Starting /dee2/code/volunteer_pipeline.sh SRR5030838
    current disk space = 160666533888
    free memory = 1041645012 
SRR5030838 SRAfilesize
9aa94be0ce2ef817401b3a4279f9a6b0  SRR5030838.sra
SRR5030838.sra file validated
SRR5030838 is single end
SRR5030838 is conventional basespace
SRR5030838 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030838_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.45275	34.0	31.0	34.0	31.0	34.0
2	32.75025	34.0	31.0	34.0	31.0	34.0
3	32.74625	34.0	31.0	34.0	31.0	34.0
4	36.3425	37.0	37.0	37.0	35.0	37.0
5	36.34975	37.0	37.0	37.0	35.0	37.0
6	36.21425	37.0	37.0	37.0	35.0	37.0
7	36.1825	37.0	36.0	37.0	35.0	37.0
8	36.19975	37.0	36.0	37.0	35.0	37.0
9	37.9905	39.0	38.0	39.0	35.0	39.0
10	37.912	39.0	38.0	39.0	35.0	39.0
11	37.873	39.0	38.0	39.0	35.0	39.0
12	37.74875	39.0	38.0	39.0	35.0	39.0
13	37.74525	39.0	38.0	39.0	35.0	39.0
14	39.15825	40.0	39.0	41.0	36.0	41.0
15	39.2775	41.0	39.0	41.0	36.0	41.0
16	39.26875	40.0	39.0	41.0	36.0	41.0
17	39.24475	40.0	39.0	41.0	36.0	41.0
18	39.38175	41.0	39.0	41.0	36.0	41.0
19	39.254	41.0	39.0	41.0	36.0	41.0
20	39.0805	40.0	39.0	41.0	35.0	41.0
21	39.09625	40.0	39.0	41.0	36.0	41.0
22	39.28075	41.0	39.0	41.0	36.0	41.0
23	39.13775	41.0	39.0	41.0	36.0	41.0
24	38.25975	40.0	38.0	41.0	33.0	41.0
25	38.3095	40.0	38.0	41.0	33.0	41.0
26	38.6055	40.0	38.0	41.0	34.0	41.0
27	38.76925	40.0	38.0	41.0	35.0	41.0
28	38.56925	40.0	38.0	41.0	34.0	41.0
29	38.03625	40.0	38.0	41.0	33.0	41.0
30	38.29475	40.0	38.0	41.0	34.0	41.0
31	38.777	40.0	38.0	41.0	35.0	41.0
32	38.68075	40.0	38.0	41.0	34.0	41.0
33	37.7185	40.0	38.0	41.0	32.0	41.0
34	37.7195	40.0	37.0	41.0	33.0	41.0
35	37.6305	40.0	37.0	41.0	32.0	41.0
36	33.6005	38.0	30.0	40.0	18.0	41.0
37	35.795	38.0	34.0	40.0	30.0	41.0
38	37.1655	39.0	37.0	40.0	32.0	41.0
39	37.364	39.0	37.0	40.0	33.0	41.0
40	37.24625	39.0	37.0	40.0	32.0	41.0
41	37.12	39.0	37.0	40.0	32.0	41.0
42	37.0405	39.0	36.0	40.0	31.0	41.0
43	37.215	39.0	37.0	41.0	32.0	41.0
44	37.444	40.0	37.0	41.0	33.0	41.0
45	37.01125	39.0	37.0	41.0	31.0	41.0
46	34.889	38.0	34.0	40.0	26.0	41.0
47	35.866	39.0	35.0	40.0	29.0	41.0
48	35.858	39.0	35.0	40.0	30.0	41.0
49	35.0155	38.0	34.0	40.0	27.0	41.0
50	31.002	34.0	28.0	39.0	15.0	40.0
>>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	2.0
15	0.0
16	2.0
17	2.0
18	2.0
19	3.0
20	1.0
21	7.0
22	7.0
23	5.0
24	7.0
25	10.0
26	20.0
27	25.0
28	30.0
29	54.0
30	39.0
31	67.0
32	78.0
33	104.0
34	185.0
35	237.0
36	305.0
37	519.0
38	1036.0
39	1253.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.955126598144899	24.768112308849336	48.583604913512154	15.69315617949361
2	20.775	27.400000000000002	19.275000000000002	32.550000000000004
3	25.731432858214554	20.880220055013755	23.13078269567392	30.257564391097773
4	30.325000000000003	28.475	15.325	25.874999999999996
5	19.45	44.05	23.75	12.75
6	33.300000000000004	17.375	35.099999999999994	14.224999999999998
7	19.525000000000002	19.35	25.324999999999996	35.8
8	23.9	31.65	14.625	29.825000000000003
9	23.150000000000002	32.300000000000004	30.099999999999998	14.45
10	23.400000000000002	19.900000000000002	31.3	25.4
11	27.474999999999998	15.2	17.175	40.150000000000006
12	15.275	20.025000000000002	31.125000000000004	33.575
13	30.85	20.7	28.299999999999997	20.150000000000002
14	28.775000000000002	34.775	18.375	18.075
15	33.375	25.75	26.400000000000002	14.475
16	15.325	22.400000000000002	22.0	40.275
17	21.75	19.675	43.25	15.325
18	23.75	19.2	32.975	24.075
19	37.1	14.899999999999999	29.125	18.875
20	41.199999999999996	17.849999999999998	26.625	14.325
21	22.025	20.75	26.200000000000003	31.025000000000002
22	28.175	14.725	44.7	12.4
23	28.025	13.775	40.325	17.875
24	48.9	16.05	25.275	9.775
25	46.475	24.325	15.1	14.099999999999998
26	28.225	43.575	15.299999999999999	12.9
27	18.5	44.4	23.75	13.350000000000001
28	13.25	25.924999999999997	45.800000000000004	15.024999999999999
29	10.475	15.5	52.900000000000006	21.125
30	11.725	9.325	35.525	43.425000000000004
31	16.25	7.775	43.4	32.574999999999996
32	27.625	9.15	21.725	41.5
33	49.9	11.075	16.125	22.900000000000002
34	56.825	9.950000000000001	16.85	16.375
35	58.75	9.125	19.125	13.0
36	43.175000000000004	9.525	31.75	15.55
37	42.675000000000004	10.9	20.525	25.900000000000002
38	23.9	15.425	15.65	45.025
39	18.675	25.074999999999996	10.875	45.375
40	16.35	45.15	14.6	23.9
41	26.150000000000002	45.074999999999996	11.55	17.224999999999998
42	46.949999999999996	29.049999999999997	13.25	10.75
43	47.075	30.55	11.375	11.0
44	31.624999999999996	46.800000000000004	8.125	13.450000000000001
45	19.25	48.949999999999996	13.225000000000001	18.575
46	13.100000000000001	29.049999999999997	20.3	37.55
47	10.65	17.875	37.75	33.725
48	13.42835708927232	13.003250812703177	20.80520130032508	52.76319079769942
49	15.075	20.5	15.85	48.575
50	20.180045011252815	34.133533383345835	13.80345086271568	31.882970742685675
>>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	0.5
10	1.0
11	0.5
12	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	1.0
22	2.0
23	1.5
24	1.0
25	1.0
26	1.0
27	2.5
28	4.0
29	3.0
30	2.0
31	14.5
32	27.0
33	26.5
34	26.0
35	36.5
36	47.0
37	67.0
38	87.0
39	77.5
40	68.0
41	69.0
42	70.0
43	108.0
44	146.0
45	201.5
46	257.0
47	322.0
48	387.0
49	498.0
50	609.0
51	691.0
52	773.0
53	595.5
54	418.0
55	434.5
56	451.0
57	358.0
58	265.0
59	167.5
60	70.0
61	61.0
62	52.0
63	71.0
64	90.0
65	68.5
66	47.0
67	32.0
68	17.0
69	16.5
70	16.0
71	28.5
72	41.0
73	24.5
74	8.0
75	5.0
76	2.0
77	3.5
78	5.0
79	6.0
80	7.0
81	4.0
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	0.27499999999999997
2	0.0
3	0.025
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	0.025
49	0.0
50	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	41.325
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.80157289776164	31.324999999999996
2	10.042347247428918	8.3
3	4.295220810647308	5.325
4	2.1778584392014517	3.5999999999999996
5	1.3914095583787054	2.875
6	1.1494252873563218	2.85
7	0.48396854204476714	1.4000000000000001
8	0.7259528130671506	2.4
