Starting /dee2/code/volunteer_pipeline.sh SRR5031056
    current disk space = 160511639552
    free memory = 73928384 
SRR5031056 SRAfilesize
b1d06fc69cfab0b2cb878549ab7a4b27  SRR5031056.sra
SRR5031056.sra file validated
SRR5031056 is single end
SRR5031056 is conventional basespace
SRR5031056 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031056_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	32.33425	33.0	31.0	34.0	30.0	34.0
2	32.56225	34.0	31.0	34.0	31.0	34.0
3	32.59475	34.0	31.0	34.0	31.0	34.0
4	36.1365	37.0	35.0	37.0	35.0	37.0
5	35.79375	37.0	35.0	37.0	35.0	37.0
6	35.769	37.0	35.0	37.0	33.0	37.0
7	35.8775	37.0	35.0	37.0	35.0	37.0
8	35.757	37.0	35.0	37.0	35.0	37.0
9	37.5565	39.0	37.0	39.0	35.0	39.0
10	37.77125	39.0	38.0	39.0	35.0	39.0
11	37.5655	39.0	37.0	39.0	35.0	39.0
12	37.6235	39.0	37.0	39.0	35.0	39.0
13	37.5765	39.0	37.0	39.0	35.0	39.0
14	38.94925	40.0	38.0	41.0	35.0	41.0
15	38.876	40.0	38.0	41.0	35.0	41.0
16	38.87825	40.0	38.0	41.0	35.0	41.0
17	38.86775	40.0	38.0	41.0	35.0	41.0
18	38.87025	40.0	38.0	41.0	35.0	41.0
19	38.7015	40.0	38.0	41.0	34.0	41.0
20	38.79475	40.0	38.0	41.0	34.0	41.0
21	38.7135	40.0	38.0	41.0	34.0	41.0
22	38.8935	40.0	39.0	41.0	35.0	41.0
23	38.75275	40.0	38.0	41.0	35.0	41.0
24	38.832	40.0	38.0	41.0	35.0	41.0
25	39.02475	41.0	39.0	41.0	35.0	41.0
26	38.83025	40.0	38.0	41.0	35.0	41.0
27	38.82575	40.0	38.0	41.0	35.0	41.0
28	38.78825	40.0	38.0	41.0	35.0	41.0
29	38.203	40.0	38.0	41.0	33.0	41.0
30	37.97225	40.0	38.0	41.0	32.0	41.0
31	38.20575	40.0	38.0	41.0	33.0	41.0
32	37.997	40.0	38.0	41.0	33.0	41.0
33	37.96125	40.0	38.0	41.0	33.0	41.0
34	38.12425	40.0	38.0	41.0	33.0	41.0
35	38.08125	40.0	38.0	41.0	33.0	41.0
36	37.77275	40.0	37.0	41.0	33.0	41.0
37	37.22575	40.0	37.0	41.0	31.0	41.0
38	36.93775	39.0	36.0	41.0	30.0	41.0
39	37.44	40.0	37.0	41.0	32.0	41.0
40	37.58175	40.0	37.0	41.0	32.0	41.0
41	37.67675	40.0	37.0	41.0	32.0	41.0
42	37.85225	40.0	37.0	41.0	33.0	41.0
43	37.993	40.0	38.0	41.0	33.0	41.0
44	37.67175	40.0	37.0	41.0	33.0	41.0
45	37.61075	40.0	37.0	41.0	33.0	41.0
46	37.55	40.0	37.0	41.0	33.0	41.0
47	37.06275	40.0	36.0	41.0	31.0	41.0
48	36.867	40.0	36.0	41.0	31.0	41.0
49	37.101	40.0	36.0	41.0	32.0	41.0
50	36.59925	39.0	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
15	1.0
16	1.0
17	6.0
18	1.0
19	1.0
20	3.0
21	8.0
22	6.0
23	10.0
24	3.0
25	8.0
26	21.0
27	24.0
28	36.0
29	29.0
30	51.0
31	75.0
32	68.0
33	106.0
34	162.0
35	192.0
36	268.0
37	394.0
38	740.0
39	1786.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.775	24.075	47.099999999999994	18.05
2	22.915101427498122	26.872026045579766	18.707738542449288	31.505133984472828
3	23.474999999999998	19.525000000000002	20.549999999999997	36.449999999999996
4	31.35	26.674999999999997	16.0	25.974999999999998
5	23.3	37.025000000000006	27.625	12.049999999999999
6	35.75	12.825000000000001	33.800000000000004	17.625
7	16.35	24.15	24.175	35.325
8	25.900000000000002	26.85	16.7	30.55
9	21.875	33.85	26.85	17.424999999999997
10	21.8	22.075	27.950000000000003	28.175
11	32.125	11.4	17.25	39.225
12	17.95	17.675	28.799999999999997	35.575
13	29.775000000000002	18.875	32.7	18.65
14	29.025000000000002	30.275000000000002	21.475	19.225
15	34.699999999999996	22.8	27.675	14.825
16	20.175	22.025	21.925	35.875
17	28.025	22.025	35.5	14.45
18	22.900000000000002	18.45	30.625000000000004	28.025
19	36.15	15.0	29.125	19.725
20	43.375	14.725	28.975	12.925
21	26.400000000000002	19.475	25.2	28.925
22	26.950000000000003	15.45	46.675	10.925
23	26.325	14.000000000000002	44.05	15.625
24	50.349999999999994	15.075	25.174999999999997	9.4
25	48.425000000000004	22.75	16.3	12.525
26	27.250000000000004	44.35	14.75	13.65
