Starting /dee2/code/volunteer_pipeline.sh SRR5030871
    current disk space = 160663027712
    free memory = 56715092 
SRR5030871 SRAfilesize
6f9ab151d447596b1307de12a94b230f  SRR5030871.sra
SRR5030871.sra file validated
SRR5030871 is single end
SRR5030871 is conventional basespace
SRR5030871 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030871_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.43125	34.0	31.0	34.0	31.0	34.0
2	32.703	34.0	31.0	34.0	31.0	34.0
3	32.75625	34.0	31.0	34.0	31.0	34.0
4	36.27675	37.0	37.0	37.0	35.0	37.0
5	36.2905	37.0	37.0	37.0	35.0	37.0
6	36.184	37.0	37.0	37.0	35.0	37.0
7	36.12075	37.0	36.0	37.0	35.0	37.0
8	36.19375	37.0	36.0	37.0	35.0	37.0
9	37.9925	39.0	38.0	39.0	35.0	39.0
10	37.932	39.0	38.0	39.0	35.0	39.0
11	37.834	39.0	38.0	39.0	35.0	39.0
12	37.78275	39.0	38.0	39.0	35.0	39.0
13	37.8335	39.0	38.0	39.0	35.0	39.0
14	39.07025	40.0	39.0	41.0	36.0	41.0
15	39.16425	41.0	39.0	41.0	36.0	41.0
16	39.13675	40.0	39.0	41.0	36.0	41.0
17	39.14425	40.0	39.0	41.0	36.0	41.0
18	39.339	41.0	39.0	41.0	36.0	41.0
19	39.3995	41.0	39.0	41.0	36.0	41.0
20	39.16	41.0	39.0	41.0	36.0	41.0
21	39.11425	41.0	39.0	41.0	36.0	41.0
22	39.2075	41.0	39.0	41.0	36.0	41.0
23	39.28425	41.0	39.0	41.0	36.0	41.0
24	38.55675	40.0	38.0	41.0	34.0	41.0
25	38.701	40.0	38.0	41.0	34.0	41.0
26	38.907	41.0	38.0	41.0	35.0	41.0
27	39.05925	41.0	39.0	41.0	35.0	41.0
28	38.69575	40.0	38.0	41.0	34.0	41.0
29	38.027	40.0	38.0	41.0	32.0	41.0
30	38.2525	40.0	38.0	41.0	33.0	41.0
31	38.77875	40.0	38.0	41.0	35.0	41.0
32	38.76625	40.0	38.0	41.0	35.0	41.0
33	37.388	40.0	37.0	41.0	31.0	41.0
34	37.663	40.0	37.0	41.0	31.0	41.0
35	37.59825	40.0	37.0	41.0	32.0	41.0
36	33.77425	38.0	30.0	40.0	21.0	41.0
37	35.856	38.0	34.0	40.0	30.0	41.0
38	37.23025	39.0	37.0	40.0	32.0	41.0
39	37.245	39.0	37.0	40.0	32.0	41.0
40	37.19725	39.0	37.0	40.0	32.0	41.0
41	36.9835	39.0	36.0	40.0	31.0	41.0
42	36.933	39.0	36.0	40.0	31.0	41.0
43	37.081	39.0	37.0	41.0	31.0	41.0
44	37.12125	39.0	37.0	41.0	32.0	41.0
45	36.97575	39.0	36.0	41.0	32.0	41.0
46	34.53975	38.0	33.0	40.0	24.0	41.0
47	35.42575	38.0	35.0	40.0	28.0	41.0
48	35.53175	39.0	35.0	40.0	29.0	41.0
49	34.7305	38.0	34.0	40.0	27.0	41.0
50	30.983	34.0	29.0	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	3.0
19	4.0
20	4.0
21	7.0
22	6.0
23	7.0
24	12.0
25	17.0
26	10.0
27	29.0
28	36.0
29	45.0
30	59.0
31	77.0
32	84.0
33	118.0
34	152.0
35	199.0
36	305.0
37	471.0
38	1111.0
39	1241.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.506265664160402	21.503759398496243	47.092731829573935	18.897243107769423
2	22.7	23.3	20.875	33.125
3	23.23080770192548	20.305076269067268	19.754938734683673	36.70917729432358
4	31.574999999999996	25.224999999999998	15.7	27.500000000000004
5	20.95	41.625	23.150000000000002	14.274999999999999
6	34.125	15.675	32.775	17.424999999999997
7	18.75	21.525	24.875	34.849999999999994
8	25.825	27.525	18.25	28.4
9	22.8	32.1	27.700000000000003	17.4
10	23.175	21.975	31.175000000000004	23.674999999999997
11	29.2	14.499999999999998	16.150000000000002	40.150000000000006
12	16.1	22.400000000000002	29.175	32.324999999999996
13	28.175	21.175	31.324999999999996	19.325
14	24.95	32.300000000000004	20.974999999999998	21.775
15	33.85	27.025	23.849999999999998	15.275
16	21.75	25.224999999999998	20.575	32.45
17	21.825	25.85	38.15	14.174999999999999
18	20.849999999999998	19.875	30.525000000000002	28.749999999999996
19	39.925	14.174999999999999	26.85	19.05
20	38.95	15.75	30.9	14.399999999999999
21	26.3	17.75	24.85	31.1
22	27.450000000000003	14.325	44.574999999999996	13.65
23	26.375	14.05	39.550000000000004	20.025000000000002
24	50.5	15.825	22.825	10.85
25	44.2	25.15	15.45	15.2
26	25.224999999999998	42.025	15.425	17.325
27	18.125	42.275	22.400000000000002	17.2
28	14.95	22.3	43.475	19.275000000000002
29	14.625	15.275	51.324999999999996	18.775
30	11.475	9.950000000000001	30.725	47.85
31	15.8	8.125	47.575	28.499999999999996
32	29.425	9.25	20.075000000000003	41.25
33	49.05	15.65	14.625	20.674999999999997
34	52.449999999999996	11.200000000000001	19.45	16.900000000000002
35	58.5	9.15	19.0	13.350000000000001
36	41.949999999999996	9.475	33.475	15.1
37	43.45	14.099999999999998	19.475	22.975
38	22.25	19.475	15.125	43.15
39	17.525	22.975	14.75	44.75
40	16.950000000000003	42.699999999999996	17.525	22.825
41	23.724999999999998	42.925000000000004	13.700000000000001	19.650000000000002
42	45.75	25.825	17.75	10.674999999999999
43	46.425	27.325	13.100000000000001	13.15
44	31.25	44.375	11.475	12.9
45	22.5	47.575	13.775	16.150000000000002
46	17.375	26.525	18.6	37.5
47	12.475	16.775000000000002	40.9	29.849999999999998
48	15.728932233058265	12.628157039259817	20.130032508127034	51.51287821955489
49	16.1	18.275	17.4	48.225
50	18.45	34.075	16.525000000000002	30.95
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.5
4	1.0
5	0.5
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	3.0
28	5.0
29	3.5
30	2.0
31	13.5
32	25.0
33	26.0
34	27.0
35	34.5
36	42.0
37	51.5
38	61.0
39	70.5
40	80.0
41	70.0
42	60.0
43	91.5
44	123.0
45	178.0
46	233.0
47	309.5
48	386.0
49	484.0
50	582.0
51	663.0
52	744.0
53	596.0
54	448.0
55	458.5
56	469.0
57	368.0
58	267.0
59	172.5
60	78.0
61	63.0
62	48.0
63	118.0
64	188.0
65	116.5
66	45.0
67	31.5
68	18.0
69	17.0
70	16.0
71	18.5
72	21.0
73	12.5
74	4.0
75	4.0
76	4.0
77	4.5
78	5.0
79	8.0
80	11.0
81	8.0
82	5.0
83	2.5
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	0.25
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	0.0
>>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	76.22504537205081	31.5
2	9.195402298850574	7.6
3	4.11373260738052	5.1
4	2.722323049001815	4.5
5	1.572897761645493	3.25
6	1.4519056261343013	3.5999999999999996
