Starting /dee2/code/volunteer_pipeline.sh SRR5031067
    current disk space = 160512065536
    free memory = 73932200 
SRR5031067 SRAfilesize
109b0366c1f05cabe535bf57d4c9b196  SRR5031067.sra
SRR5031067.sra file validated
SRR5031067 is single end
SRR5031067 is conventional basespace
SRR5031067 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031067_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	32.35125	33.0	31.0	34.0	31.0	34.0
2	32.59525	34.0	31.0	34.0	31.0	34.0
3	32.65475	34.0	31.0	34.0	31.0	34.0
4	36.18875	37.0	35.0	37.0	35.0	37.0
5	35.90375	37.0	35.0	37.0	35.0	37.0
6	35.9045	37.0	35.0	37.0	35.0	37.0
7	35.95325	37.0	35.0	37.0	35.0	37.0
8	35.821	37.0	35.0	37.0	35.0	37.0
9	37.5685	39.0	37.0	39.0	35.0	39.0
10	37.77225	39.0	37.0	39.0	35.0	39.0
11	37.602	39.0	37.0	39.0	35.0	39.0
12	37.61575	39.0	37.0	39.0	35.0	39.0
13	37.59475	39.0	37.0	39.0	35.0	39.0
14	39.104	41.0	38.0	41.0	36.0	41.0
15	38.85625	40.0	38.0	41.0	35.0	41.0
16	38.91	40.0	38.0	41.0	35.0	41.0
17	38.85225	40.0	38.0	41.0	35.0	41.0
18	39.004	40.0	38.0	41.0	35.0	41.0
19	38.702	40.0	38.0	41.0	34.0	41.0
20	38.77375	40.0	38.0	41.0	34.0	41.0
21	38.7465	40.0	38.0	41.0	34.0	41.0
22	38.93525	40.0	39.0	41.0	35.0	41.0
23	38.82675	40.0	38.0	41.0	35.0	41.0
24	38.835	40.0	38.0	41.0	35.0	41.0
25	39.11025	41.0	39.0	41.0	35.0	41.0
26	38.94725	40.0	38.0	41.0	35.0	41.0
27	38.9395	40.0	39.0	41.0	35.0	41.0
28	38.89125	40.0	38.0	41.0	35.0	41.0
29	38.46	40.0	38.0	41.0	34.0	41.0
30	38.60475	40.0	38.0	41.0	34.0	41.0
31	38.701	40.0	38.0	41.0	35.0	41.0
32	38.66175	40.0	38.0	41.0	34.0	41.0
33	38.598	40.0	38.0	41.0	35.0	41.0
34	38.77575	40.0	38.0	41.0	35.0	41.0
35	38.57475	40.0	38.0	41.0	35.0	41.0
36	38.245	40.0	38.0	41.0	34.0	41.0
37	37.68875	40.0	37.0	41.0	32.0	41.0
38	37.07075	39.0	36.0	41.0	30.0	41.0
39	37.684	40.0	37.0	41.0	33.0	41.0
40	37.85225	40.0	37.0	41.0	33.0	41.0
41	38.131	40.0	38.0	41.0	33.0	41.0
42	38.24125	40.0	38.0	41.0	34.0	41.0
43	38.39725	40.0	38.0	41.0	34.0	41.0
44	38.101	40.0	38.0	41.0	33.0	41.0
45	38.0885	40.0	38.0	41.0	33.0	41.0
46	37.95325	40.0	37.0	41.0	33.0	41.0
47	37.51375	40.0	37.0	41.0	32.0	41.0
48	37.186	40.0	36.0	41.0	32.0	41.0
49	37.354	40.0	37.0	41.0	32.0	41.0
50	36.841	40.0	36.0	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
17	2.0
18	2.0
19	2.0
20	0.0
21	4.0
22	3.0
23	9.0
24	4.0
25	7.0
26	14.0
27	12.0
28	20.0
29	33.0
30	41.0
31	55.0
32	91.0
33	111.0
34	154.0
35	196.0
36	239.0
37	439.0
38	668.0
39	1894.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.3	27.05	51.225	13.425
2	23.667750813109834	27.9459594696022	18.689016762571928	29.697272954716038
3	23.625	20.9	22.725	32.75
4	32.25	28.249999999999996	14.000000000000002	25.5
5	21.275	40.975	26.75	11.0
6	34.775	16.55	33.800000000000004	14.875
7	14.35	20.625	22.650000000000002	42.375
8	24.2	29.45	16.35	30.0
9	20.599999999999998	36.65	27.85	14.899999999999999
10	21.55	23.425	27.275	27.750000000000004
11	31.324999999999996	8.875	17.75	42.05
12	14.549999999999999	17.9	32.1	35.449999999999996
13	31.35	17.65	32.074999999999996	18.925
14	33.35	31.525	19.375	15.75
15	34.575	25.650000000000002	25.974999999999998	13.8
16	19.875	18.15	22.25	39.725
17	24.474999999999998	23.1	38.3	14.124999999999998
18	26.150000000000002	17.925	27.325	28.599999999999998
19	35.625	12.35	34.025	18.0
20	43.95	14.35	28.050000000000004	13.65
21	22.3	21.475	28.475	27.750000000000004
22	29.75	11.075	49.325	9.85
23	26.674999999999997	11.825	46.875	14.625
24	54.125	12.675	26.150000000000002	7.049999999999999
25	52.575	24.775	14.499999999999998	8.15
26	28.4	49.875	11.899999999999999	9.825000000000001
27	14.475	50.05	24.15	11.325000000000001
28	8.799999999999999	24.875	51.975	14.35
29	10.325	12.575	58.025000000000006	19.075
30	8.35	4.8	39.275	47.575
31	13.075000000000001	3.675	48.5	34.75
32	27.775	4.1000000000000005	21.025	47.099999999999994
33	57.125	7.449999999999999	13.5	21.925
34	65.575	5.6000000000000005	14.524999999999999	14.299999999999999
35	67.675	5.575	18.975	7.775
36	43.125	6.25	38.85	11.774999999999999
37	47.25	8.924999999999999	19.925	23.9
38	22.650000000000002	14.625	12.5	50.224999999999994
39	15.225	23.724999999999998	8.799999999999999	52.25
40	13.575000000000001	51.025	9.25	26.150000000000002
41	24.4	50.775000000000006	8.35	16.475
42	51.6	29.825000000000003	10.225	8.35
43	54.0	30.325000000000003	6.8500000000000005	8.825
44	31.275	50.824999999999996	6.05	11.85
45	17.7	51.725	11.5	19.075
46	11.225	26.275	18.6	43.9
47	7.9750000000000005	14.575	40.425	37.025000000000006
48	9.2	11.725	20.05	59.025000000000006
49	11.4	18.725	13.775	56.10000000000001
50	18.224999999999998	38.625	12.55	30.599999999999998
>>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	0.5
