Starting /dee2/code/volunteer_pipeline.sh SRR5030962
    current disk space = 160572030976
    free memory = 73925428 
SRR5030962 SRAfilesize
dddb91486b3036834b53acb08b59e7bb  SRR5030962.sra
SRR5030962.sra file validated
SRR5030962 is single end
SRR5030962 is conventional basespace
SRR5030962 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030962_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	32.4095	33.0	31.0	34.0	31.0	34.0
2	32.688	34.0	31.0	34.0	31.0	34.0
3	32.69175	34.0	31.0	34.0	31.0	34.0
4	36.2185	37.0	37.0	37.0	35.0	37.0
5	36.2625	37.0	37.0	37.0	35.0	37.0
6	36.17125	37.0	36.0	37.0	35.0	37.0
7	36.1735	37.0	35.0	37.0	35.0	37.0
8	36.198	37.0	36.0	37.0	35.0	37.0
9	37.91625	39.0	38.0	39.0	35.0	39.0
10	37.846	39.0	38.0	39.0	35.0	39.0
11	37.85725	39.0	38.0	39.0	35.0	39.0
12	37.6515	39.0	38.0	39.0	35.0	39.0
13	37.7395	39.0	38.0	39.0	35.0	39.0
14	39.048	40.0	39.0	41.0	36.0	41.0
15	39.2235	41.0	39.0	41.0	36.0	41.0
16	39.19475	40.0	38.0	41.0	36.0	41.0
17	39.184	40.0	39.0	41.0	36.0	41.0
18	39.3525	41.0	39.0	41.0	36.0	41.0
19	39.261	41.0	39.0	41.0	36.0	41.0
20	38.99	41.0	39.0	41.0	35.0	41.0
21	39.06575	40.0	39.0	41.0	36.0	41.0
22	39.17025	40.0	39.0	41.0	36.0	41.0
23	39.18675	41.0	39.0	41.0	36.0	41.0
24	38.431	40.0	38.0	41.0	34.0	41.0
25	38.61125	40.0	38.0	41.0	34.0	41.0
26	38.86	40.0	38.0	41.0	34.0	41.0
27	39.03225	40.0	39.0	41.0	36.0	41.0
28	38.70575	40.0	38.0	41.0	34.0	41.0
29	38.01125	40.0	38.0	41.0	32.0	41.0
30	38.25375	40.0	38.0	41.0	33.0	41.0
31	38.6305	40.0	38.0	41.0	34.0	41.0
32	38.59425	40.0	38.0	41.0	35.0	41.0
33	37.27025	40.0	37.0	41.0	31.0	41.0
34	37.108	39.0	37.0	41.0	30.0	41.0
35	37.06425	39.0	37.0	40.0	31.0	41.0
36	32.66275	38.0	30.0	40.0	15.0	41.0
37	35.352	38.0	33.0	40.0	27.0	41.0
38	36.766	39.0	36.0	40.0	31.0	41.0
39	37.038	39.0	37.0	40.0	31.0	41.0
40	36.94475	39.0	37.0	40.0	31.0	41.0
41	36.63175	39.0	36.0	40.0	31.0	41.0
42	36.7415	39.0	36.0	40.0	31.0	41.0
43	36.7205	39.0	36.0	40.0	30.0	41.0
44	36.8935	39.0	37.0	41.0	32.0	41.0
45	36.39225	39.0	36.0	40.0	31.0	41.0
46	33.92425	38.0	33.0	40.0	23.0	41.0
47	35.00575	38.0	34.0	40.0	28.0	41.0
48	35.07725	38.0	35.0	40.0	28.0	41.0
49	34.24525	38.0	34.0	40.0	24.0	41.0
50	29.658	34.0	27.0	38.0	2.0	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
15	1.0
16	5.0
17	3.0
18	4.0
19	4.0
20	4.0
21	5.0
22	11.0
23	14.0
24	13.0
25	9.0
26	19.0
27	25.0
28	52.0
29	38.0
30	63.0
31	84.0
32	79.0
33	110.0
34	172.0
35	219.0
36	325.0
37	560.0
38	1069.0
39	1112.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.794191286930396	23.15973960941412	47.32098147220831	16.72508763144717
2	20.724999999999998	25.95	20.625	32.7
3	26.724999999999998	19.2	22.025	32.05
4	31.1	29.075	15.575	24.25
5	19.400000000000002	43.125	22.7	14.774999999999999
6	27.400000000000002	17.724999999999998	40.275	14.6
7	21.2	20.45	23.474999999999998	34.875
8	23.425	31.45	14.725	30.4
9	25.1	30.125	29.75	15.024999999999999
10	25.0	17.424999999999997	34.025	23.549999999999997
11	29.15	17.974999999999998	16.1	36.775000000000006
12	15.4	21.775	33.275	29.549999999999997
13	28.425	21.5	27.55	22.525000000000002
14	24.95	34.2	21.125	19.725
15	36.125	24.5	23.974999999999998	15.4
16	16.05	24.55	23.175	36.225
17	22.55	21.625	39.0	16.825000000000003
18	20.825	18.85	36.875	23.45
19	37.4	16.55	29.275000000000002	16.775000000000002
20	42.025	18.3	24.05	15.625
21	22.125	19.8	25.85	32.225
22	28.15	15.075	43.6	13.175
23	27.35	14.475	40.475	17.7
24	47.025	18.375	23.275000000000002	11.325000000000001
25	44.65	23.799999999999997	16.25	15.299999999999999
26	26.625	42.05	16.875	14.45
27	18.575	42.75	23.95	14.725
28	14.224999999999998	24.525	44.375	16.875
29	10.375	15.7	53.77499999999999	20.150000000000002
30	11.55	10.4	32.074999999999996	45.975
31	17.45	8.450000000000001	43.95	30.15
32	28.275	9.925	20.575	41.225
33	50.025	12.85	15.225	21.9
34	53.425	12.025	18.5	16.05
35	58.12500000000001	9.75	18.15	13.975000000000001
36	40.625	10.775	31.674999999999997	16.925
37	42.775	12.275	19.075	25.874999999999996
38	21.725	18.05	14.6	45.625
39	18.125	23.9	12.5	45.475
40	19.425	42.85	14.975	22.75
41	26.900000000000002	43.025000000000006	13.950000000000001	16.125
42	47.65	27.875	13.25	11.225
43	46.125	30.725	12.0	11.15
44	29.099999999999998	45.300000000000004	10.975	14.625
45	20.275000000000002	46.625	15.85	17.25
46	14.35	26.825	20.125	38.7
47	11.799999999999999	17.75	38.2	32.25
48	14.499999999999998	15.575	20.225	49.7
49	19.45	19.425	16.1	45.025
50	21.45	33.025	17.675	27.85
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	1.0
12	2.0
13	1.5
14	1.0
15	0.5
16	0.0
17	1.0
18	2.0
19	1.0
20	0.0
21	0.0
22	0.0
23	1.0
24	2.0
25	1.5
26	1.0
27	2.0
28	3.0
29	3.5
30	4.0
31	20.5
32	37.0
33	36.5
34	36.0
35	53.5
36	71.0
37	85.5
38	100.0
39	95.0
40	90.0
41	88.0
42	86.0
43	123.0
44	160.0
45	207.5
46	255.0
47	330.0
48	405.0
49	449.0
50	493.0
51	567.5
52	642.0
53	519.0
54	396.0
55	467.5
56	539.0
57	420.5
58	302.0
59	198.5
60	95.0
61	75.5
62	56.0
63	70.0
64	84.0
65	60.0
66	36.0
67	25.0
68	14.0
69	15.5
70	17.0
71	27.0
72	37.0
73	21.5
74	6.0
75	5.5
76	5.0
77	6.0
78	7.0
79	10.0
80	13.0
81	8.0
82	3.0
83	1.5
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	0.15
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	43.225
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.18796992481202	32.5
2	10.294968189705033	8.9
3	5.205320994794679	6.75
4	1.850780798149219	3.2
5	0.6940427993059572	1.5
6	1.5615962984384038	4.05
7	0.8097165991902834	2.45
8	0.8097165991902834	2.8000000000000003
9	0.2891844997108155	1.125
>10	3.007518796992481	25.624999999999996
>50	0.1735106998264893	4.9
>100	0.11567379988432619	6.2
