Starting /dee2/code/volunteer_pipeline.sh SRR5030873
    current disk space = 160656408576
    free memory = 73947484 
SRR5030873 SRAfilesize
1db6ca1e667aa51892fe9d56cd6c8525  SRR5030873.sra
SRR5030873.sra file validated
SRR5030873 is single end
SRR5030873 is conventional basespace
SRR5030873 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030873_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3645	33.0	31.0	34.0	31.0	34.0
2	32.686	34.0	31.0	34.0	31.0	34.0
3	32.832	34.0	31.0	34.0	31.0	34.0
4	36.304	37.0	37.0	37.0	35.0	37.0
5	36.34525	37.0	37.0	37.0	35.0	37.0
6	36.07775	37.0	36.0	37.0	35.0	37.0
7	36.1325	37.0	35.0	37.0	35.0	37.0
8	36.17	37.0	36.0	37.0	35.0	37.0
9	37.93275	39.0	38.0	39.0	35.0	39.0
10	37.93025	39.0	38.0	39.0	35.0	39.0
11	37.83125	39.0	38.0	39.0	35.0	39.0
12	37.88775	39.0	38.0	39.0	35.0	39.0
13	37.81275	39.0	38.0	39.0	35.0	39.0
14	39.261	41.0	39.0	41.0	36.0	41.0
15	39.167	40.0	39.0	41.0	36.0	41.0
16	39.20925	40.0	39.0	41.0	36.0	41.0
17	39.303	41.0	39.0	41.0	36.0	41.0
18	39.318	41.0	39.0	41.0	36.0	41.0
19	39.027	41.0	38.0	41.0	35.0	41.0
20	39.06275	41.0	39.0	41.0	35.0	41.0
21	39.11425	40.0	39.0	41.0	36.0	41.0
22	39.14775	41.0	39.0	41.0	36.0	41.0
23	39.049	40.0	39.0	41.0	36.0	41.0
24	38.71075	40.0	38.0	41.0	35.0	41.0
25	38.83325	40.0	38.0	41.0	35.0	41.0
26	38.66925	40.0	38.0	41.0	34.0	41.0
27	38.83425	40.0	38.0	41.0	35.0	41.0
28	38.6615	40.0	38.0	41.0	34.0	41.0
29	37.96275	40.0	38.0	41.0	33.0	41.0
30	38.32975	40.0	38.0	41.0	33.0	41.0
31	38.718	40.0	38.0	41.0	35.0	41.0
32	38.97875	40.0	38.0	41.0	35.0	41.0
33	38.36075	40.0	38.0	41.0	34.0	41.0
34	38.2895	40.0	38.0	41.0	33.0	41.0
35	38.06325	40.0	38.0	41.0	34.0	41.0
36	34.2735	38.0	31.0	40.0	23.0	41.0
37	35.9675	38.0	34.0	40.0	30.0	41.0
38	37.137	39.0	37.0	40.0	32.0	41.0
39	37.301	39.0	37.0	40.0	32.0	41.0
40	37.331	39.0	37.0	41.0	32.0	41.0
41	37.4065	39.0	37.0	41.0	32.0	41.0
42	37.55575	40.0	38.0	41.0	33.0	41.0
43	37.37525	40.0	37.0	41.0	32.0	41.0
44	37.36325	40.0	37.0	41.0	33.0	41.0
45	36.92125	40.0	37.0	41.0	31.0	41.0
46	35.39225	38.0	34.0	40.0	27.0	41.0
47	35.94625	39.0	35.0	40.0	29.0	41.0
48	36.41025	39.0	36.0	41.0	30.0	41.0
49	35.549	39.0	35.0	41.0	29.0	41.0
50	30.78075	34.0	28.0	38.0	16.0	40.0
>>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
17	1.0
18	3.0
19	1.0
20	3.0
21	3.0
22	3.0
23	8.0
24	15.0
25	17.0
26	18.0
27	21.0
28	29.0
29	36.0
30	44.0
31	63.0
32	83.0
33	112.0
34	178.0
35	198.0
36	316.0
37	514.0
38	972.0
39	1362.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.210737581535374	23.507275464124437	51.35474159558454	14.927245358755645
2	22.825	25.825	21.375	29.975
3	27.474999999999998	19.925	20.849999999999998	31.75
4	31.65	29.65	14.124999999999998	24.575
5	20.200000000000003	43.875	23.925	12.0
6	33.625	16.625	35.175	14.575
7	18.125	18.9	24.0	38.975
8	22.15	31.974999999999998	15.775	30.099999999999998
9	23.65	33.2	29.075	14.075
10	23.200000000000003	21.575	31.275	23.95
11	28.075	12.7	18.175	41.05
12	14.274999999999999	18.95	33.725	33.050000000000004
13	31.3	21.575	29.5	17.625
14	30.099999999999998	33.875	20.125	15.9
15	37.684421105276314	24.33108277069267	23.730932733183295	14.253563390847713
16	17.7	21.15	22.475	38.675
17	21.075	22.3	42.25	14.374999999999998
18	24.75	21.05	31.175000000000004	23.025000000000002
19	38.925	12.950000000000001	29.975	18.15
20	43.275000000000006	15.575	27.35	13.8
21	22.45	18.625	29.4	29.525000000000002
22	28.675	12.174999999999999	48.775	10.375
23	27.875	12.7	45.475	13.950000000000001
24	53.525	14.6	23.549999999999997	8.325000000000001
25	49.675000000000004	25.575	14.499999999999998	10.25
26	25.575	49.175000000000004	14.75	10.5
27	16.3	47.075	25.825	10.8
28	12.25	22.975	50.349999999999994	14.424999999999999
29	9.45	12.825000000000001	56.15	21.575
30	9.875	6.65	36.25	47.225
31	15.25	5.65	46.175	32.925
32	29.799999999999997	6.0	20.200000000000003	44.0
33	57.275	7.8	13.05	21.875
34	63.224999999999994	7.7	15.775	13.3
35	63.025	7.925	19.25	9.8
36	43.35	8.475000000000001	34.925	13.25
37	44.824999999999996	10.35	19.725	25.1
38	21.6	16.125	12.225	50.05
39	14.475	27.275	8.375	49.875
40	15.7	50.349999999999994	10.225	23.724999999999998
41	26.125	49.375	8.774999999999999	15.725
42	52.47500000000001	29.4	9.175	8.95
43	49.675000000000004	32.95	7.725	9.65
44	27.325	51.55	7.6499999999999995	13.475000000000001
45	16.775000000000002	49.65	13.075000000000001	20.5
46	11.325000000000001	25.7	20.1	42.875
47	7.7	15.975	39.375	36.95
48	9.975000000000001	13.475000000000001	18.125	58.425000000000004
49	13.025	21.725	13.275	51.975
50	19.400000000000002	38.525	13.25	28.825
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.5
4	1.0
5	0.5
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	1.0
28	2.0
29	3.0
30	4.0
31	11.0
32	18.0
33	17.0
34	16.0
35	24.0
36	32.0
37	42.0
38	52.0
39	49.5
40	47.0
41	46.5
42	46.0
43	89.0
44	132.0
45	184.0
46	236.0
47	361.0
48	486.0
49	595.5
50	705.0
51	719.5
52	734.0
53	569.5
54	405.0
55	455.0
56	505.0
57	383.0
58	261.0
59	168.0
60	75.0
61	64.5
62	54.0
63	74.0
64	94.0
65	64.0
66	34.0
67	25.0
68	16.0
69	12.0
70	8.0
71	16.5
72	25.0
73	14.5
74	4.0
75	3.5
76	3.0