14	1.0
15	0.5
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	0.5
26	1.0
27	0.5
28	0.0
29	0.5
30	1.0
31	6.0
32	11.0
33	10.0
34	9.0
35	10.0
36	11.0
37	15.0
38	19.0
39	21.0
40	23.0
41	30.5
42	38.0
43	75.5
44	113.0
45	151.5
46	190.0
47	326.5
48	463.0
49	607.0
50	751.0
51	835.0
52	919.0
53	678.5
54	438.0
55	449.5
56	461.0
57	340.5
58	220.0
59	133.5
60	47.0
61	43.5
62	40.0
63	85.5
64	131.0
65	76.5
66	22.0
67	19.0
68	16.0
69	16.0
70	16.0
71	31.5
72	47.0
73	27.0
74	7.0
75	3.5
76	0.0
77	0.5
78	1.0
79	1.5
80	2.0
81	2.0
82	2.0
83	1.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.075
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	35.525
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.15833919774806	26.700000000000003
2	9.078114004222378	6.45
3	4.714989444053484	5.025
4	2.322308233638283	3.3000000000000003
5	1.688951442646024	3.0
6	1.4074595355383532	3.0
7	0.49261083743842365	1.225
8	0.7741027445460943	2.1999999999999997
9	0.3518648838845883	1.125
>10	3.3075299085151304	21.3
>50	0.3518648838845883	9.9
>100	0.3518648838845883	16.775000000000002
>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	175	4.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	138	3.45	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	129	3.225	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	117	2.9250000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	81	2.025	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	80	2.0	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	79	1.975	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	59	1.4749999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	38	0.95	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	23	0.575	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	21	0.525	RNA PCR Primer, Index 1 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTC	13	0.325	RNA PCR Primer, Index 39 (100% over 44bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGC	11	0.27499999999999997	RNA PCR Primer, Index 39 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	8	0.2	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
AAGGGATTCTGATGTTGGTCACTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	5	0.125	No Hit
ATCATGATGGGCTCCTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.275	0.0	0.0	0.0
2	0.0	0.325	0.0	0.0	0.0
3	0.0	0.4	0.0	0.0	0.0
4	0.0	0.425	0.0	0.0	0.0
5	0.0	0.45	0.0	0.0	0.0
6	0.0	0.475	0.0	0.0	0.0
7	0.0	0.85	0.0	0.0	0.0
8	0.0	1.0	0.0	0.0	0.0
9	0.0	1.075	0.0	0.0	0.0
10	0.0	1.2	0.0	0.0	0.0
11	0.0	1.35	0.0	0.0	0.0
12	0.0	1.575	0.0	0.0	0.0
13	0.0	1.675	0.0	0.0	0.0
14	0.0	1.85	0.0	0.0	0.0
15	0.0	2.1	0.0	0.0	0.0
16	0.0	3.0	0.0	0.0	0.0
17	0.0	3.525	0.0	0.0	0.0
18	0.0	4.3	0.0	0.0	0.0
19	0.0	4.65	0.0	0.0	0.0
20	0.0	5.4	0.0	0.0	0.0
21	0.0	10.575	0.0	0.0	0.0
22	0.0	23.45	0.0	0.0	0.0
23	0.0	55.775	0.0	0.0	0.0
24	0.0	69.625	0.0	0.0	0.0
25	0.0	76.875	0.0	0.0	0.0
26	0.0	78.275	0.0	0.0	0.0
27	0.0	78.775	0.0	0.0	0.0
28	0.0	79.35	0.0	0.0	0.0
29	0.0	79.95	0.0	0.0	0.0
30	0.0	80.575	0.0	0.0	0.0
31	0.0	81.275	0.0	0.0	0.0
32	0.0	82.2	0.0	0.0	0.0
33	0.0	83.35	0.0	0.0	0.0
34	0.0	86.35	0.0	0.0	0.0
35	0.0	87.325	0.0	0.0	0.0
36	0.0	88.3	0.0	0.0	0.0
37	0.0	89.375	0.0	0.0	0.0
38	0.0	89.625	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGATGAA	20	6.952051E-4	44.000004	6
AACGCTG	20	6.952051E-4	44.000004	8
ACGCTGT	20	6.952051E-4	44.000004	9
TTCAACG	20	6.952051E-4	44.000004	5
TCGGTGA	20	6.952051E-4	44.000004	15
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
ATTCAAC	20	6.952051E-4	44.000004	4
CAACGCT	20	6.952051E-4	44.000004	7
CGCTGTC	20	6.952051E-4	44.000004	10
ACTGTTG	25	3.6958358E-5	44.0	18
GTTGAAG	25	3.6958358E-5	44.0	10
AAGTAAT	30	1.9515464E-6	44.0	4
TCAAGTA	30	1.9515464E-6	44.0	2
CAGTTGA	25	3.6958358E-5	44.0	8
ATCCAGG	30	1.9515464E-6	44.0	9
AACTGTT	25	3.6958358E-5	44.0	17
TTCAAGT	30	1.9515464E-6	44.0	1
AGGATAG	30	1.9515464E-6	44.0	13
ATAGGCT	30	1.9515464E-6	44.0	16
>>END_MODULE
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
Read 193008 spots for SRR5031067.sra
Written 193008 spots for SRR5031067.sra
SRR ids: ['SRR5031067.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_0v8cdra4
SRR5031067.sra spots: 2316096
blocks: [[1, 193008], [193009, 386016], [386017, 579024], [579025, 772032], [772033, 965040], [965041, 1158048], [1158049, 1351056], [1351057, 1544064], [1544065, 1737072], [1737073, 1930080], [1930081, 2123088], [2123089, 2316096]]
SRR5031067 file size 400363
SRR5031067 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031067 SRR5031067_1.fastq
Input file:	SRR5031067_1.fastq
trimmed:	SRR5031067-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 07:17:21 2020 >> started

