Starting /dee2/code/volunteer_pipeline.sh SRR5031043
    current disk space = 160489259008
    free memory = 73917348 
SRR5031043 SRAfilesize
4d435df7a063ec7afe629ac5dd417e18  SRR5031043.sra
SRR5031043.sra file validated
SRR5031043 is single end
SRR5031043 is conventional basespace
SRR5031043 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031043_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	32.3085	33.0	31.0	34.0	31.0	34.0
2	32.5885	34.0	31.0	34.0	31.0	34.0
3	32.612	34.0	31.0	34.0	31.0	34.0
4	36.213	37.0	35.0	37.0	35.0	37.0
5	35.80725	37.0	35.0	37.0	35.0	37.0
6	35.8925	37.0	35.0	37.0	35.0	37.0
7	35.962	37.0	35.0	37.0	35.0	37.0
8	35.7555	37.0	35.0	37.0	33.0	37.0
9	37.54025	39.0	37.0	39.0	34.0	39.0
10	37.7935	39.0	37.0	39.0	35.0	39.0
11	37.6285	39.0	37.0	39.0	35.0	39.0
12	37.61375	39.0	37.0	39.0	35.0	39.0
13	37.70175	39.0	37.0	39.0	35.0	39.0
14	39.02575	40.0	38.0	41.0	36.0	41.0
15	38.931	40.0	38.0	41.0	35.0	41.0
16	38.88575	40.0	38.0	41.0	35.0	41.0
17	38.87275	40.0	38.0	41.0	35.0	41.0
18	38.98675	40.0	38.0	41.0	35.0	41.0
19	38.64825	40.0	38.0	41.0	34.0	41.0
20	38.78575	40.0	38.0	41.0	34.0	41.0
21	38.79775	40.0	38.0	41.0	34.0	41.0
22	38.96675	40.0	39.0	41.0	35.0	41.0
23	38.74375	40.0	38.0	41.0	35.0	41.0
24	38.73775	40.0	38.0	41.0	34.0	41.0
25	39.058	41.0	39.0	41.0	35.0	41.0
26	38.80775	40.0	38.0	41.0	35.0	41.0
27	38.74575	40.0	38.0	41.0	34.0	41.0
28	38.67775	40.0	38.0	41.0	34.0	41.0
29	38.274	40.0	38.0	41.0	33.0	41.0
30	38.17675	40.0	38.0	41.0	33.0	41.0
31	38.437	40.0	38.0	41.0	34.0	41.0
32	38.2965	40.0	38.0	41.0	34.0	41.0
33	38.103	40.0	38.0	41.0	33.0	41.0
34	38.21225	40.0	38.0	41.0	34.0	41.0
35	38.0375	40.0	38.0	41.0	33.0	41.0
36	37.78375	40.0	37.0	41.0	33.0	41.0
37	37.41375	40.0	37.0	41.0	31.0	41.0
38	36.64075	39.0	36.0	41.0	30.0	41.0
39	37.26275	39.0	37.0	41.0	31.0	41.0
40	37.505	40.0	37.0	41.0	32.0	41.0
41	37.65775	40.0	37.0	41.0	32.0	41.0
42	37.96725	40.0	38.0	41.0	33.0	41.0
43	38.15675	40.0	38.0	41.0	33.0	41.0
44	37.881	40.0	38.0	41.0	33.0	41.0
45	37.84325	40.0	38.0	41.0	33.0	41.0
46	37.77025	40.0	37.0	41.0	33.0	41.0
47	37.26925	40.0	37.0	41.0	31.0	41.0
48	36.80325	40.0	36.0	41.0	31.0	41.0
49	36.95225	40.0	36.0	41.0	31.0	41.0
50	36.394	39.0	35.0	41.0	30.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
13	1.0
14	1.0
15	0.0
16	2.0
17	0.0
18	3.0
19	3.0
20	3.0
21	4.0
22	8.0
23	1.0
24	5.0
25	16.0
26	11.0
27	25.0
28	24.0
29	34.0
30	46.0
31	65.0
32	108.0
33	103.0
34	137.0
35	205.0
36	256.0
37	431.0
38	705.0
39	1803.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.85	24.6	50.64999999999999	14.899999999999999
2	23.15973960941412	28.693039559339006	20.305458187280923	27.84176264396595
3	23.575	18.775	22.125	35.525
4	34.325	28.775000000000002	13.675	23.225
5	21.349999999999998	36.975	28.675	13.0
6	27.775	16.425	39.825	15.975
7	17.325	21.325	20.0	41.349999999999994
8	22.0	29.849999999999998	18.425	29.725
9	23.674999999999997	33.475	26.974999999999998	15.875
10	22.725	20.549999999999997	29.775000000000002	26.950000000000003
11	34.4	11.125	17.299999999999997	37.175000000000004
12	14.649999999999999	21.4	32.15	31.8
13	26.900000000000002	17.925	35.4	19.775000000000002
14	30.375000000000004	30.4	20.775	18.45
15	36.075	23.974999999999998	24.975	14.975
16	20.075000000000003	19.075	24.0	36.85
17	27.35	24.85	34.725	13.075000000000001
18	26.125	17.150000000000002	32.324999999999996	24.4
19	35.925000000000004	15.65	32.9	15.525
20	44.675	16.05	25.15	14.124999999999998
21	24.125	21.925	24.975	28.975
22	31.15	12.225	47.9	8.725
23	26.25	13.200000000000001	44.3	16.25
24	50.849999999999994	14.549999999999999	25.674999999999997	8.924999999999999
25	49.625	25.124999999999996	15.425	9.825000000000001
26	26.3	46.7	14.149999999999999	12.85
27	15.6	46.949999999999996	24.349999999999998	13.100000000000001
28	11.75	22.825	49.225	16.2
29	13.15	12.475	54.825	19.55
30	10.15	6.3	35.9	47.65
31	14.224999999999998	5.475	47.125	33.175
32	28.299999999999997	5.949999999999999	21.625	44.125
33	54.525	9.275	13.900000000000002	22.3
34	60.95	7.825	16.35	14.875
35	64.47500000000001	6.9750000000000005	18.825	9.725
36	43.05	7.5249999999999995	36.35	13.075000000000001
37	45.975	11.65	19.25	23.125
38	23.95	17.150000000000002	11.425	47.475
39	15.0	24.925	11.425	48.65
40	15.2	48.725	11.675	24.4
41	24.2	48.449999999999996	9.875	17.474999999999998
42	48.525	28.875	12.7	9.9
43	50.7	28.425	8.9	11.975
44	30.8	47.85	7.6499999999999995	13.700000000000001
45	19.675	50.075	11.899999999999999	18.35
46	14.149999999999999	25.324999999999996	17.625	42.9
47	9.950000000000001	14.124999999999998	40.45	35.475
48	12.225	12.525	20.175	55.074999999999996
49	13.15	19.45	13.8	53.6
50	18.6	36.475	13.525	31.4
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	0.0
28	0.0
29	0.5
30	1.0
31	2.5
32	4.0
33	10.5
34	17.0
35	22.0
36	27.0
37	22.5
38	18.0
39	30.0
40	42.0
41	48.5
42	55.0
43	97.5
44	140.0
45	164.0
46	188.0
47	319.5
48	451.0
49	576.5
50	702.0
51	779.5
52	857.0
53	651.5
54	446.0
55	465.0
56	484.0
57	351.0
58	218.0
59	144.5
60	71.0
61	59.5
62	48.0
63	91.0
64	134.0
65	75.0
66	16.0
67	14.0
68	12.0
69	10.0
70	8.0
71	28.5
72	49.0
73	27.5
74	6.0
75	3.0
76	0.0