77	2.5
78	2.0
79	1.0
80	0.0
81	0.0
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	0.35000000000000003
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	0.025
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	39.625
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.52996845425868	30.325000000000003
2	8.580441640378549	6.800000000000001
3	4.037854889589906	4.8
4	3.1545741324921135	5.0
5	1.38801261829653	2.75
6	1.0725552050473186	2.55
7	0.8201892744479496	2.275
8	0.6309148264984227	2.0
9	0.5047318611987383	1.7999999999999998
>10	2.7129337539432177	20.724999999999998
>50	0.3785488958990536	10.5
>100	0.1892744479495268	10.475
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	142	3.55	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	92	2.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	86	2.15	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	63	1.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	59	1.4749999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	52	1.3	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	49	1.225	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	40	1.0	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	24	0.6	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	22	0.5499999999999999	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTC	21	0.525	RNA PCR Primer, Index 7 (100% over 44bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	19	0.475	RNA PCR Primer, Index 7 (100% over 35bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 33bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	16	0.4	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	13	0.325	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	10	0.25	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	9	0.22499999999999998	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 7 (100% over 50bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	8	0.2	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	8	0.2	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	7	0.17500000000000002	RNA PCR Primer, Index 2 (100% over 34bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	7	0.17500000000000002	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	6	0.15	No Hit
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	6	0.15	No Hit
TTGTGCTTGATCTAACCATGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	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)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	5	0.125	No Hit
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	5	0.125	No Hit
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	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	0.225	0.0	0.0	0.0
2	0.0	0.225	0.0	0.0	0.0
3	0.0	0.325	0.0	0.0	0.0
4	0.0	0.35	0.0	0.0	0.0
5	0.0	0.4	0.0	0.0	0.0
6	0.0	0.425	0.0	0.0	0.0
7	0.0	1.0	0.0	0.0	0.0
8	0.0	1.1	0.0	0.0	0.0
9	0.0	1.2	0.0	0.0	0.0
10	0.0	1.375	0.0	0.0	0.0
11	0.0	1.5	0.0	0.0	0.0
12	0.0	1.725	0.0	0.0	0.0
13	0.0	2.1	0.0	0.0	0.0
14	0.0	2.275	0.0	0.0	0.0
15	0.0	2.675	0.0	0.0	0.0
16	0.0	3.7	0.0	0.0	0.0
17	0.0	4.45	0.0	0.0	0.0
18	0.0	5.55	0.0	0.0	0.0
19	0.0	6.075	0.0	0.0	0.0
20	0.0	7.45	0.0	0.0	0.0
21	0.0	13.45	0.0	0.0	0.0
22	0.0	26.475	0.0	0.0	0.0
23	0.0	56.8	0.0	0.0	0.0
24	0.0	68.5	0.0	0.0	0.0
25	0.0	74.1	0.0	0.0	0.0
26	0.0	75.675	0.0	0.0	0.0
27	0.0	76.05	0.0	0.0	0.0
28	0.0	76.575	0.0	0.0	0.0
29	0.0	77.1	0.0	0.0	0.0
30	0.0	77.35	0.0	0.0	0.0
31	0.0	77.85	0.0	0.0	0.0
32	0.0	79.25	0.0	0.0	0.0
33	0.0	80.075	0.0	0.0	0.0
34	0.0	82.0	0.0	0.0	0.0
35	0.0	82.85	0.0	0.0	0.0
36	0.0	83.5	0.0	0.0	0.0
37	0.0	84.125	0.0	0.0	0.0
38	0.0	84.325	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	40	5.315087E-9	44.000004	8
GAGGTAG	20	6.952051E-4	44.000004	2
ACGCTGT	40	5.315087E-9	44.000004	9
AACCGGT	20	6.952051E-4	44.000004	9
CTGAGCT	40	5.315087E-9	44.000004	11
TTCAACG	40	5.315087E-9	44.000004	5
TCGGTGA	40	5.315087E-9	44.000004	15
GGTCTCT	20	6.952051E-4	44.000004	13
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	40	5.315087E-9	44.000004	1
GGCTGGA	20	6.952051E-4	44.000004	19
GTCTGAG	40	5.315087E-9	44.000004	9
CATTCAA	40	5.315087E-9	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
CGGATCC	40	5.315087E-9	44.000004	2
ACATTCA	40	5.315087E-9	44.000004	2
>>END_MODULE
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331576 spots for SRR5030873.sra
Written 331576 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
Read 331568 spots for SRR5030873.sra
Written 331568 spots for SRR5030873.sra
SRR ids: ['SRR5030873.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_lzxvyrds
SRR5030873.sra spots: 3978824
blocks: [[1, 331568], [331569, 663136], [663137, 994704], [994705, 1326272], [1326273, 1657840], [1657841, 1989408], [1989409, 2320976], [2320977, 2652544], [2652545, 2984112], [2984113, 3315680], [3315681, 3647248], [3647249, 3978824]]
SRR5030873 file size 688545
SRR5030873 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030873 SRR5030873_1.fastq
Input file:	SRR5030873_1.fastq
trimmed:	SRR5030873-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 06:34:01 2020 >> started