Wed Mar  4 07:17:22 2020 >> done (1.685s)
2316096 reads processed; of these:
    169 ( 0.01%) short reads filtered out after trimming by size control
      8 ( 0.00%) empty reads filtered out after trimming by size control
2315919 (99.99%) reads available; of these:
 112118 ( 4.84%) trimmed reads available after processing
2203801 (95.16%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     57	  0.00%
 19	     65	  0.00%
 20	    131	  0.01%
 21	    143	  0.01%
 22	    269	  0.01%
 23	    317	  0.01%
 24	    369	  0.02%
 25	    450	  0.02%
 26	    364	  0.02%
 27	    522	  0.02%
 28	    590	  0.03%
 29	   1030	  0.04%
 30	    522	  0.02%
 31	    615	  0.03%
 32	    719	  0.03%
 33	    892	  0.04%
 34	   1127	  0.05%
 35	   2179	  0.09%
 36	   1877	  0.08%
 37	   2235	  0.10%
 38	   1943	  0.08%
 39	   2087	  0.09%
 40	   2427	  0.10%
 41	   2436	  0.11%
 42	   3267	  0.14%
 43	   4671	  0.20%
 44	   6367	  0.27%
 45	   7607	  0.33%
 46	  10618	  0.46%
 47	  13911	  0.60%
 48	  21814	  0.94%
 49	  20497	  0.89%
 50	2203801	 95.16%
2315919 reads passed initial QC


