Starting /dee2/code/volunteer_pipeline.sh SRR5030979
    current disk space = 160584581120
    free memory = 1053816000 
SRR5030979 SRAfilesize
3688273a8d32c7cd906086f31fda3ac3  SRR5030979.sra
SRR5030979.sra file validated
SRR5030979 is single end
SRR5030979 is conventional basespace
SRR5030979 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030979_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.428	33.0	31.0	34.0	31.0	34.0
2	32.76525	34.0	31.0	34.0	31.0	34.0
3	32.76175	34.0	31.0	34.0	31.0	34.0
4	36.24975	37.0	37.0	37.0	35.0	37.0
5	36.11425	37.0	37.0	37.0	35.0	37.0
6	35.96425	37.0	35.0	37.0	35.0	37.0
7	36.09825	37.0	35.0	37.0	35.0	37.0
8	36.1065	37.0	36.0	37.0	35.0	37.0
9	37.75225	39.0	38.0	39.0	35.0	39.0
10	37.88125	39.0	38.0	39.0	35.0	39.0
11	37.73225	39.0	38.0	39.0	35.0	39.0
12	37.74075	39.0	38.0	39.0	35.0	39.0
13	37.73675	39.0	38.0	39.0	35.0	39.0
14	39.014	40.0	38.0	41.0	35.0	41.0
15	39.14425	40.0	39.0	41.0	36.0	41.0
16	39.135	40.0	39.0	41.0	36.0	41.0
17	39.17625	41.0	39.0	41.0	36.0	41.0
18	39.23625	41.0	39.0	41.0	36.0	41.0
19	38.94525	40.0	38.0	41.0	35.0	41.0
20	38.93225	40.0	38.0	41.0	35.0	41.0
21	38.897	40.0	38.0	41.0	35.0	41.0
22	38.9025	40.0	38.0	41.0	35.0	41.0
23	38.6645	40.0	38.0	41.0	34.0	41.0
24	38.78025	40.0	38.0	41.0	35.0	41.0
25	38.726	40.0	38.0	41.0	34.0	41.0
26	38.46325	40.0	38.0	41.0	34.0	41.0
27	38.59625	40.0	38.0	41.0	34.0	41.0
28	38.21325	40.0	38.0	41.0	33.0	41.0
29	37.5565	40.0	37.0	41.0	31.0	41.0
30	37.86425	40.0	38.0	41.0	32.0	41.0
31	38.144	40.0	38.0	41.0	33.0	41.0
32	38.0905	40.0	38.0	41.0	33.0	41.0
33	38.21775	40.0	38.0	41.0	33.0	41.0
34	38.17475	40.0	38.0	41.0	34.0	41.0
35	37.9725	40.0	37.0	41.0	33.0	41.0
36	37.3485	39.0	37.0	41.0	31.0	41.0
37	36.74475	39.0	36.0	41.0	30.0	41.0
38	37.037	39.0	36.0	41.0	30.0	41.0
39	37.57125	39.0	37.0	41.0	33.0	41.0
40	37.5185	40.0	37.0	41.0	33.0	41.0
41	37.46725	40.0	37.0	41.0	32.0	41.0
42	37.5875	40.0	37.0	41.0	33.0	41.0
43	37.7745	40.0	37.0	41.0	33.0	41.0
44	37.4855	39.0	37.0	41.0	33.0	41.0
45	37.243	39.0	37.0	41.0	32.0	41.0
46	36.791	39.0	36.0	41.0	31.0	41.0
47	36.20125	39.0	35.0	41.0	28.0	41.0
48	35.84575	39.0	35.0	41.0	28.0	41.0
49	36.189	39.0	35.0	41.0	30.0	41.0
50	35.69575	39.0	34.0	40.0	29.0	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	2.0
17	1.0
18	2.0
19	0.0
20	3.0
21	5.0
22	5.0
23	4.0
24	10.0
25	10.0
26	19.0
27	20.0
28	29.0
29	42.0
30	58.0
31	57.0
32	74.0
33	134.0
34	154.0
35	192.0
36	272.0
37	492.0
38	849.0
39	1565.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.952488122030507	23.730932733183295	48.612153038259564	17.704426106526633
2	24.175	27.075	19.275000000000002	29.475
3	24.25	18.575	22.425	34.75
4	33.900000000000006	27.675	15.45	22.975
5	23.325000000000003	38.324999999999996	26.05	12.3
6	33.6	14.475	34.25	17.675
7	14.75	23.9	23.7	37.65
8	25.074999999999996	26.950000000000003	17.675	30.3
9	23.425	31.25	27.500000000000004	17.825
10	21.65	22.925	27.975	27.450000000000003
11	31.525	10.95	18.4	39.125
12	17.625	16.6	30.875000000000004	34.9
13	31.35	16.8	33.275	18.575
14	31.25	28.849999999999998	20.150000000000002	19.75
15	36.35	22.2	27.0	14.45
16	20.5	18.125	23.3	38.074999999999996
17	28.000000000000004	20.65	37.625	13.725000000000001
18	26.174999999999997	17.1	28.775000000000002	27.950000000000003
19	38.05	13.575000000000001	29.75	18.625
20	44.1	14.85	28.275	12.775
21	24.775	19.975	27.6	27.650000000000002
