Starting /dee2/code/volunteer_pipeline.sh SRR5031057
    current disk space = 160512425984
    free memory = 73950900 
SRR5031057 SRAfilesize
0439976655fce8dee3560e987dd3a409  SRR5031057.sra
SRR5031057.sra file validated
SRR5031057 is single end
SRR5031057 is conventional basespace
SRR5031057 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031057_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	32.3885	33.0	31.0	34.0	31.0	34.0
2	32.63975	34.0	31.0	34.0	31.0	34.0
3	32.69625	34.0	31.0	34.0	31.0	34.0
4	36.21675	37.0	37.0	37.0	35.0	37.0
5	35.9925	37.0	35.0	37.0	35.0	37.0
6	35.96825	37.0	35.0	37.0	35.0	37.0
7	35.9955	37.0	35.0	37.0	35.0	37.0
8	35.758	37.0	35.0	37.0	33.0	37.0
9	37.61825	39.0	37.0	39.0	35.0	39.0
10	37.81725	39.0	38.0	39.0	35.0	39.0
11	37.6155	39.0	37.0	39.0	35.0	39.0
12	37.62775	39.0	37.0	39.0	35.0	39.0
13	37.62425	39.0	37.0	39.0	35.0	39.0
14	38.88025	40.0	38.0	41.0	35.0	41.0
15	38.899	40.0	38.0	41.0	35.0	41.0
16	38.81625	40.0	38.0	41.0	35.0	41.0
17	38.827	40.0	38.0	41.0	35.0	41.0
18	38.96175	40.0	38.0	41.0	35.0	41.0
19	38.61975	40.0	38.0	41.0	34.0	41.0
20	38.8615	40.0	38.0	41.0	35.0	41.0
21	38.82225	40.0	38.0	41.0	35.0	41.0
22	38.87175	40.0	38.0	41.0	35.0	41.0
23	38.56425	40.0	38.0	41.0	34.0	41.0
24	38.6735	40.0	38.0	41.0	34.0	41.0
25	38.93675	40.0	39.0	41.0	35.0	41.0
26	38.5875	40.0	38.0	41.0	34.0	41.0
27	38.6055	40.0	38.0	41.0	34.0	41.0
28	38.661	40.0	38.0	41.0	35.0	41.0
29	38.21575	40.0	38.0	41.0	33.0	41.0
30	38.04975	40.0	38.0	41.0	33.0	41.0
31	38.27175	40.0	38.0	41.0	33.0	41.0
32	38.272	40.0	38.0	41.0	33.0	41.0
33	38.4385	40.0	38.0	41.0	34.0	41.0
34	38.55075	40.0	38.0	41.0	34.0	41.0
35	38.2345	40.0	38.0	41.0	33.0	41.0
36	37.8665	40.0	37.0	41.0	32.0	41.0
37	37.5315	40.0	37.0	41.0	31.0	41.0
38	36.82875	39.0	36.0	41.0	30.0	41.0
39	37.183	39.0	37.0	41.0	31.0	41.0
40	37.54175	40.0	37.0	41.0	33.0	41.0
41	37.49775	40.0	37.0	41.0	32.0	41.0
42	37.60075	40.0	37.0	41.0	32.0	41.0
43	38.0015	40.0	38.0	41.0	33.0	41.0
44	37.6895	40.0	37.0	41.0	33.0	41.0
45	37.6375	40.0	37.0	41.0	33.0	41.0
46	37.60225	40.0	37.0	41.0	33.0	41.0
47	37.05075	40.0	36.0	41.0	31.0	41.0
48	36.78675	40.0	36.0	41.0	31.0	41.0
49	36.9605	40.0	36.0	41.0	31.0	41.0
50	36.49	39.0	35.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
14	1.0
15	0.0
16	0.0
17	2.0
18	5.0
19	3.0
20	6.0
21	5.0
22	3.0
23	7.0
24	11.0
25	6.0
26	12.0
27	20.0
28	22.0
29	39.0
30	45.0
31	63.0
32	84.0
33	119.0
34	162.0
35	201.0
36	263.0
37	426.0
38	749.0
39	1746.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.674999999999999	24.675	49.0	15.65
2	24.730913642052567	27.759699624530665	18.02252816020025	29.486858573216523
3	27.150000000000002	15.675	21.675	35.5
4	32.300000000000004	30.775000000000002	14.799999999999999	22.125
5	20.8	41.225	25.775	12.2
6	29.575000000000003	14.424999999999999	39.45	16.55
7	16.775000000000002	19.7	22.925	40.6
8	20.625	29.025000000000002	17.075000000000003	33.275
9	24.2	31.574999999999996	27.825	16.400000000000002
10	20.275000000000002	20.349999999999998	29.875	29.5
11	36.0	11.875	15.049999999999999	37.075
12	16.375	20.775	31.45	31.4
13	30.2	16.6	32.225	20.974999999999998
14	28.65	30.175	21.5	19.675
15	37.65	23.65	25.275	13.425
16	19.05	20.0	20.849999999999998	40.1
17	27.775	22.0	34.725	15.5
18	24.875	19.225	30.9	25.0
19	35.699999999999996	16.25	30.925000000000004	17.125
20	46.425	15.15	25.474999999999998	12.950000000000001
21	27.224999999999998	21.25	22.650000000000002	28.875
22	29.75	16.175	44.675	9.4
23	25.525	15.7	41.725	17.05
24	49.85	14.7	24.65	10.8
25	46.300000000000004	24.6	17.95	11.15
26	26.25	44.35	13.25	16.150000000000002
27	16.525000000000002	44.125	23.625	15.725
28	11.65	25.874999999999996	45.425	17.05
29	15.675	13.175	52.400000000000006	18.75
30	9.575	7.425	37.325	45.675
31	13.375	5.2749999999999995	46.0	35.35
32	28.349999999999998	8.799999999999999	20.525	42.325
33	52.2	10.7	13.575000000000001	23.525
34	57.574999999999996	8.15	15.975	18.3
35	61.925	10.475	18.675	8.924999999999999
36	40.925	11.575000000000001	34.25	13.25
37	43.675000000000004	11.25	19.325	25.75
38	22.15	16.875	15.525	45.45
39	15.075	26.75	11.575000000000001	46.6
40	15.15	48.225	12.3	24.325
41	23.200000000000003	45.675	12.6	18.525
42	46.075	27.775	12.775	13.375
43	48.75	28.325	11.95	10.975
44	30.825000000000003	45.050000000000004	7.775	16.35
45	23.25	46.675	13.075000000000001	17.0
46	14.45	24.75	20.474999999999998	40.325
47	9.975000000000001	17.974999999999998	38.1	33.95
48	12.075	12.049999999999999	21.95	53.925
49	16.0	18.4	13.600000000000001	52.0
50	17.175	36.125	12.525	34.175
>>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	0.5
12	1.0
13	0.5
14	0.0
15	0.0
16	0.0
17	1.0
18	2.0
19	1.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	2.5
28	5.0
29	4.5
30	4.0
31	5.0
32	6.0
33	11.0
34	16.0
35	14.5
36	13.0
37	23.5
38	34.0
39	41.0
40	48.0
41	49.0
42	50.0
43	78.5
44	107.0
45	135.0
46	163.0
47	289.0
48	415.0
49	552.5
50	690.0
51	775.5
52	861.0
53	621.5
54	382.0
55	465.0
56	548.0
57	396.0
58	244.0
59	156.5
60	69.0
61	61.0
62	53.0
63	107.5
64	162.0
65	95.0
66	28.0
67	21.5
68	15.0
69	19.0
70	23.0
71	34.0
72	45.0
73	25.0
74	5.0
75	3.5
76	2.0