9	0.48396854204476714	1.7999999999999998
>10	2.9643073200241985	24.224999999999998
>50	0.42347247428917123	13.225000000000001
>100	0.06049606775559589	2.675
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	107	2.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	99	2.475	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	94	2.35	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	76	1.9	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	69	1.725	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	63	1.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	54	1.35	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	49	1.225	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	42	1.05	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	20	0.5	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCC	19	0.475	RNA PCR Primer, Index 5 (97% over 35bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTC	19	0.475	RNA PCR Primer, Index 36 (100% over 44bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	18	0.44999999999999996	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	17	0.42500000000000004	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	16	0.4	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	16	0.4	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	15	0.375	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	14	0.35000000000000003	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	13	0.325	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	11	0.27499999999999997	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	10	0.25	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	10	0.25	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGAAGAAAGGT	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	9	0.22499999999999998	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	9	0.22499999999999998	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 36 (100% over 50bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	9	0.22499999999999998	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	8	0.2	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	7	0.17500000000000002	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	7	0.17500000000000002	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	6	0.15	No Hit
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	6	0.15	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	6	0.15	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	6	0.15	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	6	0.15	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	6	0.15	No Hit
CAACGGAATCCCAAAAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GACCCTGTTGATCTCAAATACTAATTGCCAGTTTTGTCTGATGTGGAATT	5	0.125	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	5	0.125	No Hit
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	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	0.275	0.0	0.0	0.0
2	0.0	0.275	0.0	0.0	0.0
3	0.0	0.35	0.0	0.0	0.0
4	0.0	0.35	0.0	0.0	0.0
5	0.0	0.375	0.0	0.0	0.0
6	0.0	0.375	0.0	0.0	0.0
7	0.0	0.975	0.0	0.0	0.0
8	0.0	1.075	0.0	0.0	0.0
9	0.0	1.125	0.0	0.0	0.0
10	0.0	1.275	0.0	0.0	0.0
11	0.0	1.525	0.0	0.0	0.0
12	0.0	1.65	0.0	0.0	0.0
13	0.0	1.975	0.0	0.0	0.0
14	0.0	2.05	0.0	0.0	0.0
15	0.0	2.25	0.0	0.0	0.0
16	0.0	3.025	0.0	0.0	0.0
17	0.0	3.4	0.0	0.0	0.0
18	0.0	4.2	0.0	0.0	0.0
19	0.0	4.525	0.0	0.0	0.0
20	0.0	5.225	0.0	0.0	0.0
21	0.0	9.85	0.0	0.0	0.0
22	0.0	20.85	0.0	0.0	0.0
23	0.0	46.425	0.0	0.0	0.0
24	0.0	57.7	0.0	0.0	0.0
25	0.0	63.6	0.0	0.0	0.0
26	0.0	65.125	0.0	0.0	0.0
27	0.0	65.85	0.0	0.0	0.0
28	0.0	66.475	0.0	0.0	0.0
29	0.0	66.9	0.0	0.0	0.0
30	0.0	67.3	0.0	0.0	0.0
31	0.0	67.775	0.0	0.0	0.0
32	0.0	68.75	0.0	0.0	0.0
33	0.0	69.75	0.0	0.0	0.0
34	0.0	72.125	0.0	0.0	0.0
35	0.0	73.05	0.0	0.0	0.0
36	0.0	73.9	0.0	0.0	0.0
37	0.0	75.05	0.0	0.0	0.0
38	0.0	75.775	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
ACTGTTG	20	6.952051E-4	44.000004	18
AACGCTG	45	2.728484E-10	44.000004	8
GGTGAGT	45	2.728484E-10	44.000004	17
GTTGAAG	20	6.952051E-4	44.000004	10
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
ACGCTGT	45	2.728484E-10	44.000004	9
CTGAGAC	20	6.952051E-4	44.000004	4
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
TTCAAGT	20	6.952051E-4	44.000004	1
TTCAACG	45	2.728484E-10	44.000004	5
AGGATAG	20	6.952051E-4	44.000004	13
GCTGGAA	20	6.952051E-4	44.000004	20
CCTGAGA	20	6.952051E-4	44.000004	3
GGCTGGA	20	6.952051E-4	44.000004	19
CATTCAA	45	2.728484E-10	44.000004	3
TCAACGC	45	2.728484E-10	44.000004	6
GAAGAAC	20	6.952051E-4	44.000004	13
>>END_MODULE
Read 79701 spots for SRR5030838.sra
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SRR ids: ['SRR5030838.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ri81go9k
SRR5030838.sra spots: 3825674
blocks: [[1, 79701], [79702, 159402], [159403, 239103], [239104, 318804], [318805, 398505], [398506, 478206], [478207, 557907], [557908, 637608], [637609, 717309], [717310, 797010], [797011, 876711], [876712, 956412], [956413, 1036113], [1036114, 1115814], [1115815, 1195515], [1195516, 1275216], [1275217, 1354917], [1354918, 1434618], [1434619, 1514319], [1514320, 1594020], [1594021, 1673721], [1673722, 1753422], [1753423, 1833123], [1833124, 1912824], [1912825, 1992525], [1992526, 2072226], [2072227, 2151927], [2151928, 2231628], [2231629, 2311329], [2311330, 2391030], [2391031, 2470731], [2470732, 2550432], [2550433, 2630133], [2630134, 2709834], [2709835, 2789535], [2789536, 2869236], [2869237, 2948937], [2948938, 3028638], [3028639, 3108339], [3108340, 3188040], [3188041, 3267741], [3267742, 3347442], [3347443, 3427143], [3427144, 3506844], [3506845, 3586545], [3586546, 3666246], [3666247, 3745947], [3745948, 3825674]]
SRR5030838 file size 661997
SRR5030838 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5030838 SRR5030838_1.fastq
Input file:	SRR5030838_1.fastq
trimmed:	SRR5030838-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 06:24:24 2020 >> started