criterion=sequence-density
sequence-density=88.61
sequence-density-rank=1
fanout-score=20.76
fanout-score-rank=1
prefix-density=90.30
prefix-fanout=20.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGCC


criterion=fanout-score
sequence-density=88.61
sequence-density-rank=1
fanout-score=20.76
fanout-score-rank=1
prefix-density=90.30
prefix-fanout=20.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGCC -o SRR5031067 -
Input file:	STDIN
trimmed:	SRR5031067-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGCC
-- 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 07:17:36 2020 >> started

Wed Mar  4 07:17:40 2020 >> done (3.609s)
2263876 reads processed; of these:
  98645 ( 4.36%) short reads filtered out after trimming by size control
  12563 ( 0.55%) empty reads filtered out after trimming by size control
2152668 (95.09%) reads available; of these:
2077653 (96.52%) trimmed reads available after processing
  75015 ( 3.48%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11065	  0.51%
 19	  21615	  1.00%
 20	 120687	  5.61%
 21	 292467	 13.59%
 22	 725900	 33.72%
 23	 322190	 14.97%
 24	 149285	  6.93%
 25	  36916	  1.71%
 26	  18627	  0.87%
 27	  15066	  0.70%
 28	  16402	  0.76%
 29	  12659	  0.59%
 30	  17960	  0.83%
 31	  20655	  0.96%
 32	  27190	  1.26%
 33	  67457	  3.13%
 34	  22939	  1.07%
 35	  16896	  0.78%
 36	  20434	  0.95%
 37	   9536	  0.44%
 38	  10894	  0.51%
 39	  10034	  0.47%
 40	  16211	  0.75%
 41	  21071	  0.98%
 42	  24022	  1.12%
 43	  16199	  0.75%
 44	  11733	  0.55%
 45	  14693	  0.68%
 46	  10102	  0.47%
 47	   8155	  0.38%
 48	    770	  0.04%
 49	    988	  0.05%
 50	  61850	  2.87%


criterion=sequence-density
sequence-density=7.45
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=0.02
sequence-density-rank=38
fanout-score=95.49
fanout-score-rank=1
prefix-density=2.25
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:18:17
                             Started mapping on |	Mar 04 07:18:18
                                    Finished on |	Mar 04 07:18:43
       Mapping speed, Million of reads per hour |	317.48

                          Number of input reads |	2204711
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1166611
                        Uniquely mapped reads % |	52.91%
                          Average mapped length |	23.98
                       Number of splices: Total |	1447
            Number of splices: Annotated (sjdb) |	336
                       Number of splices: GT/AG |	1366
                       Number of splices: GC/AG |	24
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	57
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.68
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	782696
             % of reads mapped to multiple loci |	35.50%
        Number of reads mapped to too many loci |	37771
             % of reads mapped to too many loci |	1.71%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.39%
                     % of reads unmapped: other |	0.49%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	255404	255404	255404
N_multimapping	782696	782696	782696
N_noFeature	50974	63259	809509
N_ambiguous	660665	351871	9263
UnstrandedReadsAssigned:454972 PositiveStrandReadsAssigned:751481 NegativeStrandReadsAssigned:347839
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031067 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: SRR5031067-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,204,711 reads, 572,649 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,112 rounds

 109283 SRR5031067.ke.tsv
  52636 SRR5031067.se.tsv
 161919 total
==> SRR5031067.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

==> SRR5031067.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031067 completed mapping pipeline successfully