77	2.5
78	3.0
79	4.0
80	5.0
81	2.5
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.125
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	37.724999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.01656726308813	28.299999999999997
2	9.343936381709742	7.049999999999999
3	4.970178926441352	5.625
4	2.4519549370444005	3.6999999999999997
5	1.5904572564612325	3.0
6	1.2591119946984757	2.85
7	0.8614976805831678	2.275
8	0.46388336646785955	1.4000000000000001
9	0.46388336646785955	1.575
>10	2.9158383035122597	18.3
>50	0.26507620941020543	7.6
>100	0.3976143141153081	18.325
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	140	3.5000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	123	3.075	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	123	3.075	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGC	118	2.9499999999999997	RNA PCR Primer, Index 29 (100% over 50bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	115	2.875	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	114	2.85	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	100	2.5	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	88	2.1999999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	63	1.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	53	1.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	48	1.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	28	0.7000000000000001	RNA PCR Primer, Index 7 (100% over 35bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	16	0.4	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	15	0.375	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTC	15	0.375	RNA PCR Primer, Index 29 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	12	0.3	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	12	0.3	RNA PCR Primer, Index 1 (100% over 33bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	11	0.27499999999999997	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	11	0.27499999999999997	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	9	0.22499999999999998	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	7	0.17500000000000002	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	6	0.15	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	6	0.15	RNA PCR Primer, Index 2 (100% over 34bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	5	0.125	No Hit
TCTCACACAGAAATCGCACCCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAA	5	0.125	RNA PCR Primer, Index 2 (97% over 36bp)
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	5	0.125	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	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	3.225	0.0	0.0	0.0
2	0.0	3.225	0.0	0.0	0.0
3	0.0	3.275	0.0	0.0	0.0
4	0.0	3.3	0.0	0.0	0.0
5	0.0	3.325	0.0	0.0	0.0
6	0.0	3.45	0.0	0.0	0.0
7	0.0	3.925	0.0	0.0	0.0
8	0.0	4.05	0.0	0.0	0.0
9	0.0	4.125	0.0	0.0	0.0
10	0.0	4.175	0.0	0.0	0.0
11	0.0	4.225	0.0	0.0	0.0
12	0.0	4.4	0.0	0.0	0.0
13	0.0	4.675	0.0	0.0	0.0
14	0.0	4.975	0.0	0.0	0.0
15	0.0	5.4	0.0	0.0	0.0
16	0.0	6.6	0.0	0.0	0.0
17	0.0	7.275	0.0	0.0	0.0
18	0.0	8.175	0.0	0.0	0.0
19	0.0	8.6	0.0	0.0	0.0
20	0.0	9.1	0.0	0.0	0.0
21	0.0	14.175	0.0	0.0	0.0
22	0.0	24.875	0.0	0.0	0.0
23	0.0	52.475	0.0	0.0	0.0
24	0.0	63.925	0.0	0.0	0.0
25	0.0	70.0	0.0	0.0	0.0
26	0.0	71.475	0.0	0.0	0.0
27	0.0	72.075	0.0	0.0	0.0
28	0.0	72.45	0.0	0.0	0.0
29	0.0	73.25	0.0	0.0	0.0
30	0.0	73.7	0.0	0.0	0.0
31	0.0	74.6	0.0	0.0	0.0
32	0.0	75.85	0.0	0.0	0.0
33	0.0	77.15	0.0	0.0	0.0
34	0.0	81.3	0.0	0.0	0.0
35	0.0	83.05	0.0	0.0	0.0
36	0.0	84.1	0.0	0.0	0.0
37	0.0	85.4	0.0	0.0	0.0
38	0.0	85.95	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
AACGCTG	40	5.315087E-9	44.000004	8
ACGCTGT	40	5.315087E-9	44.000004	9
CTGAGAC	20	6.952051E-4	44.000004	4
TTCAACG	40	5.315087E-9	44.000004	5
TCGGTGA	40	5.315087E-9	44.000004	15
CCTGAGA	20	6.952051E-4	44.000004	3
CATTCAA	40	5.315087E-9	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
ACATCCT	20	6.952051E-4	44.000004	6
ACATTCA	40	5.315087E-9	44.000004	2
CTTGGCT	20	6.952051E-4	44.000004	16
GCTGTCG	40	5.315087E-9	44.000004	11
CCCTGAG	20	6.952051E-4	44.000004	2
GACTGGA	20	6.952051E-4	44.000004	14
AGACCCT	20	6.952051E-4	44.000004	7
CTGTCGG	40	5.315087E-9	44.000004	12
ATTCAAC	40	5.315087E-9	44.000004	4
CGACTGG	20	6.952051E-4	44.000004	13
GTCGGTG	40	5.315087E-9	44.000004	14
>>END_MODULE
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302246 spots for SRR5031057.sra
Written 302246 spots for SRR5031057.sra
Read 302247 spots for SRR5031057.sra
Written 302247 spots for SRR5031057.sra
SRR ids: ['SRR5031057.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_tbatxaqw
SRR5031057.sra spots: 3626953
blocks: [[1, 302246], [302247, 604492], [604493, 906738], [906739, 1208984], [1208985, 1511230], [1511231, 1813476], [1813477, 2115722], [2115723, 2417968], [2417969, 2720214], [2720215, 3022460], [3022461, 3324706], [3324707, 3626953]]
SRR5031057 file size 627572
SRR5031057 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031057 SRR5031057_1.fastq
Input file:	SRR5031057_1.fastq
trimmed:	SRR5031057-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 07:15:07 2020 >> started