7	0.48396854204476714	1.4000000000000001
8	0.7259528130671506	2.4
9	0.3629764065335753	1.35
>10	2.722323049001815	22.95
>50	0.3024803387779794	9.75
>100	0.12099213551119178	6.6000000000000005
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	140	3.5000000000000004	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	124	3.1	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	94	2.35	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	71	1.775	RNA PCR Primer, Index 1 (100% over 30bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	54	1.35	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	50	1.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	43	1.075	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	38	0.95	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	37	0.9249999999999999	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	35	0.8750000000000001	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTC	32	0.8	RNA PCR Primer, Index 12 (100% over 44bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	21	0.525	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	18	0.44999999999999996	RNA PCR Primer, Index 1 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	17	0.42500000000000004	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	16	0.4	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	16	0.4	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	13	0.325	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	13	0.325	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	12	0.3	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	12	0.3	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	11	0.27499999999999997	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCT	11	0.27499999999999997	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	10	0.25	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 12 (100% over 50bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	9	0.22499999999999998	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	8	0.2	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	8	0.2	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	7	0.17500000000000002	No Hit
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	7	0.17500000000000002	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGAAGAAAGGT	7	0.17500000000000002	No Hit
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTGGAATTCTCGGGTGC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	6	0.15	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	6	0.15	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTG	5	0.125	RNA PCR Primer, Index 12 (100% over 37bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGCAACTCTGTGCTGAATGT	5	0.125	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	5	0.125	No Hit
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
GCGTTGGTGGTATAGTGGTGAGCATAGCTGCCTTCCAAGCAGTTGACCCG	5	0.125	No Hit
TTTCTATGATGAATCAAACTAGCTCACTATGACTGCTAATGAAAACACAG	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
GATACCCGTCGCCGCGCTCTCCCTCTCCCCCCGTCCGCCTCCCGGGCGGG	5	0.125	No Hit
AGTAATGATGATTTCTGGTGATTCTGAGTGTCTCGCTGACGCCATCACCG	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	0.375	0.0	0.0	0.0
4	0.0	0.45	0.0	0.0	0.0
5	0.0	0.5	0.0	0.0	0.0
6	0.0	0.575	0.0	0.0	0.0
7	0.0	1.6	0.0	0.0	0.0
8	0.0	1.775	0.0	0.0	0.0
9	0.0	1.825	0.0	0.0	0.0
10	0.0	1.925	0.0	0.0	0.0
11	0.0	2.125	0.0	0.0	0.0
12	0.0	2.35	0.0	0.0	0.0
13	0.0	2.65	0.0	0.0	0.0
14	0.0	3.075	0.0	0.0	0.0
15	0.0	3.4	0.0	0.0	0.0
16	0.0	4.2	0.0	0.0	0.0
17	0.0	4.525	0.0	0.0	0.0
18	0.0	5.35	0.0	0.0	0.0
19	0.0	5.9	0.0	0.0	0.0
20	0.0	6.45	0.0	0.0	0.0
21	0.0	10.975	0.0	0.0	0.0
22	0.0	20.0	0.0	0.0	0.0
23	0.0	45.55	0.0	0.0	0.0
24	0.0	54.85	0.0	0.0	0.0
25	0.0	59.875	0.0	0.0	0.0
26	0.0	61.275	0.0	0.0	0.0
27	0.0	61.95	0.0	0.0	0.0
28	0.0	62.325	0.0	0.0	0.0
29	0.0	62.9	0.0	0.0	0.0
30	0.0	63.225	0.0	0.0	0.0
31	0.0	63.875	0.0	0.0	0.0
32	0.0	64.775	0.0	0.0	0.0
33	0.0	65.875	0.0	0.0	0.0
34	0.0	71.025	0.0	0.0	0.0
35	0.0	72.375	0.0	0.0	0.0
36	0.0	73.4	0.0	0.0	0.0
37	0.0	74.4	0.0	0.0	0.0
38	0.0	75.125	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AAGTAAT	45	2.728484E-10	44.000004	4
TCAAGTA	45	2.728484E-10	44.000004	2
AATCCAG	45	2.728484E-10	44.000004	8
ATCCAGG	45	2.728484E-10	44.000004	9
TTCAAGT	45	2.728484E-10	44.000004	1
AGGATAG	45	2.728484E-10	44.000004	13
CTCTTTT	20	6.952051E-4	44.000004	16
ATAGGCT	45	2.728484E-10	44.000004	16
TCCAGGA	45	2.728484E-10	44.000004	10
GGATAGG	45	2.728484E-10	44.000004	14
CTTGGCT	20	6.952051E-4	44.000004	16
AGTAATC	45	2.728484E-10	44.000004	5
TAATCCA	45	2.728484E-10	44.000004	7
GCTTGGC	20	6.952051E-4	44.000004	15
TTGGCTT	20	6.952051E-4	44.000004	17
CAGGATA	45	2.728484E-10	44.000004	12
GTAATCC	45	2.728484E-10	44.000004	6
GATAGGC	45	2.728484E-10	44.000004	15
TGGCTTG	20	6.952051E-4	44.000004	18
CCAGGAT	45	2.728484E-10	44.000004	11
>>END_MODULE
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240619 spots for SRR5030871.sra
Written 240619 spots for SRR5030871.sra
Read 240628 spots for SRR5030871.sra
Written 240628 spots for SRR5030871.sra
SRR ids: ['SRR5030871.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_eb80l42f
SRR5030871.sra spots: 2887437
blocks: [[1, 240619], [240620, 481238], [481239, 721857], [721858, 962476], [962477, 1203095], [1203096, 1443714], [1443715, 1684333], [1684334, 1924952], [1924953, 2165571], [2165572, 2406190], [2406191, 2646809], [2646810, 2887437]]
SRR5030871 file size 499377
SRR5030871 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030871 SRR5030871_1.fastq
Input file:	SRR5030871_1.fastq
trimmed:	SRR5030871-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 06:32:58 2020 >> started