Wed Mar  4 06:24:26 2020 >> done (2.174s)
3825674 reads processed; of these:
    278 ( 0.01%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
3825386 (99.99%) reads available; of these:
 296906 ( 7.76%) trimmed reads available after processing
3528480 (92.24%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     91	  0.00%
 19	     74	  0.00%
 20	    241	  0.01%
 21	    324	  0.01%
 22	    461	  0.01%
 23	    562	  0.01%
 24	    656	  0.02%
 25	    731	  0.02%
 26	    657	  0.02%
 27	    819	  0.02%
 28	    980	  0.03%
 29	   1381	  0.04%
 30	   1038	  0.03%
 31	   1425	  0.04%
 32	   1736	  0.05%
 33	   3043	  0.08%
 34	   8004	  0.21%
 35	   4193	  0.11%
 36	   3140	  0.08%
 37	   3579	  0.09%
 38	   5035	  0.13%
 39	   4870	  0.13%
 40	   7421	  0.19%
 41	   5856	  0.15%
 42	   9232	  0.24%
 43	   7904	  0.21%
 44	  19680	  0.51%
 45	  20615	  0.54%
 46	  20071	  0.52%
 47	  24984	  0.65%
 48	  57375	  1.50%
 49	  80728	  2.11%
 50	3528480	 92.24%
3825386 reads passed initial QC