22	29.799999999999997	12.925	46.150000000000006	11.125
23	27.05	12.85	43.4	16.7
24	51.0	16.0	25.5	7.5
25	47.675	26.1	15.6	10.625
26	28.349999999999998	44.15	15.1	12.4
27	16.275000000000002	45.074999999999996	24.6	14.05
28	13.525	23.5	46.725	16.25
29	13.900000000000002	12.6	54.175	19.325
30	12.025	7.074999999999999	35.825	45.074999999999996
31	15.45	4.875	45.1	34.575
32	29.7	5.375	21.775	43.15
33	52.05	10.525	13.425	24.0
34	59.52499999999999	9.3	17.224999999999998	13.950000000000001
35	63.375	7.6	19.075	9.950000000000001
36	43.1	7.6	35.525	13.775
37	42.725	11.899999999999999	19.075	26.3
38	23.849999999999998	18.775	11.200000000000001	46.175
39	14.45	25.650000000000002	10.975	48.925000000000004
40	15.625	46.775	12.950000000000001	24.65
41	24.4	46.375	9.775	19.45
42	46.075	28.225	11.55	14.149999999999999
43	48.675000000000004	29.175	8.649999999999999	13.5
44	31.624999999999996	46.650000000000006	6.9	14.825
45	18.95	48.025	13.775	19.25
46	14.274999999999999	24.6	18.825	42.3
47	9.325	15.049999999999999	38.025	37.6
48	10.424999999999999	12.8	20.8	55.974999999999994
49	12.675	19.8	15.125	52.400000000000006
50	18.4	34.225	13.350000000000001	34.025
>>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	0.0
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	1.0
28	1.0
29	2.0
30	3.0
31	7.5
32	12.0
33	9.5
34	7.0
35	13.0
36	19.0
37	21.5
38	24.0
39	25.5
40	27.0
41	30.5
42	34.0
43	58.0
44	82.0
45	119.5
46	157.0
47	286.5
48	416.0
49	508.0
50	600.0
51	720.0
52	840.0
53	642.5
54	445.0
55	518.0
56	591.0
57	448.5
58	306.0
59	197.0
60	88.0
61	74.5
62	61.0
63	99.0
64	137.0
65	93.5
66	50.0
67	33.5
68	17.0
69	16.5
70	16.0
71	35.5
72	55.0
73	28.5
74	2.0
75	2.0
76	2.0
77	2.5
78	3.0
79	2.0
80	1.0
81	1.0
82	1.0
83	0.5
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	0.025
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	0.0
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	37.6
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.66489361702128	28.449999999999996
2	9.308510638297872	7.000000000000001
3	4.25531914893617	4.8
4	2.5265957446808507	3.8
5	1.7287234042553192	3.25
6	1.0638297872340425	2.4
7	0.8643617021276596	2.275
8	0.598404255319149	1.7999999999999998
9	0.598404255319149	2.025
>10	2.859042553191489	23.775
>50	0.3324468085106383	10.95
>100	0.19946808510638298	9.475
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	140	3.5000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	126	3.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	113	2.825	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	98	2.45	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	94	2.35	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	85	2.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	64	1.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	50	1.25	RNA PCR Primer, Index 5 (97% over 35bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	45	1.