Wed Mar  4 06:34:03 2020 >> done (2.234s)
3978824 reads processed; of these:
    233 ( 0.01%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
3978581 (99.99%) reads available; of these:
 213325 ( 5.36%) trimmed reads available after processing
3765256 (94.64%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     89	  0.00%
 19	     90	  0.00%
 20	    176	  0.00%
 21	    206	  0.01%
 22	    397	  0.01%
 23	    497	  0.01%
 24	    497	  0.01%
 25	    585	  0.01%
 26	    465	  0.01%
 27	    625	  0.02%
 28	    788	  0.02%
 29	   1225	  0.03%
 30	    784	  0.02%
 31	   1086	  0.03%
 32	    991	  0.02%
 33	   1369	  0.03%
 34	   2962	  0.07%
 35	   3000	  0.08%
 36	   2305	  0.06%
 37	   2481	  0.06%
 38	   2867	  0.07%
 39	   2930	  0.07%
 40	   3273	  0.08%
 41	   3944	  0.10%
 42	   4913	  0.12%
 43	   6997	  0.18%
 44	  12465	  0.31%
 45	  15178	  0.38%
 46	  13878	  0.35%
 47	  20279	  0.51%
 48	  44263	  1.11%
 49	  61720	  1.55%
 50	3765256	 94.64%
3978581 reads passed initial QC


