Starting /dee2/code/volunteer_pipeline.sh SRR5030943
    current disk space = 160606617600
    free memory = 73945332 
SRR5030943 SRAfilesize
2b8e51c4e7e54cf161aa6c8eb296b5fa  SRR5030943.sra
SRR5030943.sra file validated
SRR5030943 is single end
SRR5030943 is conventional basespace
SRR5030943 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030943_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	32.469	34.0	31.0	34.0	31.0	34.0
2	32.72775	34.0	31.0	34.0	31.0	34.0
3	32.8895	34.0	31.0	34.0	31.0	34.0
4	36.3265	37.0	37.0	37.0	35.0	37.0
5	36.34625	37.0	37.0	37.0	35.0	37.0
6	36.1455	37.0	36.0	37.0	35.0	37.0
7	36.18425	37.0	36.0	37.0	35.0	37.0
8	36.26825	37.0	36.0	37.0	35.0	37.0
9	38.09525	39.0	38.0	39.0	35.0	39.0
10	38.07825	39.0	39.0	39.0	35.0	39.0
11	37.875	39.0	38.0	39.0	35.0	39.0
12	37.9445	39.0	38.0	39.0	35.0	39.0
13	37.86425	39.0	38.0	39.0	35.0	39.0
14	39.277	41.0	39.0	41.0	36.0	41.0
15	39.308	41.0	39.0	41.0	36.0	41.0
16	39.27825	41.0	39.0	41.0	36.0	41.0
17	39.4375	41.0	39.0	41.0	36.0	41.0
18	39.41625	41.0	39.0	41.0	36.0	41.0
19	39.08075	40.0	39.0	41.0	35.0	41.0
20	39.1405	41.0	39.0	41.0	36.0	41.0
21	39.20275	41.0	39.0	41.0	36.0	41.0
22	39.2205	41.0	39.0	41.0	36.0	41.0
23	39.02325	41.0	39.0	41.0	36.0	41.0
24	38.6005	40.0	38.0	41.0	34.0	41.0
25	38.86925	40.0	39.0	41.0	35.0	41.0
26	38.91475	40.0	38.0	41.0	35.0	41.0
27	39.07575	40.0	39.0	41.0	36.0	41.0
28	38.83075	40.0	38.0	41.0	35.0	41.0
29	38.11175	40.0	38.0	41.0	33.0	41.0
30	38.51425	40.0	38.0	41.0	34.0	41.0
31	38.8495	40.0	38.0	41.0	35.0	41.0
32	39.092	41.0	39.0	41.0	35.0	41.0
33	38.59675	40.0	38.0	41.0	34.0	41.0
34	38.06425	40.0	38.0	41.0	32.0	41.0
35	37.73525	39.0	37.0	41.0	33.0	41.0
36	34.03075	38.0	30.0	40.0	23.0	41.0
37	35.721	38.0	34.0	40.0	30.0	41.0
38	37.098	39.0	37.0	40.0	31.0	41.0
39	37.091	39.0	37.0	40.0	31.0	41.0
40	37.14725	39.0	37.0	40.0	31.0	41.0
41	37.062	39.0	36.0	40.0	31.0	41.0
42	37.47075	40.0	37.0	41.0	33.0	41.0
43	37.241	40.0	37.0	41.0	32.0	41.0
44	37.143	40.0	37.0	41.0	31.0	41.0
45	36.98825	40.0	37.0	41.0	31.0	41.0
46	35.33475	38.0	34.0	40.0	26.0	41.0
47	35.971	39.0	35.0	40.0	29.0	41.0
48	36.449	39.0	36.0	41.0	30.0	41.0
49	35.10425	38.0	34.0	40.0	29.0	41.0
50	30.363	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	1.0
17	1.0
18	1.0
19	1.0
20	2.0
21	4.0
22	6.0
23	9.0
24	12.0
25	9.0
26	16.0
27	23.0
28	28.0
29	38.0
30	49.0
31	60.0
32	86.0
33	129.0
34	153.0
35	200.0
36	302.0
37	549.0
38	1018.0
39	1302.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.992486851990984	23.94189832206361	51.96594039569247	14.099674430252943
2	20.025000000000002	27.05	20.424999999999997	32.5
3	28.875	17.65	21.975	31.5
4	35.275	27.925	13.175	23.625
5	18.975	42.525	23.875	14.625
6	27.3	17.8	41.725	13.175
7	19.650000000000002	18.875	21.224999999999998	40.25
8	20.4	31.5	15.425	32.675
9	27.474999999999998	31.95	26.174999999999997	14.399999999999999
10	23.65	16.275000000000002	34.75	25.324999999999996
11	28.525	14.674999999999999	16.275000000000002	40.525
12	13.975000000000001	19.675	36.875	29.475
13	30.65	19.075	28.425	21.85
14	27.3	35.65	21.125	15.925
15	37.974999999999994	21.85	23.599999999999998	16.575
16	16.175	20.25	23.974999999999998	39.6
17	22.75	20.5	40.775	15.975
18	24.4	16.475	36.8	22.325
19	37.05	14.575	32.6	15.775
20	47.175	16.0	22.55	14.274999999999999
21	20.175	19.900000000000002	27.450000000000003	32.475
22	29.65	13.950000000000001	46.25	10.15
23	29.65	12.35	45.0	13.0
24	51.05	15.775	24.45	8.725
25	49.575	25.624999999999996	14.875	9.925
26	25.95	47.325	16.650000000000002	10.075000000000001
27	15.7	46.75	26.650000000000002	10.9
28	12.049999999999999	23.45	49.2	15.299999999999999
29	9.175	13.100000000000001	58.025000000000006	19.7
30	9.875	7.249999999999999	35.15	47.725
31	16.975	5.65	44.625	32.75
32	29.525000000000002	6.625	20.575	43.275000000000006
33	57.3	7.675	12.85	22.175
34	60.8	8.05	16.875	14.274999999999999
35	63.65	8.125	18.475	9.75
36	41.175	8.450000000000001	35.225	15.15
37	44.45	9.225	19.2	27.125
38	22.3	16.35	12.75	48.6
39	15.75	27.525	8.6	48.125
40	17.525	49.575	9.775	23.125
41	28.525	47.875	8.3	15.299999999999999
42	50.349999999999994	30.575000000000003	9.075	10.0
43	49.275000000000006	34.025	8.15	8.55
44	26.8	49.975	7.775	15.45
45	15.0	50.2	15.475	19.325
46	10.9	25.124999999999996	19.75	44.224999999999994
47	8.799999999999999	15.2	37.625	38.375
48	9.2	15.6	18.825	56.375
49	15.275	21.9	13.325000000000001	49.5
50	20.630157539384847	37.05926481620405	14.403600900225054	27.906976744186046
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.5
14	1.0
15	1.5
16	2.0
17	1.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.5
26	2.0
27	1.5
28	1.0
29	1.0
30	1.0
31	9.0
32	17.0
33	19.0
34	21.0
35	31.5
36	42.0
37	43.5
38	45.0
39	51.0
40	57.0
41	64.5
42	72.0
43	100.5
44	129.0
45	170.0
46	211.0
47	331.5
48	452.0
49	546.5
50	641.0
51	701.5
52	762.0
53	564.0
54	366.0
55	484.5
56	603.0
57	439.0
58	275.0
59	176.0
60	77.0
61	58.0
62	39.0
63	51.0
64	63.0
65	44.0
66	25.0
67	17.5
68	10.0
69	14.5
70	19.0
71	39.0
72	59.0
73	31.0
74	3.0
75	2.0
76	1.0
77	1.0
78	1.0
79	1.5
80	2.0
81	1.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.17500000000000002
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	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	40.65