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	43	1.075	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	40	1.0	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTC	33	0.8250000000000001	RNA PCR Primer, Index 46 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	30	0.75	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGC	20	0.5	RNA PCR Primer, Index 46 (100% over 50bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	17	0.42500000000000004	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 31bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	14	0.35000000000000003	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	13	0.325	RNA PCR Primer, Index 3 (100% over 34bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTAT	12	0.3	RNA PCR Primer, Index 46 (100% over 48bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	9	0.22499999999999998	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	9	0.22499999999999998	RNA PCR Primer, Index 3 (100% over 34bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	8	0.2	RNA PCR Primer, Index 1 (100% over 24bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	8	0.2	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
CTGCGTTCGCGCTCTCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCG	7	0.17500000000000002	RNA PCR Primer, Index 46 (100% over 45bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGCACTCCAGTCACTC	7	0.17500000000000002	RNA PCR Primer, Index 45 (97% over 35bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGA	6	0.15	RNA PCR Primer, Index 46 (100% over 39bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	6	0.15	RNA PCR Primer, Index 5 (97% over 35bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCG	6	0.15	RNA PCR Primer, Index 46 (100% over 38bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ATCACATTGCCAGGGATTACCACTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
AAACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GACCCTGTTGATCTCAAATACTAATTGCCAGTTTTGTCTGATGTGGAATT	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCC	5	0.125	RNA PCR Primer, Index 46 (100% over 37bp)
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TATTGCACTCGTCCCGGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	5	0.125	No Hit
ATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATCATGATGGGCTCCTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.575	0.0	0.0	0.0
2	0.0	0.6	0.0	0.0	0.0
3	0.0	0.95	0.0	0.0	0.0
4	0.0	0.975	0.0	0.0	0.0
5	0.0	1.025	0.0	0.0	0.0
6	0.0	1.4	0.0	0.0	0.0
7	0.0	2.5	0.0	0.0	0.0
8	0.0	2.775	0.0	0.0	0.0
9	0.0	2.85	0.0	0.0	0.0
10	0.0	3.15	0.0	0.0	0.0
11	0.0	3.3	0.0	0.0	0.0
12	0.0	3.8	0.0	0.0	0.0
13	0.0	4.125	0.0	0.0	0.0
14	0.0	4.425	0.0	0.0	0.0
15	0.0	4.825	0.0	0.0	0.0
16	0.0	6.95	0.0	0.0	0.0
17	0.0	8.05	0.0	0.0	0.0
18	0.0	9.7	0.0	0.0	0.0
19	0.0	10.425	0.0	0.0	0.0
20	0.0	11.575	0.0	0.0	0.0
21	0.0	17.175	0.0	0.0	0.0
22	0.0	28.95	0.0	0.0	0.0
23	0.0	56.7	0.0	0.0	0.0
24	0.0	69.3	0.0	0.0	0.0
25	0.0	74.5	0.0	0.0	0.0
26	0.0	76.2	0.0	0.0	0.0
27	0.0	77.1	0.0	0.0	0.0
28	0.0	77.85	0.0	0.0	0.0
29	0.0	78.4	0.0	0.0	0.0
30	0.0	78.95	0.0	0.0	0.0
31	0.0	79.725	0.0	0.0	0.0
32	0.0	80.775	0.0	0.0	0.0
33	0.0	81.95	0.0	0.0	0.0
34	0.0	85.425	0.0	0.0	0.0
35	0.0	86.625	0.0	0.0	0.0
36	0.0	87.35	0.0	0.0	0.0
37	0.0	88.25	0.0	0.0	0.0
38	0.0	88.875	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCCAA	20	6.952051E-4	44.000004	8
TTGCACT	20	6.952051E-4	44.000004	3
AATCCCA	20	6.952051E-4	44.000004	7
TCCCAAA	20	6.952051E-4	44.000004	9
CCAAAAG	20	6.952051E-4	44.000004	11
CCCGGCC	20	6.952051E-4	44.000004	13
TATTGCA	20	6.952051E-4	44.000004	1
ACATTCA	20	6.952051E-4	44.000004	2
AGCAGCT	20	6.952051E-4	44.000004	16
CGGAATC	20	6.952051E-4	44.000004	4
GTCCCGG	20	6.952051E-4	44.000004	11
AAAAGCA	20	6.952051E-4	44.000004	13
CCCAAAA	20	6.952051E-4	44.000004	10