Wed Mar  4 07:15:09 2020 >> done (1.672s)
3626953 reads processed; of these:
    248 ( 0.01%) short reads filtered out after trimming by size control
     18 ( 0.00%) empty reads filtered out after trimming by size control
3626687 (99.99%) reads available; of these:
 182724 ( 5.04%) trimmed reads available after processing
3443963 (94.96%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     90	  0.00%
 19	    117	  0.00%
 20	    235	  0.01%
 21	    303	  0.01%
 22	    486	  0.01%
 23	    537	  0.01%
 24	    620	  0.02%
 25	    727	  0.02%
 26	    646	  0.02%
 27	    797	  0.02%
 28	    968	  0.03%
 29	   1577	  0.04%
 30	    974	  0.03%
 31	   1071	  0.03%
 32	   1198	  0.03%
 33	   1540	  0.04%
 34	   1741	  0.05%
 35	   3396	  0.09%
 36	   2977	  0.08%
 37	   3317	  0.09%
 38	   3156	  0.09%
 39	   3488	  0.10%
 40	   4621	  0.13%
 41	   4156	  0.11%
 42	   5121	  0.14%
 43	   7243	  0.20%
 44	   9774	  0.27%
 45	  12267	  0.34%
 46	  18010	  0.50%
 47	  23124	  0.64%
 48	  34513	  0.95%
 49	  33934	  0.94%
 50	3443963	 94.96%
3626687 reads passed initial QC