27	16.05	45.5	23.575	14.875
28	12.475	24.125	47.125	16.275000000000002
29	14.124999999999998	12.575	54.775	18.525
30	12.375	7.3	35.199999999999996	45.125
31	14.975	6.35	45.5	33.175
32	27.85	7.074999999999999	22.225	42.85
33	51.6	10.35	14.524999999999999	23.525
34	58.425000000000004	8.725	16.45	16.400000000000002
35	62.35000000000001	8.85	17.7	11.1
36	40.175	10.0	35.925000000000004	13.900000000000002
37	43.75	13.275	20.625	22.35
38	24.075	17.75	12.725	45.45
39	17.5	22.575	11.200000000000001	48.725
40	15.925	46.175	13.25	24.65
41	23.775	47.199999999999996	10.95	18.075
42	47.3	27.650000000000002	13.075000000000001	11.975
43	50.675000000000004	27.800000000000004	10.174999999999999	11.35
44	31.924999999999997	46.7	7.625	13.750000000000002
45	20.424999999999997	49.125	12.85	17.599999999999998
46	14.95	26.125	18.0	40.925
47	10.375	16.7	38.824999999999996	34.1
48	12.225	13.575000000000001	20.825	53.37499999999999
49	12.65	19.950000000000003	13.8	53.6
50	17.474999999999998	38.25	12.775	31.5
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.5
2	1.0
3	0.5
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.5
10	1.0
11	1.0
12	1.0
13	0.5
14	0.0
15	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	2.5
28	4.0
29	4.5
30	5.0
31	9.0
32	13.0
33	12.5
34	12.0
35	20.0
36	28.0
37	33.5
38	39.0
39	39.0
40	39.0
41	41.0
42	43.0
43	68.0
44	93.0
45	128.5
46	164.0
47	289.5
48	415.0
49	506.5
50	598.0
51	757.0
52	916.0
53	676.5
54	437.0
55	469.5
56	502.0
57	383.0
58	264.0
59	177.0
60	90.0
61	68.5
62	47.0
63	95.0
64	143.0
65	92.5
66	42.0
67	29.5
68	17.0
69	18.0
70	19.0
71	36.0
72	53.0
73	28.0
74	3.0
75	1.5
76	0.0
77	1.5
78	3.0
79	3.5
80	4.0
81	2.5
82	1.0
83	0.5
84	0.0
85	0.0
86	0.0
87	0.5
88	1.0
89	0.5
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	0.17500000000000002
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	40.375
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.40866873065015	30.85
2	8.978328173374612	7.249999999999999
3	4.891640866873065	5.925
4	2.786377708978328	4.5
5	1.1764705882352942	2.375
6	0.9287925696594427	2.25
7	0.24767801857585142	0.7000000000000001
8	0.6811145510835914	2.1999999999999997
9	0.49535603715170284	1.7999999999999998
>10	2.910216718266254	22.0
>50	0.30959752321981426	10.75
>100	0.18575851393188852	9.4
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	141	3.5249999999999995	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	116	2.9000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	100	2.5	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	92	2.3	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	81	2.025	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	79	1.975	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	78	1.95	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	47	1.175	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	40	1.0	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	37	0.9249999999999999	RNA PCR Primer, Index 7 (100% over 35bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGC	35	0.8750000000000001	RNA PCR Primer, Index 28 (100% over 50bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	22	0.5499999999999999	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	18	0.44999999999999996	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTC	14	0.35000000000000003	RNA PCR Primer, Index 28 (100% over 44bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	14	0.35000000000000003	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	13	0.325	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	11	0.27499999999999997	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 31bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	10	0.25	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	8	0.2	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	7	0.17500000000000002	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