GCTGTCG	20	6.952051E-4	44.000004	11
ATTGCAC	20	6.952051E-4	44.000004	2
GAATCCC	20	6.952051E-4	44.000004	6
TCCCGGC	20	6.952051E-4	44.000004	12
CTGTCGG	20	6.952051E-4	44.000004	12
AAAGCAG	20	6.952051E-4	44.000004	14
AACGGAA	20	6.952051E-4	44.000004	2
>>END_MODULE
Read 50182 spots for SRR5030979.sra
Written 50182 spots for SRR5030979.sra
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Read 50201 spots for SRR5030979.sra
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SRR ids: ['SRR5030979.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_n2xjp_zs
SRR5030979.sra spots: 2408755
blocks: [[1, 50182], [50183, 100364], [100365, 150546], [150547, 200728], [200729, 250910], [250911, 301092], [301093, 351274], [351275, 401456], [401457, 451638], [451639, 501820], [501821, 552002], [552003, 602184], [602185, 652366], [652367, 702548], [702549, 752730], [752731, 802912], [802913, 853094], [853095, 903276], [903277, 953458], [953459, 1003640], [1003641, 1053822], [1053823, 1104004], [1104005, 1154186], [1154187, 1204368], [1204369, 1254550], [1254551, 1304732], [1304733, 1354914], [1354915, 1405096], [1405097, 1455278], [1455279, 1505460], [1505461, 1555642], [1555643, 1605824], [1605825, 1656006], [1656007, 1706188], [1706189, 1756370], [1756371, 1806552], [1806553, 1856734], [1856735, 1906916], [1906917, 1957098], [1957099, 2007280], [2007281, 2057462], [2057463, 2107644], [2107645, 2157826], [2157827, 2208008], [2208009, 2258190], [2258191, 2308372], [2308373, 2358554], [2358555, 2408755]]
SRR5030979 file size 416416
SRR5030979 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5030979 SRR5030979_1.fastq
Input file:	SRR5030979_1.fastq
trimmed:	SRR5030979-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):	32
Wed Mar  4 06:58:36 2020 >> started

Wed Mar  4 06:58:37 2020 >> done (1.470s)
2408755 reads processed; of these:
    233 ( 0.01%) short reads filtered out after trimming by size control
      8 ( 0.00%) empty reads filtered out after trimming by size control
2408514 (99.99%) reads available; of these:
 174122 ( 7.23%) trimmed reads available after processing
2234392 (92.77%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     78	  0.00%
 19	    106	  0.00%
 20	    154	  0.01%
 21	    212	  0.01%
 22	    319	  0.01%
 23	    396	  0.02%
 24	    456	  0.02%
 25	    561	  0.02%
 26	    511	  0.02%
 27	    629	  0.03%
 28	    760	  0.03%
 29	    875	  0.04%
 30	    663	  0.03%
 31	    806	  0.03%
 32	    914	  0.04%
 33	   1107	  0.05%
 34	   1392	  0.06%
 35	   2479	  0.10%
 36	   2381	  0.10%
 37	   2506	  0.10%
 38	   2607	  0.11%
 39	   2979	  0.12%
 40	   3490	  0.14%
 41	   3674	  0.15%
 42	   5033	  0.21%
 43	   6642	  0.28%
 44	   9651	  0.40%
 45	  12292	  0.51%
 46	  18551	  0.77%
 47	  19096	  0.79%
 48	  29820	  1.24%
 49	  42982	  1.78%
 50	2234392	 92.77%
2408514 reads passed initial QC


criterion=sequence-density
sequence-density=88.44
sequence-density-rank=1
fanout-score=19.59
fanout-score-rank=1
prefix-density=89.92
prefix-fanout=19.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC


criterion=fanout-score
sequence-density=88.44
sequence-density-rank=1
fanout-score=19.59
fanout-score-rank=1
prefix-density=89.92
prefix-fanout=19.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC -o SRR5030979 -
Input file:	STDIN