Wed Mar  4 06:32:59 2020 >> done (1.788s)
2887437 reads processed; of these:
    161 ( 0.01%) short reads filtered out after trimming by size control
     11 ( 0.00%) empty reads filtered out after trimming by size control
2887265 (99.99%) reads available; of these:
 214628 ( 7.43%) trimmed reads available after processing
2672637 (92.57%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     40	  0.00%
 19	     52	  0.00%
 20	    141	  0.00%
 21	    168	  0.01%
 22	    260	  0.01%
 23	    334	  0.01%
 24	    404	  0.01%
 25	    505	  0.02%
 26	    421	  0.01%
 27	    535	  0.02%
 28	    661	  0.02%
 29	    874	  0.03%
 30	    771	  0.03%
 31	   1006	  0.03%
 32	   1304	  0.05%
 33	   2241	  0.08%
 34	   7174	  0.25%
 35	   3441	  0.12%
 36	   2375	  0.08%
 37	   2915	  0.10%
 38	   3673	  0.13%
 39	   3571	  0.12%
 40	   5147	  0.18%
 41	   4335	  0.15%
 42	   6417	  0.22%
 43	   5844	  0.20%
 44	  14909	  0.52%
 45	  15420	  0.53%
 46	  14830	  0.51%
 47	  17724	  0.61%
 48	  40461	  1.40%
 49	  56675	  1.96%
 50	2672637	 92.57%
2887265 reads passed initial QC