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	139	3.4750000000000005	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	109	2.725	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	75	1.875	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	59	1.4749999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	50	1.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	49	1.225	RNA PCR Primer, Index 1 (100% over 27bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	41	1.0250000000000001	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	38	0.95	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	31	0.775	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	27	0.675	RNA PCR Primer, Index 1 (97% over 35bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	25	0.625	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTC	21	0.525	RNA PCR Primer, Index 20 (100% over 44bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	20	0.5	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	14	0.35000000000000003	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	14	0.35000000000000003	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGC	14	0.35000000000000003	RNA PCR Primer, Index 20 (100% over 50bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	13	0.325	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	13	0.325	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	13	0.325	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	12	0.3	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	12	0.3	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	12	0.3	No Hit
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	10	0.25	No Hit
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	10	0.25	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	9	0.22499999999999998	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	9	0.22499999999999998	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	9	0.22499999999999998	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	8	0.2	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	8	0.2	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	8	0.2	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCT	8	0.2	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GATACCCGTCGCCGCGCTCTCCCTCTCCCCCCGTCCGCCTCCCGGGCGGG	8	0.2	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	7	0.17500000000000002	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	7	0.17500000000000002	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	7	0.17500000000000002	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAG	6	0.15	No Hit
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCTTGGAATT	6	0.15	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	6	0.15	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTAT	6	0.15	RNA PCR Primer, Index 20 (100% over 48bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (96% over 30bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCAGATGATGAATTCAACTGTTCAACTGCTGAATGAGCCAAACATGAACT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	5	0.125	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	5	0.125	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGCTATGATGAAGGCTATGTTGGTAGGGACAACTGAGCTTGTTGATGAAT	5	0.125	No Hit
TGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAATA	5	0.125	No Hit
GGTCAATGATGACAACCCAATGTCATGAACAAAGGTGATGACATAAAATT	5	0.125	No Hit
TTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCAT	5	0.125	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.375	0.0	0.0	0.0
2	0.0	0.425	0.0	0.0	0.0
3	0.0	0.6	0.0	0.0	0.0
4	0.0	0.675	0.0	0.0	0.0
5	0.0	0.75	0.0	0.0	0.0
6	0.0	0.85	0.0	0.0	0.0
7	0.0	1.4	0.0	0.0	0.0
8	0.0	1.525	0.0	0.0	0.0
9	0.0	1.575	0.0	0.0	0.0
10	0.0	1.625	0.0	0.0	0.0
11	0.0	1.75	0.0	0.0	0.0
12	0.0	1.9	0.0	0.0	0.0
13	0.0	2.125	0.0	0.0	0.0
14	0.0	2.3	0.0	0.0	0.0
15	0.0	2.775	0.0	0.0	0.0
16	0.0	3.85	0.0	0.0	0.0
17	0.0	4.3	0.0	0.0	0.0
18	0.0	5.05	0.0	0.0	0.0
19	0.0	5.35	0.0	0.0	0.0
20	0.0	6.1	0.0	0.0	0.0
21	0.0	11.9	0.0	0.0	0.0
22	0.0	20.85	0.0	0.0	0.0
23	0.0	46.325	0.0	0.0	0.0
24	0.0	55.65	0.0	0.0	0.0
25	0.0	60.65	0.0	0.0	0.0
26	0.0	61.925	0.0	0.0	0.0
27	0.0	62.55	0.0	0.0	0.0
28	0.0	63.0	0.0	0.0	0.0
29	0.0	63.575	0.0	0.0	0.0
30	0.0	63.975	0.0	0.0	0.0
31	0.0	64.8	0.0	0.0	0.0
32	0.0	65.575	0.0	0.0	0.0
33	0.0	66.5	0.0	0.0	0.0
34	0.0	68.775	0.0	0.0	0.0
35	0.0	69.775	0.0	0.0	0.0
36	0.0	70.6	0.0	0.0	0.0
37	0.0	71.375	0.0	0.0	0.0
38	0.0	72.05	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
AATCCAG	20	6.952051E-4	44.000004	8
ATCCAGG	20	6.952051E-4	44.000004	9
TTCAAGT	20	6.952051E-4	44.000004	1
AGGATAG	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
ACCCGTA	20	6.952051E-4	44.000004	2
TCCAGGA	20	6.952051E-4	44.000004	10
CTTGGTG	20	6.952051E-4	44.000004	16
GGATAGG	20	6.952051E-4	44.000004	14
CCGTAGA	20	6.952051E-4	44.000004	4
CCCGTAG	20	6.952051E-4	44.000004	3
AGTAATC	20	6.952051E-4	44.000004	5
TAATCCA	20	6.952051E-4	44.000004	7
GCTTGGT	20	6.952051E-4	44.000004	15
TTGGCTT	20	6.952051E-4	44.000004	17
TGGTGGA	20	6.952051E-4	44.000004	18
CAGGATA	20	6.952051E-4	44.000004	12
GTAATCC	20	6.952051E-4	44.000004	6
>>END_MODULE
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292034 spots for SRR5030962.sra
Written 292034 spots for SRR5030962.sra
Read 292044 spots for SRR5030962.sra
Written 292044 spots for SRR5030962.sra
SRR ids: ['SRR5030962.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ox7_xph2
SRR5030962.sra spots: 3504418
blocks: [[1, 292034], [292035, 584068], [584069, 876102], [876103, 1168136], [1168137, 1460170], [1460171, 1752204], [1752205, 2044238], [2044239, 2336272], [2336273, 2628306], [2628307, 2920340], [2920341, 3212374], [3212375, 3504418]]
SRR5030962 file size 606315
SRR5030962 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030962 SRR5030962_1.fastq
Input file:	SRR5030962_1.fastq
trimmed:	SRR5030962-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 06:55:19 2020 >> started