criterion=sequence-density
sequence-density=75.28
sequence-density-rank=1
fanout-score=20.72
fanout-score-rank=2
prefix-density=77.69
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC


criterion=fanout-score
sequence-density=1.72
sequence-density-rank=7
fanout-score=137.12
fanout-score-rank=1
prefix-density=77.35
prefix-fanout=3.1
sequence=GAATTCTCGGGGGCCAAGGAACT
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC -o SRR5030838 -
Input file:	STDIN
trimmed:	SRR5030838-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC
-- 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 06:24:44 2020 >> started

Wed Mar  4 06:24:49 2020 >> done (5.660s)
3724718 reads processed; of these:
 166795 ( 4.48%) short reads filtered out after trimming by size control
   7269 ( 0.20%) empty reads filtered out after trimming by size control
3550654 (95.33%) reads available; of these:
3034476 (85.46%) trimmed reads available after processing
 516178 (14.54%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15677	  0.44%
 19	  30435	  0.86%
 20	 183805	  5.18%
 21	 386127	 10.87%
 22	 986919	 27.80%
 23	 427069	 12.03%
 24	 207278	  5.84%
 25	  57082	  1.61%
 26	  27563	  0.78%
 27	  20492	  0.58%
 28	  22166	  0.62%
 29	  16557	  0.47%
 30	  26770	  0.75%
 31	  43341	  1.22%
 32	  35735	  1.01%
 33	  85909	  2.42%
 34	  38854	  1.09%
 35	  33247	  0.94%
 36	  40468	  1.14%
 37	  20234	  0.57%
 38	  21748	  0.61%
 39	  23203	  0.65%
 40	  36968	  1.04%
 41	  48263	  1.36%
 42	  58176	  1.64%
 43	  41040	  1.16%
 44	  34478	  0.97%
 45	  47732	  1.34%
 46	  36705	  1.03%
 47	  26958	  0.76%
 48	   6606	  0.19%
 49	  18473	  0.52%
 50	 444576	 12.52%


criterion=sequence-density
sequence-density=4.66
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=22
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.03
sequence-density-rank=36
fanout-score=32.53
fanout-score-rank=1
prefix-density=0.94
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:25:30
                             Started mapping on |	Mar 04 06:25:30
                                    Finished on |	Mar 04 06:25:58
       Mapping speed, Million of reads per hour |	469.46

                          Number of input reads |	3651322
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2167570
                        Uniquely mapped reads % |	59.36%
                          Average mapped length |	28.57
                       Number of splices: Total |	1465
            Number of splices: Annotated (sjdb) |	334
                       Number of splices: GT/AG |	1312
                       Number of splices: GC/AG |	21
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	132
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.48
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1035448
             % of reads mapped to multiple loci |	28.36%
        Number of reads mapped to too many loci |	84348
             % of reads mapped to too many loci |	2.31%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.33%
                     % of reads unmapped: other |	0.64%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	448304	448304	448304
N_multimapping	1035448	1035448	1035448
N_noFeature	108560	136352	1528520
N_ambiguous	1180026	632272	28619
UnstrandedReadsAssigned:878984 PositiveStrandReadsAssigned:1398946 NegativeStrandReadsAssigned:610431
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030838 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: SRR5030838-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,651,322 reads, 951,817 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 820 rounds

 109283 SRR5030838.ke.tsv
  52636 SRR5030838.se.tsv
 161919 total
==> SRR5030838.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

==> SRR5030838.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030838 completed mapping pipeline successfully