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.47724477244773	30.275000000000002
2	10.209102091020911	8.3
3	4.366543665436654	5.325
4	3.198031980319803	5.2
5	1.2915129151291513	2.625
6	1.107011070110701	2.7
7	0.6150061500615006	1.7500000000000002
8	0.7995079950799507	2.6
9	0.24600246002460024	0.8999999999999999
>10	3.198031980319803	20.45
>50	0.36900369003690037	12.049999999999999
>100	0.12300123001230012	7.825
>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	180	4.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	133	3.325	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	90	2.25	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	88	2.1999999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	87	2.175	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	81	2.025	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	29	0.7250000000000001	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	23	0.575	RNA PCR Primer, Index 5 (100% over 35bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	18	0.44999999999999996	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	14	0.35000000000000003	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	13	0.325	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTC	13	0.325	RNA PCR Primer, Index 8 (100% over 44bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	12	0.3	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	11	0.27499999999999997	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGC	10	0.25	RNA PCR Primer, Index 8 (100% over 50bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	10	0.25	RNA PCR Primer, Index 1 (96% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	9	0.22499999999999998	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	8	0.2	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTGTGCTTGATCTAACCATGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	8	0.2	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	8	0.2	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	8	0.2	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	7	0.17500000000000002	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CAGGATCACAGAAAAAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (100% over 33bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
GACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	6	0.15	RNA PCR Primer, Index 5 (100% over 35bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	6	0.15	No Hit
AGCTCGACTCATGGTTTGAACCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCAGCATCAGTGATTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	5	0.125	No Hit
AACCCGTAGATCCGAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.275	0.0	0.0	0.0
2	0.0	0.325	0.0	0.0	0.0
3	0.0	0.45	0.0	0.0	0.0
4	0.0	0.45	0.0	0.0	0.0
5	0.0	0.55	0.0	0.0	0.0
6	0.0	0.625	0.0	0.0	0.0
7	0.0	1.0	0.0	0.0	0.0
8	0.0	1.225	0.0	0.0	0.0
9	0.0	1.275	0.0	0.0	0.0
10	0.0	1.45	0.0	0.0	0.0
11	0.0	1.625	0.0	0.0	0.0
12	0.0	1.85	0.0	0.0	0.0
13	0.0	2.1	0.0	0.0	0.0
14	0.0	2.325	0.0	0.0	0.0
15	0.0	2.85	0.0	0.0	0.0
16	0.0	4.0	0.0	0.0	0.0
17	0.0	4.625	0.0	0.0	0.0
18	0.0	5.85	0.0	0.0	0.0
19	0.0	6.35	0.0	0.0	0.0
20	0.0	7.15	0.0	0.0	0.0
21	0.0	14.9	0.0	0.0	0.0
22	0.0	26.85	0.0	0.0	0.0
23	0.0	56.65	0.0	0.0	0.0
24	0.0	68.125	0.0	0.0	0.0
25	0.0	73.675	0.0	0.0	0.0
26	0.0	75.0	0.0	0.0	0.0
27	0.0	75.65	0.0	0.0	0.0
28	0.0	76.125	0.0	0.0	0.0
29	0.0	76.5	0.0	0.0	0.0
30	0.0	76.825	0.0	0.0	0.0
31	0.0	77.6	0.0	0.0	0.0
32	0.0	78.625	0.0	0.0	0.0
33	0.0	79.35	0.0	0.0	0.0
34	0.0	80.55	0.0	0.0	0.0
35	0.0	81.225	0.0	0.0	0.0
36	0.0	81.85	0.0	0.0	0.0
37	0.0	82.575	0.0	0.0	0.0
38	0.0	82.925	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	20	6.952051E-4	44.000004	2
ACTGTAG	20	6.952051E-4	44.000004	12
GAAGCAC	20	6.952051E-4	44.000004	7
ATGAAGC	20	6.952051E-4	44.000004	5
CACTGTA	20	6.952051E-4	44.000004	11
GGCTGGA	20	6.952051E-4	44.000004	19
GATGAAG	20	6.952051E-4	44.000004	4
CTTGGTG	20	6.952051E-4	44.000004	16
GGCTTGG	40	5.315087E-9	44.000004	19
TGAAGCA	20	6.952051E-4	44.000004	6
TGTAGCT	20	6.952051E-4	44.000004	14
GGTAGTA	20	6.952051E-4	44.000004	4
GCTTGGT	20	6.952051E-4	44.000004	15
AGATGAA	20	6.952051E-4	44.000004	3
TGAGGTA	20	6.952051E-4	44.000004	1
AGCACTG	20	6.952051E-4	44.000004	9
TTGGTGG	20	6.952051E-4	44.000004	17
GCACTGT	20	6.952051E-4	44.000004	10
AGGTAGT	20	6.952051E-4	44.000004	3
TGGTGGA	20	6.952051E-4	44.000004	18
>>END_MODULE
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327087 spots for SRR5030943.sra
Written 327087 spots for SRR5030943.sra
Read 327096 spots for SRR5030943.sra
Written 327096 spots for SRR5030943.sra
SRR ids: ['SRR5030943.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_cmrp8nsb
SRR5030943.sra spots: 3925053
blocks: [[1, 327087], [327088, 654174], [654175, 981261], [981262, 1308348], [1308349, 1635435], [1635436, 1962522], [1962523, 2289609], [2289610, 2616696], [2616697, 2943783], [2943784, 3270870], [3270871, 3597957], [3597958, 3925053]]
SRR5030943 file size 679226
SRR5030943 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030943 SRR5030943_1.fastq
Input file:	SRR5030943_1.fastq
trimmed:	SRR5030943-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 06:50:36 2020 >> started