Wed Mar  4 06:55:21 2020 >> done (2.030s)
3504418 reads processed; of these:
    158 ( 0.00%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3504254 (100.00%) reads available; of these:
 297091 ( 8.48%) trimmed reads available after processing
3207163 (91.52%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     53	  0.00%
 19	     63	  0.00%
 20	    196	  0.01%
 21	    213	  0.01%
 22	    352	  0.01%
 23	    436	  0.01%
 24	    516	  0.01%
 25	    595	  0.02%
 26	    569	  0.02%
 27	    835	  0.02%
 28	    979	  0.03%
 29	   1335	  0.04%
 30	   1142	  0.03%
 31	   1540	  0.04%
 32	   2089	  0.06%
 33	   3281	  0.09%
 34	   8978	  0.26%
 35	   3997	  0.11%
 36	   3020	  0.09%
 37	   3617	  0.10%
 38	   4749	  0.14%
 39	   5015	  0.14%
 40	   7704	  0.22%
 41	   5651	  0.16%
 42	  10061	  0.29%
 43	   7879	  0.22%
 44	  20706	  0.59%
 45	  20940	  0.60%
 46	  20402	  0.58%
 47	  24515	  0.70%
 48	  52829	  1.51%
 49	  82834	  2.36%
 50	3207163	 91.52%
3504254 reads passed initial QC