77	0.5
78	1.0
79	2.5
80	4.0
81	2.0
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	0.15
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	38.6
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.6761658031088	28.825
2	10.297927461139897	7.95
3	4.533678756476684	5.25
4	2.7202072538860103	4.2
5	1.7487046632124352	3.375
6	0.9715025906735751	2.25
7	0.582901554404145	1.575
8	0.9715025906735751	3.0
9	0.38860103626943004	1.35
>10	2.461139896373057	16.400000000000002
>50	0.3238341968911917	10.549999999999999
>100	0.3238341968911917	15.275
>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
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	126	3.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	125	3.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	123	3.075	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	122	3.05	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	115	2.875	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	99	2.475	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	98	2.45	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	77	1.925	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	51	1.275	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	24	0.6	RNA PCR Primer, Index 1 (100% over 35bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	19	0.475	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	17	0.42500000000000004	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	14	0.35000000000000003	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTC	13	0.325	RNA PCR Primer, Index 15 (100% over 44bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGC	13	0.325	RNA PCR Primer, Index 15 (100% over 50bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	10	0.25	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	9	0.22499999999999998	No Hit
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATG	9	0.22499999999999998	RNA PCR Primer, Index 15 (100% over 36bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	8	0.2	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	8	0.2	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGT	8	0.2	RNA PCR Primer, Index 15 (100% over 37bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	6	0.15	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
CTAGACTGAGGCTCCTTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATCATGATGGGCTCCTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGAATTGTGGCTGGACATCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC	5	0.125	RNA PCR Primer, Index 15 (98% over 50bp)
ACGCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTC	5	0.125	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.375	0.0	0.0	0.0
2	0.0	0.425	0.0	0.0	0.0
3	0.0	0.525	0.0	0.0	0.0
4	0.0	0.525	0.0	0.0	0.0
5	0.0	0.55	0.0	0.0	0.0
6	0.0	0.65	0.0	0.0	0.0
7	0.0	1.025	0.0	0.0	0.0
8	0.0	1.2	0.0	0.0	0.0
9	0.0	1.3	0.0	0.0	0.0
10	0.0	1.45	0.0	0.0	0.0
11	0.0	1.6	0.0	0.0	0.0
12	0.0	1.8	0.0	0.0	0.0
13	0.0	1.975	0.0	0.0	0.0
14	0.0	2.4	0.0	0.0	0.0
15	0.0	2.975	0.0	0.0	0.0
16	0.0	4.025	0.0	0.0	0.0
17	0.0	4.75	0.0	0.0	0.0
18	0.0	5.875	0.0	0.0	0.0
19	0.0	6.425	0.0	0.0	0.0
20	0.0	7.425	0.0	0.0	0.0
21	0.0	12.925	0.0	0.0	0.0
22	0.0	24.2	0.0	0.0	0.0
23	0.0	53.975	0.0	0.0	0.0
24	0.0	66.525	0.0	0.0	0.0
25	0.0	72.5	0.0	0.0	0.0
26	0.0	73.95	0.0	0.0	0.0
27	0.0	74.7	0.0	0.0	0.0
28	0.0	75.375	0.0	0.0	0.0
29	0.0	75.9	0.0	0.0	0.0
30	0.0	76.425	0.0	0.0	0.0
31	0.0	77.325	0.0	0.0	0.0
32	0.0	78.1	0.0	0.0	0.0
33	0.0	79.05	0.0	0.0	0.0
34	0.0	83.325	0.0	0.0	0.0
35	0.0	84.925	0.0	0.0	0.0
36	0.0	86.1	0.0	0.0	0.0
37	0.0	87.275	0.0	0.0	0.0
38	0.0	87.9	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	45	2.728484E-10	44.000004	8
ACGCTGT	45	2.728484E-10	44.000004	9
TTCAACG	45	2.728484E-10	44.000004	5
CATTCAA	45	2.728484E-10	44.000004	3
TCAACGC	45	2.728484E-10	44.000004	6
GGTAGTA	20	6.952051E-4	44.000004	4
GCTTGGC	40	5.315087E-9	44.000004	15
TGAGGTA	20	6.952051E-4	44.000004	1
AGGTAGT	20	6.952051E-4	44.000004	3
ATTCAAC	45	2.728484E-10	44.000004	4
TGGCTTG	20	6.952051E-4	44.000004	18
GTAGTAG	20	6.952051E-4	44.000004	5
CAACGCT	45	2.728484E-10	44.000004	7
CGCTGTC	45	2.728484E-10	44.000004	10
GAGGTAG	25	3.6958358E-5	44.0	2
GGTGAGT	35	1.02281774E-7	44.0	17
TCGGTGA	35	1.02281774E-7	44.0	15
GAGCTTG	55	0.0	44.0	13
GGATCCG	55	0.0	44.0	3
CCGTCTG	55	0.0	44.0	7
>>END_MODULE
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217334 spots for SRR5031043.sra
Written 217334 spots for SRR5031043.sra
Read 217337 spots for SRR5031043.sra
Written 217337 spots for SRR5031043.sra
SRR ids: ['SRR5031043.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_vbj8x860
SRR5031043.sra spots: 2608011
blocks: [[1, 217334], [217335, 434668], [434669, 652002], [652003, 869336], [869337, 1086670], [1086671, 1304004], [1304005, 1521338], [1521339, 1738672], [1738673, 1956006], [1956007, 2173340], [2173341, 2390674], [2390675, 2608011]]
SRR5031043 file size 450960
SRR5031043 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031043 SRR5031043_1.fastq
Input file:	SRR5031043_1.fastq
trimmed:	SRR5031043-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 07:12:54 2020 >> started

