	   3148	  0.10%
 50	 110121	  3.46%


criterion=sequence-density
sequence-density=6.62
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=38
fanout-score=82.93
fanout-score-rank=1
prefix-density=1.69
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:07:40
                             Started mapping on |	Mar 04 07:07:41
                                    Finished on |	Mar 04 07:08:07
       Mapping speed, Million of reads per hour |	451.75

                          Number of input reads |	3262644
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1760729
                        Uniquely mapped reads % |	53.97%
                          Average mapped length |	24.34
                       Number of splices: Total |	1743
            Number of splices: Annotated (sjdb) |	353
                       Number of splices: GT/AG |	1635
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	89
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.77
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1102906
             % of reads mapped to multiple loci |	33.80%
        Number of reads mapped to too many loci |	64856
             % of reads mapped to too many loci |	1.99%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.64%
                     % of reads unmapped: other |	0.60%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	399009	399009	399009
N_multimapping	1102906	1102906	1102906
N_noFeature	75410	95300	1199285
N_ambiguous	977342	490293	16682
UnstrandedReadsAssigned:707977 PositiveStrandReadsAssigned:1175136 NegativeStrandReadsAssigned:544762
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031016 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: SRR5031016-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,262,644 reads, 850,894 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,146 rounds

 109283 SRR5031016.ke.tsv
  52636 SRR5031016.se.tsv
 161919 total
==> SRR5031016.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

==> SRR5031016.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031016 completed mapping pipeline successfully