criterion=sequence-density
sequence-density=86.29
sequence-density-rank=1
fanout-score=20.60
fanout-score-rank=1
prefix-density=85.53
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC


criterion=fanout-score
sequence-density=86.29
sequence-density-rank=1
fanout-score=20.60
fanout-score-rank=1
prefix-density=85.53
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC -o SRR5031057 -
Input file:	STDIN
trimmed:	SRR5031057-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC
-- 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 07:15:25 2020 >> started

Wed Mar  4 07:15:29 2020 >> done (3.989s)
3543315 reads processed; of these:
 167200 ( 4.72%) short reads filtered out after trimming by size control
 126397 ( 3.57%) empty reads filtered out after trimming by size control
3249718 (91.71%) reads available; of these:
3094740 (95.23%) trimmed reads available after processing
 154978 ( 4.77%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16707	  0.51%
 19	  28533	  0.88%
 20	 185539	  5.71%
 21	 365451	 11.25%
 22	1002941	 30.86%
 23	 431835	 13.29%
 24	 202208	  6.22%
 25	  58122	  1.79%
 26	  29527	  0.91%
 27	  25231	  0.78%
 28	  27602	  0.85%
 29	  21315	  0.66%
 30	  33024	  1.02%
 31	  40886	  1.26%
 32	  44933	  1.38%
 33	 157504	  4.85%
 34	  51383	  1.58%
 35	  40730	  1.25%
 36	  45787	  1.41%
 37	  21299	  0.66%
 38	  24738	  0.76%
 39	  22170	  0.68%
 40	  34238	  1.05%
 41	  39660	  1.22%
 42	  43454	  1.34%
 43	  29426	  0.91%
 44	  23656	  0.73%
 45	  28626	  0.88%
 46	  21573	  0.66%
 47	  17164	  0.53%
 48	   1621	  0.05%
 49	   2517	  0.08%
 50	 130318	  4.01%


criterion=sequence-density
sequence-density=3.51
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=13
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCT


criterion=fanout-score
sequence-density=0.72
sequence-density-rank=20
fanout-score=12.03
fanout-score-rank=1
prefix-density=8.65
prefix-fanout=1.0
sequence=TGAGCTTGGCTAT
                                 Started job on |	Mar 04 07:15:50
                             Started mapping on |	Mar 04 07:15:51
                                    Finished on |	Mar 04 07:16:15
       Mapping speed, Million of reads per hour |	499.96

                          Number of input reads |	3333090
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1802489
                        Uniquely mapped reads % |	54.08%
                          Average mapped length |	24.89
                       Number of splices: Total |	2044
            Number of splices: Annotated (sjdb) |	398
                       Number of splices: GT/AG |	1898
                       Number of splices: GC/AG |	36
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	109
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1048949
             % of reads mapped to multiple loci |	31.47%
        Number of reads mapped to too many loci |	82718
             % of reads mapped to too many loci |	2.48%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.03%
                     % of reads unmapped: other |	0.93%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	481652	481652	481652
N_multimapping	1048949	1048949	1048949
N_noFeature	82306	107474	1191512
N_ambiguous	999861	464080	15307
UnstrandedReadsAssigned:720322 PositiveStrandReadsAssigned:1230935 NegativeStrandReadsAssigned:595670
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031057 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: SRR5031057-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,333,090 reads, 861,175 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 825 rounds

 109283 SRR5031057.ke.tsv
  52636 SRR5031057.se.tsv
 161919 total
==> SRR5031057.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

==> SRR5031057.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031057 completed mapping pipeline successfully