Wed Mar  4 06:50:38 2020 >> done (1.809s)
3925053 reads processed; of these:
    187 ( 0.00%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3924860 (100.00%) reads available; of these:
 224982 ( 5.73%) trimmed reads available after processing
3699878 (94.27%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     57	  0.00%
 19	     68	  0.00%
 20	    177	  0.00%
 21	    215	  0.01%
 22	    344	  0.01%
 23	    459	  0.01%
 24	    441	  0.01%
 25	    516	  0.01%
 26	    425	  0.01%
 27	    603	  0.02%
 28	    755	  0.02%
 29	   1170	  0.03%
 30	    832	  0.02%
 31	   1025	  0.03%
 32	    951	  0.02%
 33	   1505	  0.04%
 34	   3638	  0.09%
 35	   3589	  0.09%
 36	   2346	  0.06%
 37	   2687	  0.07%
 38	   3104	  0.08%
 39	   3320	  0.08%
 40	   3645	  0.09%
 41	   4054	  0.10%
 42	   5001	  0.13%
 43	   7267	  0.19%
 44	  12706	  0.32%
 45	  15054	  0.38%
 46	  14265	  0.36%
 47	  21191	  0.54%
 48	  48044	  1.22%
 49	  65528	  1.67%
 50	3699878	 94.27%
3924860 reads passed initial QC