criterion=sequence-density
sequence-density=75.42
sequence-density-rank=1
fanout-score=19.33
fanout-score-rank=2
prefix-density=77.98
prefix-fanout=18.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC


criterion=fanout-score
sequence-density=1.67
sequence-density-rank=5
fanout-score=144.67
fanout-score-rank=1
prefix-density=77.61
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 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC -o SRR5030871 -
Input file:	STDIN
trimmed:	SRR5030871-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC
-- 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 06:33:14 2020 >> started

Wed Mar  4 06:33:19 2020 >> done (4.353s)
2811284 reads processed; of these:
 145630 ( 5.18%) short reads filtered out after trimming by size control
  12330 ( 0.44%) empty reads filtered out after trimming by size control
2653324 (94.38%) reads available; of these:
2274939 (85.74%) trimmed reads available after processing
 378385 (14.26%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13742	  0.52%
 19	  21618	  0.81%
 20	 126970	  4.79%
 21	 270158	 10.18%
 22	 735683	 27.73%
 23	 278468	 10.50%
 24	 139378	  5.25%
 25	  41065	  1.55%
 26	  20623	  0.78%
 27	  16160	  0.61%
 28	  17051	  0.64%
 29	  14357	  0.54%
 30	  19929	  0.75%
 31	  26930	  1.01%
 32	  27867	  1.05%
 33	 129906	  4.90%
 34	  36807	  1.39%
 35	  29562	  1.11%
 36	  35310	  1.33%
 37	  17203	  0.65%
 38	  18360	  0.69%
 39	  19817	  0.75%
 40	  28383	  1.07%
 41	  35657	  1.34%
 42	  43443	  1.64%
 43	  29738	  1.12%
 44	  27489	  1.04%
 45	  31973	  1.21%
 46	  25211	  0.95%
 47	  23723	  0.89%
 48	   4784	  0.18%
 49	  13869	  0.52%
 50	 332090	 12.52%


criterion=sequence-density
sequence-density=5.68
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=12
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=35
fanout-score=48.61
fanout-score-rank=1
prefix-density=0.75
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:33:40
                             Started mapping on |	Mar 04 06:33:40
                                    Finished on |	Mar 04 06:34:04
       Mapping speed, Million of reads per hour |	409.40

                          Number of input reads |	2729305
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1545226
                        Uniquely mapped reads % |	56.62%
                          Average mapped length |	28.81
                       Number of splices: Total |	1128
            Number of splices: Annotated (sjdb) |	272
                       Number of splices: GT/AG |	1004
                       Number of splices: GC/AG |	19
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	104
                      Mismatch rate per base, % |	0.25%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.34
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	764116
             % of reads mapped to multiple loci |	28.00%
        Number of reads mapped to too many loci |	85725
             % of reads mapped to too many loci |	3.14%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.70%
                     % of reads unmapped: other |	0.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	419963	419963	419963
N_multimapping	764116	764116	764116
N_noFeature	81335	102915	1114425
N_ambiguous	857120	495519	20342
UnstrandedReadsAssigned:606771 PositiveStrandReadsAssigned:946792 NegativeStrandReadsAssigned:410459
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030871 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: SRR5030871-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,729,305 reads, 730,998 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,170 rounds

 109283 SRR5030871.ke.tsv
  52636 SRR5030871.se.tsv
 161919 total
==> SRR5030871.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

==> SRR5030871.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030871 completed mapping pipeline successfully