Wed Mar  4 07:12:57 2020 >> done (2.877s)
2608011 reads processed; of these:
    163 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
2607843 (99.99%) reads available; of these:
 129069 ( 4.95%) trimmed reads available after processing
2478774 (95.05%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     48	  0.00%
 19	     67	  0.00%
 20	    154	  0.01%
 21	    191	  0.01%
 22	    286	  0.01%
 23	    341	  0.01%
 24	    356	  0.01%
 25	    529	  0.02%
 26	    372	  0.01%
 27	    549	  0.02%
 28	    644	  0.02%
 29	   1090	  0.04%
 30	    713	  0.03%
 31	    758	  0.03%
 32	    883	  0.03%
 33	   1051	  0.04%
 34	   1251	  0.05%
 35	   2518	  0.10%
 36	   2003	  0.08%
 37	   2244	  0.09%
 38	   2031	  0.08%
 39	   2271	  0.09%
 40	   2719	  0.10%
 41	   2781	  0.11%
 42	   3728	  0.14%
 43	   5423	  0.21%
 44	   7323	  0.28%
 45	   8904	  0.34%
 46	  13217	  0.51%
 47	  16003	  0.61%
 48	  23293	  0.89%
 49	  25328	  0.97%
 50	2478774	 95.05%
2607843 reads passed initial QC