criterion=sequence-density
sequence-density=84.82
sequence-density-rank=1
fanout-score=19.43
fanout-score-rank=1
prefix-density=86.24
prefix-fanout=19.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC


criterion=fanout-score
sequence-density=84.82
sequence-density-rank=1
fanout-score=19.43
fanout-score-rank=1
prefix-density=86.24
prefix-fanout=19.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC -o SRR5030873 -
Input file:	STDIN
trimmed:	SRR5030873-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC
-- 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 06:34:21 2020 >> started

Wed Mar  4 06:34:25 2020 >> done (4.864s)
3884967 reads processed; of these:
 224677 ( 5.78%) short reads filtered out after trimming by size control
  11222 ( 0.29%) empty reads filtered out after trimming by size control
3649068 (93.93%) reads available; of these:
3320879 (91.01%) trimmed reads available after processing
 328189 ( 8.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  23302	  0.64%
 19	  40708	  1.12%
 20	 238586	  6.54%
 21	 501147	 13.73%
 22	1194250	 32.73%
 23	 485456	 13.30%
 24	 210304	  5.76%
 25	  50538	  1.38%
 26	  25799	  0.71%
 27	  21567	  0.59%
 28	  21542	  0.59%
 29	  15759	  0.43%
 30	  25217	  0.69%
 31	  40398	  1.11%
 32	  29907	  0.82%
 33	  89960	  2.47%
 34	  36506	  1.00%
 35	  29837	  0.82%
 36	  34002	  0.93%
 37	  15485	  0.42%
 38	  15628	  0.43%
 39	  16724	  0.46%
 40	  19889	  0.55%
 41	  27588	  0.76%
 42	  31693	  0.87%
 43	  23326	  0.64%
 44	  20099	  0.55%
 45	  24289	  0.67%
 46	  18764	  0.51%
 47	  16075	  0.44%
 48	   3495	  0.10%
 49	  11032	  0.30%
 50	 290196	  7.95%


criterion=sequence-density
sequence-density=5.87
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=0.43
sequence-density-rank=29
fanout-score=26.90
fanout-score-rank=1
prefix-density=11.54
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 06:34:46
                             Started mapping on |	Mar 04 06:34:46
                                    Finished on |	Mar 04 06:35:13
       Mapping speed, Million of reads per hour |	499.02

                          Number of input reads |	3742682
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2136153
                        Uniquely mapped reads % |	57.08%
                          Average mapped length |	26.15
                       Number of splices: Total |	1444
            Number of splices: Annotated (sjdb) |	285
                       Number of splices: GT/AG |	1315
                       Number of splices: GC/AG |	22
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	107
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.55
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1248748
             % of reads mapped to multiple loci |	33.37%
        Number of reads mapped to too many loci |	73326
             % of reads mapped to too many loci |	1.96%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.16%
                     % of reads unmapped: other |	0.44%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	357781	357781	357781
N_multimapping	1248748	1248748	1248748
N_noFeature	101905	122307	1449178
N_ambiguous	1217586	621064	23014
UnstrandedReadsAssigned:816662 PositiveStrandReadsAssigned:1392782 NegativeStrandReadsAssigned:663961
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030873 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: SRR5030873-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,742,682 reads, 1,025,950 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,006 rounds

 109283 SRR5030873.ke.tsv
  52636 SRR5030873.se.tsv
 161919 total
==> SRR5030873.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

==> SRR5030873.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030873 completed mapping pipeline successfully