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	1.025	0.0	0.0	0.0
2	0.0	1.025	0.0	0.0	0.0
3	0.0	1.1	0.0	0.0	0.0
4	0.0	1.15	0.0	0.0	0.0
5	0.0	1.225	0.0	0.0	0.0
6	0.0	1.325	0.0	0.0	0.0
7	0.0	1.775	0.0	0.0	0.0
8	0.0	1.975	0.0	0.0	0.0
9	0.0	2.05	0.0	0.0	0.0
10	0.0	2.25	0.0	0.0	0.0
11	0.0	2.375	0.0	0.0	0.0
12	0.0	2.6	0.0	0.0	0.0
13	0.0	2.95	0.0	0.0	0.0
14	0.0	3.25	0.0	0.0	0.0
15	0.0	3.5	0.0	0.0	0.0
16	0.0	4.95	0.0	0.0	0.0
17	0.0	5.575	0.0	0.0	0.0
18	0.0	6.7	0.0	0.0	0.0
19	0.0	7.25	0.0	0.0	0.0
20	0.0	8.275	0.0	0.0	0.0
21	0.0	12.925	0.0	0.0	0.0
22	0.0	22.875	0.0	0.0	0.0
23	0.0	50.95	0.0	0.0	0.0
24	0.0	63.425	0.0	0.0	0.0
25	0.0	68.95	0.0	0.0	0.0
26	0.0	70.5	0.0	0.0	0.0
27	0.0	71.225	0.0	0.0	0.0
28	0.0	72.05	0.0	0.0	0.0
29	0.0	72.75	0.0	0.0	0.0
30	0.0	73.325	0.0	0.0	0.0
31	0.0	74.4	0.0	0.0	0.0
32	0.0	75.6	0.0	0.0	0.0
33	0.0	77.05	0.0	0.0	0.0
34	0.0	80.725	0.0	0.0	0.0
35	0.0	81.95	0.0	0.0	0.0
36	0.0	82.825	0.0	0.0	0.0
37	0.0	83.875	0.0	0.0	0.0
38	0.0	84.5	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATAGGCT	20	6.952051E-4	44.000004	16
CATTCAA	20	6.952051E-4	44.000004	3
ACATTCA	20	6.952051E-4	44.000004	2
CTTGGCT	20	6.952051E-4	44.000004	16
GGTAGTA	20	6.952051E-4	44.000004	4
GCTTGGC	20	6.952051E-4	44.000004	15
CTGTTGG	20	6.952051E-4	44.000004	19
ATTCAAC	20	6.952051E-4	44.000004	4
GATAGGC	20	6.952051E-4	44.000004	15
TGGCTTG	20	6.952051E-4	44.000004	18
GTAGTAG	20	6.952051E-4	44.000004	5
AACATTC	20	6.952051E-4	44.000004	1
GAGGTAG	25	3.6958358E-5	44.0	2
AAGTAAT	25	3.6958358E-5	44.0	4
TCAAGTA	25	3.6958358E-5	44.0	2
AATCCAG	25	3.6958358E-5	44.0	8
CTGAGCT	30	1.9515464E-6	44.0	11
AGCTTGG	30	1.9515464E-6	44.0	14
ATCCAGG	25	3.6958358E-5	44.0	9
TTCAAGT	25	3.6958358E-5	44.0	1
>>END_MODULE
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
Read 192530 spots for SRR5031056.sra
Written 192530 spots for SRR5031056.sra
SRR ids: ['SRR5031056.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ibkx8uk_
SRR5031056.sra spots: 2310360
blocks: [[1, 192530], [192531, 385060], [385061, 577590], [577591, 770120], [770121, 962650], [962651, 1155180], [1155181, 1347710], [1347711, 1540240], [1540241, 1732770], [1732771, 1925300], [1925301, 2117830], [2117831, 2310360]]
SRR5031056 file size 399370
SRR5031056 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031056 SRR5031056_1.fastq
Input file:	SRR5031056_1.fastq
trimmed:	SRR5031056-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 (1.631s)
2310360 reads processed; of these:
    199 ( 0.01%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
2310157 (99.99%) reads available; of these:
 109163 ( 4.73%) trimmed reads available after processing
2200994 (95.27%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     59	  0.00%
 19	     66	  0.00%
 20	    161	  0.01%
 21	    192	  0.01%
 22	    307	  0.01%
 23	    344	  0.01%
 24	    386	  0.02%
 25	    537	  0.02%
 26	    446	  0.02%
 27	    533	  0.02%
 28	    630	  0.03%
 29	   1103	  0.05%
 30	    645	  0.03%
 31	    734	  0.03%
 32	    780	  0.03%
 33	   1018	  0.04%
 34	   1112	  0.05%
 35	   2141	  0.09%
 36	   1986	  0.09%
 37	   2173	  0.09%
 38	   2210	  0.10%
 39	   2251	  0.10%
 40	   2669	  0.12%
 41	   2616	  0.11%
 42	   3239	  0.14%
 43	   4577	  0.20%
 44	   6189	  0.27%
 45	   7606	  0.33%
 46	  10920	  0.47%
 47	  13419	  0.58%
 48	  18399	  0.80%
 49	  19715	  0.85%
 50	2200994	 95.27%
2310157 reads passed initial QC