criterion=sequence-density
sequence-density=87.44
sequence-density-rank=1
fanout-score=21.98
fanout-score-rank=1
prefix-density=89.80
prefix-fanout=21.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC


criterion=fanout-score
sequence-density=87.44
sequence-density-rank=1
fanout-score=21.98
fanout-score-rank=1
prefix-density=89.80
prefix-fanout=21.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC -o SRR5031043 -
Input file:	STDIN
trimmed:	SRR5031043-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC
-- 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 07:13:19 2020 >> started

Wed Mar  4 07:13:26 2020 >> done (6.170s)
2548574 reads processed; of these:
 130020 ( 5.10%) short reads filtered out after trimming by size control
  10732 ( 0.42%) empty reads filtered out after trimming by size control
2407822 (94.48%) reads available; of these:
2305453 (95.75%) trimmed reads available after processing
 102369 ( 4.25%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13711	  0.57%
 19	  23808	  0.99%
 20	 138389	  5.75%
 21	 292113	 12.13%
 22	 765462	 31.79%
 23	 334128	 13.88%
 24	 148810	  6.18%
 25	  39683	  1.65%
 26	  20908	  0.87%
 27	  19946	  0.83%
 28	  20566	  0.85%
 29	  16683	  0.69%
 30	  22397	  0.93%
 31	  29441	  1.22%
 32	  32693	  1.36%
 33	 100299	  4.17%
 34	  38675	  1.61%
 35	  31176	  1.29%
 36	  38549	  1.60%
 37	  14809	  0.62%
 38	  17924	  0.74%
 39	  14307	  0.59%
 40	  20623	  0.86%
 41	  23857	  0.99%
 42	  25991	  1.08%
 43	  17880	  0.74%
 44	  13851	  0.58%
 45	  17583	  0.73%
 46	  12767	  0.53%
 47	  11089	  0.46%
 48	   1030	  0.04%
 49	   1353	  0.06%
 50	  87321	  3.63%


criterion=sequence-density
sequence-density=3.22
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AAGCTGCCAGTTGAAGAACTGT


criterion=fanout-score
sequence-density=0.65
sequence-density-rank=24
fanout-score=12.22
fanout-score-rank=1
prefix-density=7.90
prefix-fanout=1.0
sequence=TGAGCTTGGCTAT
                                 Started job on |	Mar 04 07:13:56
                             Started mapping on |	Mar 04 07:13:57
                                    Finished on |	Mar 04 07:14:22
       Mapping speed, Million of reads per hour |	355.26

                          Number of input reads |	2467091
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1294594
                        Uniquely mapped reads % |	52.47%
                          Average mapped length |	24.33
                       Number of splices: Total |	1544
            Number of splices: Annotated (sjdb) |	290
                       Number of splices: GT/AG |	1448
                       Number of splices: GC/AG |	15
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	78
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.83
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	846400
             % of reads mapped to multiple loci |	34.31%
        Number of reads mapped to too many loci |	61420
             % of reads mapped to too many loci |	2.49%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.92%
                     % of reads unmapped: other |	0.81%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	326097	326097	326097
N_multimapping	846400	846400	846400
N_noFeature	59479	76138	846626
N_ambiguous	729140	330540	9760
UnstrandedReadsAssigned:505975 PositiveStrandReadsAssigned:887916 NegativeStrandReadsAssigned:438208
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031043 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: SRR5031043-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,467,091 reads, 645,376 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,164 rounds

 109283 SRR5031043.ke.tsv
  52636 SRR5031043.se.tsv
 161919 total
==> SRR5031043.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

==> SRR5031043.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	1
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031043 completed mapping pipeline successfully