trimmed:	SRR5030979-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC
-- 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):	32
Wed Mar  4 06:58:52 2020 >> started

Wed Mar  4 06:58:55 2020 >> done (3.460s)
2354390 reads processed; of these:
 230652 ( 9.80%) short reads filtered out after trimming by size control
  15127 ( 0.64%) empty reads filtered out after trimming by size control
2108611 (89.56%) reads available; of these:
2034052 (96.46%) trimmed reads available after processing
  74559 ( 3.54%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14830	  0.70%
 19	  30003	  1.42%
 20	 121094	  5.74%
 21	 257803	 12.23%
 22	 669166	 31.73%
 23	 303160	 14.38%
 24	 135573	  6.43%
 25	  37840	  1.79%
 26	  20449	  0.97%
 27	  16401	  0.78%
 28	  17256	  0.82%
 29	  12957	  0.61%
 30	  21608	  1.02%
 31	  31386	  1.49%
 32	  26900	  1.28%
 33	  92328	  4.38%
 34	  26989	  1.28%
 35	  21026	  1.00%
 36	  23941	  1.14%
 37	  12387	  0.59%
 38	  12522	  0.59%
 39	  12010	  0.57%
 40	  15646	  0.74%
 41	  21687	  1.03%
 42	  25543	  1.21%
 43	  17808	  0.84%
 44	  12927	  0.61%
 45	  16279	  0.77%
 46	  13346	  0.63%
 47	   9456	  0.45%
 48	    990	  0.05%
 49	   1616	  0.08%
 50	  55684	  2.64%


criterion=sequence-density
sequence-density=6.87
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=0.61
sequence-density-rank=21
fanout-score=12.65
fanout-score-rank=1
prefix-density=7.72
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 06:59:34
                             Started mapping on |	Mar 04 06:59:34
                                    Finished on |	Mar 04 07:00:02
       Mapping speed, Million of reads per hour |	278.07

                          Number of input reads |	2162735
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1121217
                        Uniquely mapped reads % |	51.84%
                          Average mapped length |	24.14
                       Number of splices: Total |	1207
            Number of splices: Annotated (sjdb) |	204
                       Number of splices: GT/AG |	1139
                       Number of splices: GC/AG |	11
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	54
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.76
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	741108
             % of reads mapped to multiple loci |	34.27%
        Number of reads mapped to too many loci |	51783
             % of reads mapped to too many loci |	2.39%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.73%
                     % of reads unmapped: other |	0.76%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	300410	300410	300410
N_multimapping	741108	741108	741108
N_noFeature	64534	77527	770197
N_ambiguous	625963	323198	9547
UnstrandedReadsAssigned:430720 PositiveStrandReadsAssigned:720492 NegativeStrandReadsAssigned:341473
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030979 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: SRR5030979-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,162,735 reads, 544,093 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,118 rounds

 109283 SRR5030979.ke.tsv
  52636 SRR5030979.se.tsv
 161919 total
==> SRR5030979.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

==> SRR5030979.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030979 completed mapping pipeline successfully