criterion=sequence-density
sequence-density=82.60
sequence-density-rank=1
fanout-score=19.45
fanout-score-rank=1
prefix-density=84.17
prefix-fanout=19.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC


criterion=fanout-score
sequence-density=82.60
sequence-density-rank=1
fanout-score=19.45
fanout-score-rank=1
prefix-density=84.17
prefix-fanout=19.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC -o SRR5030943 -
Input file:	STDIN
trimmed:	SRR5030943-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC
-- 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 06:50:53 2020 >> started

Wed Mar  4 06:50:57 2020 >> done (4.013s)
3830285 reads processed; of these:
 224501 ( 5.86%) short reads filtered out after trimming by size control
  11681 ( 0.30%) empty reads filtered out after trimming by size control
3594103 (93.83%) reads available; of these:
3215398 (89.46%) trimmed reads available after processing
 378705 (10.54%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  21495	  0.60%
 19	  38842	  1.08%
 20	 275778	  7.67%
 21	 481725	 13.40%
 22	1137806	 31.66%
 23	 434956	 12.10%
 24	 211377	  5.88%
 25	  53041	  1.48%
 26	  25868	  0.72%
 27	  20311	  0.57%
 28	  21302	  0.59%
 29	  15148	  0.42%
 30	  24724	  0.69%
 31	  42002	  1.17%
 32	  29749	  0.83%
 33	  59649	  1.66%
 34	  30359	  0.84%
 35	  25144	  0.70%
 36	  25556	  0.71%
 37	  15798	  0.44%
 38	  17765	  0.49%
 39	  16758	  0.47%
 40	  24066	  0.67%
 41	  31282	  0.87%
 42	  36086	  1.00%
 43	  26197	  0.73%
 44	  20924	  0.58%
 45	  33965	  0.95%
 46	  24850	  0.69%
 47	  18037	  0.50%
 48	   4085	  0.11%
 49	  12436	  0.35%
 50	 337022	  9.38%


criterion=sequence-density
sequence-density=6.02
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.46
sequence-density-rank=34
fanout-score=23.62
fanout-score-rank=1
prefix-density=10.78
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 06:51:18
                             Started mapping on |	Mar 04 06:51:19
                                    Finished on |	Mar 04 06:51:43
       Mapping speed, Million of reads per hour |	553.30

                          Number of input reads |	3688678
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2284251
                        Uniquely mapped reads % |	61.93%
                          Average mapped length |	25.97
                       Number of splices: Total |	2080
            Number of splices: Annotated (sjdb) |	319
                       Number of splices: GT/AG |	1961
                       Number of splices: GC/AG |	33
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	86
                      Mismatch rate per base, % |	0.17%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.67
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1010969
             % of reads mapped to multiple loci |	27.41%
        Number of reads mapped to too many loci |	65013
             % of reads mapped to too many loci |	1.76%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.18%
                     % of reads unmapped: other |	0.73%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	393458	393458	393458
N_multimapping	1010969	1010969	1010969
N_noFeature	89426	111156	1453914
N_ambiguous	1309820	564243	20532
UnstrandedReadsAssigned:885005 PositiveStrandReadsAssigned:1608852 NegativeStrandReadsAssigned:809805
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030943 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: SRR5030943-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,688,678 reads, 1,076,232 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,135 rounds

 109283 SRR5030943.ke.tsv
  52636 SRR5030943.se.tsv
 161919 total
==> SRR5030943.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

==> SRR5030943.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030943 completed mapping pipeline successfully