criterion=sequence-density
sequence-density=84.42
sequence-density-rank=1
fanout-score=21.73
fanout-score-rank=1
prefix-density=86.31
prefix-fanout=21.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC


criterion=fanout-score
sequence-density=84.42
sequence-density-rank=1
fanout-score=21.73
fanout-score-rank=1
prefix-density=86.31
prefix-fanout=21.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC -o SRR5031056 -
Input file:	STDIN
trimmed:	SRR5031056-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC
-- 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 07:15:22 2020 >> started

Wed Mar  4 07:15:26 2020 >> done (3.213s)
2255800 reads processed; of these:
 131977 ( 5.85%) short reads filtered out after trimming by size control
  24662 ( 1.09%) empty reads filtered out after trimming by size control
2099161 (93.06%) reads available; of these:
1984853 (94.55%) trimmed reads available after processing
 114308 ( 5.45%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11550	  0.55%
 19	  21396	  1.02%
 20	 111738	  5.32%
 21	 236534	 11.27%
 22	 640494	 30.51%
 23	 283316	 13.50%
 24	 124939	  5.95%
 25	  36415	  1.73%
 26	  19195	  0.91%
 27	  16131	  0.77%
 28	  18994	  0.90%
 29	  15442	  0.74%
 30	  23908	  1.14%
 31	  30138	  1.44%
 32	  32755	  1.56%
 33	  86323	  4.11%
 34	  29751	  1.42%
 35	  22434	  1.07%
 36	  26003	  1.24%
 37	  14553	  0.69%
 38	  14697	  0.70%
 39	  14717	  0.70%
 40	  22620	  1.08%
 41	  28026	  1.34%
 42	  31124	  1.48%
 43	  20693	  0.99%
 44	  15543	  0.74%
 45	  21006	  1.00%
 46	  15999	  0.76%
 47	  11665	  0.56%
 48	   1186	  0.06%
 49	   1862	  0.09%
 50	  98014	  4.67%


criterion=sequence-density
sequence-density=6.55
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.63
sequence-density-rank=22
fanout-score=12.27
fanout-score-rank=1
prefix-density=7.75
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTTT
                                 Started job on |	Mar 04 07:15:46
                             Started mapping on |	Mar 04 07:15:47
                                    Finished on |	Mar 04 07:16:11
       Mapping speed, Million of reads per hour |	323.03

                          Number of input reads |	2153518
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1144037
                        Uniquely mapped reads % |	53.12%
                          Average mapped length |	25.47
                       Number of splices: Total |	1395
            Number of splices: Annotated (sjdb) |	321
                       Number of splices: GT/AG |	1313
                       Number of splices: GC/AG |	14
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	68
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.71
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	703821
             % of reads mapped to multiple loci |	32.68%
        Number of reads mapped to too many loci |	49433
             % of reads mapped to too many loci |	2.30%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.29%
                     % of reads unmapped: other |	0.61%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	305660	305660	305660
N_multimapping	703821	703821	703821
N_noFeature	59735	76173	797958
N_ambiguous	633043	342670	11230
UnstrandedReadsAssigned:451259 PositiveStrandReadsAssigned:725194 NegativeStrandReadsAssigned:334849
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031056 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: SRR5031056-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,153,518 reads, 536,997 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 872 rounds

 109283 SRR5031056.ke.tsv
  52636 SRR5031056.se.tsv
 161919 total
==> SRR5031056.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

==> SRR5031056.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031056 completed mapping pipeline successfully