criterion=sequence-density
sequence-density=71.60
sequence-density-rank=1
fanout-score=19.92
fanout-score-rank=2
prefix-density=74.35
prefix-fanout=19.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC


criterion=fanout-score
sequence-density=1.90
sequence-density-rank=7
fanout-score=122.28
fanout-score-rank=1
prefix-density=73.20
prefix-fanout=3.2
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 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC -o SRR5030962 -
Input file:	STDIN
trimmed:	SRR5030962-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC
-- 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 06:55:39 2020 >> started

Wed Mar  4 06:55:43 2020 >> done (4.584s)
3406914 reads processed; of these:
 180490 ( 5.30%) short reads filtered out after trimming by size control
  17188 ( 0.50%) empty reads filtered out after trimming by size control
3209236 (94.20%) reads available; of these:
2666660 (83.09%) trimmed reads available after processing
 542576 (16.91%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15289	  0.48%
 19	  23926	  0.75%
 20	 182250	  5.68%
 21	 318309	  9.92%
 22	 844043	 26.30%
 23	 333187	 10.38%
 24	 175535	  5.47%
 25	  49510	  1.54%
 26	  24907	  0.78%
 27	  19465	  0.61%
 28	  22033	  0.69%
 29	  16220	  0.51%
 30	  22953	  0.72%
 31	  32534	  1.01%
 32	  33840	  1.05%
 33	  80615	  2.51%
 34	  34379	  1.07%
 35	  28259	  0.88%
 36	  30310	  0.94%
 37	  22864	  0.71%
 38	  24771	  0.77%
 39	  26209	  0.82%
 40	  40480	  1.26%
 41	  49945	  1.56%
 42	  60100	  1.87%
 43	  42085	  1.31%
 44	  36018	  1.12%
 45	  49334	  1.54%
 46	  39018	  1.22%
 47	  29351	  0.91%
 48	   6901	  0.22%
 49	  20416	  0.64%
 50	 474180	 14.78%


criterion=sequence-density
sequence-density=4.46
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=0.77
sequence-density-rank=17
fanout-score=11.80
fanout-score-rank=1
prefix-density=9.01
prefix-fanout=1.0
sequence=TGAGCTTGGCTAT
                                 Started job on |	Mar 04 06:56:05
                             Started mapping on |	Mar 04 06:56:05
                                    Finished on |	Mar 04 06:56:28
       Mapping speed, Million of reads per hour |	517.55

                          Number of input reads |	3306576
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2044383
                        Uniquely mapped reads % |	61.83%
                          Average mapped length |	29.53
                       Number of splices: Total |	1431
            Number of splices: Annotated (sjdb) |	256
                       Number of splices: GT/AG |	1235
                       Number of splices: GC/AG |	15
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	180
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.45
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.06
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	831415
             % of reads mapped to multiple loci |	25.14%
        Number of reads mapped to too many loci |	82341
             % of reads mapped to too many loci |	2.49%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.48%
                     % of reads unmapped: other |	1.06%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	430778	430778	430778
N_multimapping	831415	831415	831415
N_noFeature	90476	121087	1418055
N_ambiguous	1113968	569721	23275
UnstrandedReadsAssigned:839939 PositiveStrandReadsAssigned:1353575 NegativeStrandReadsAssigned:603053
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030962 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: SRR5030962-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,306,576 reads, 894,701 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,132 rounds

 109283 SRR5030962.ke.tsv
  52636 SRR5030962.se.tsv
 161919 total
==> SRR5030962.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

==> SRR5030962.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030962 completed mapping pipeline successfully
