Starting /dee2/code/volunteer_pipeline.sh SRR5031081
    current disk space = 160501088256
    free memory = 56706172 
SRR5031081 SRAfilesize
f359de95aec1aa352e3eb59c3175cf45  SRR5031081.sra
SRR5031081.sra file validated
SRR5031081 is single end
SRR5031081 is conventional basespace
SRR5031081 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031081_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.864	31.0	31.0	34.0	30.0	34.0
2	32.385	33.0	31.0	34.0	31.0	34.0
3	32.40375	33.0	31.0	34.0	31.0	34.0
4	36.116	37.0	35.0	37.0	35.0	37.0
5	36.028	37.0	35.0	37.0	35.0	37.0
6	36.00225	37.0	35.0	37.0	35.0	37.0
7	35.769	37.0	35.0	37.0	35.0	37.0
8	35.63475	37.0	35.0	37.0	33.0	37.0
9	36.88125	39.0	37.0	39.0	33.0	39.0
10	36.35	39.0	35.0	39.0	32.0	39.0
11	37.327	39.0	37.0	39.0	34.0	39.0
12	37.67575	39.0	37.0	39.0	35.0	39.0
13	37.539	39.0	37.0	39.0	35.0	39.0
14	38.32275	40.0	38.0	41.0	33.0	41.0
15	36.43575	39.0	36.0	41.0	27.0	41.0
16	36.80325	38.0	36.0	40.0	31.0	41.0
17	36.9295	39.0	36.0	40.0	32.0	41.0
18	38.16125	39.0	37.0	41.0	34.0	41.0
19	38.75075	40.0	38.0	41.0	36.0	41.0
20	38.3865	40.0	38.0	41.0	34.0	41.0
21	38.48725	40.0	38.0	41.0	34.0	41.0
22	37.1645	39.0	37.0	40.0	31.0	41.0
23	38.02075	39.0	37.0	40.0	34.0	41.0
24	37.22275	39.0	37.0	40.0	31.0	41.0
25	38.09325	40.0	37.0	41.0	34.0	41.0
26	37.9505	40.0	38.0	41.0	33.0	41.0
27	38.24925	40.0	38.0	41.0	34.0	41.0
28	38.49125	40.0	38.0	41.0	34.0	41.0
29	38.347	40.0	38.0	41.0	34.0	41.0
30	38.78625	40.0	38.0	41.0	35.0	41.0
31	38.85675	40.0	38.0	41.0	35.0	41.0
32	38.9425	40.0	39.0	41.0	35.0	41.0
33	38.95675	40.0	39.0	41.0	35.0	41.0
34	38.1895	40.0	38.0	41.0	33.0	41.0
35	37.36775	40.0	36.0	41.0	30.0	41.0
36	32.5	35.0	30.0	39.0	21.0	41.0
37	34.7155	37.0	32.0	39.0	30.0	40.0
38	36.188	38.0	35.0	39.0	31.0	40.0
39	36.5295	38.0	36.0	40.0	31.0	40.0
40	37.0575	39.0	37.0	40.0	32.0	41.0
41	37.45625	40.0	37.0	40.0	33.0	41.0
42	37.3615	40.0	37.0	41.0	32.0	41.0
43	37.30175	40.0	37.0	41.0	32.0	41.0
44	36.2475	38.0	35.0	40.0	30.0	41.0
45	36.383	39.0	35.0	40.0	30.0	41.0
46	36.63975	39.0	36.0	40.0	30.0	41.0
47	35.634	38.0	34.0	40.0	28.0	41.0
48	36.797	39.0	36.0	40.0	31.0	41.0
49	36.88075	40.0	37.0	41.0	31.0	41.0
50	34.80325	38.0	34.0	40.0	28.0	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
10	1.0
11	0.0
12	2.0
13	2.0
14	3.0
15	0.0
16	2.0
17	1.0
18	1.0
19	3.0
20	3.0
21	7.0
22	10.0
23	2.0
24	9.0
25	10.0
26	11.0
27	20.0
28	17.0
29	31.0
30	44.0
31	68.0
32	88.0
33	135.0
34	190.0
35	304.0
36	470.0
37	792.0
38	1177.0
39	597.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.3797848386289715	25.619214410808105	54.315736802601954	13.685263947960971
2	22.942206654991242	26.1195896922692	17.137853390042533	33.80035026269702
3	27.55	18.725	17.724999999999998	36.0
4	34.125	27.325	12.6	25.95
5	22.1	41.125	25.874999999999996	10.9
6	34.525	12.725	38.574999999999996	14.174999999999999
7	11.975	23.525	22.7	41.8
8	25.900000000000002	28.575	13.425	32.1
9	25.025	33.825	28.225	12.925
10	19.075	20.5	31.75	28.675
11	31.0	8.674999999999999	16.45	43.875
12	14.374999999999998	14.649999999999999	34.8	36.175000000000004
13	32.7	16.625	32.65	18.025
14	30.475	34.375	19.8	15.35
15	39.1	17.7	24.474999999999998	18.725
16	18.95	18.9	21.099999999999998	41.05
17	24.2	20.375	40.0	15.425
18	22.675	17.375	33.25	26.700000000000003
19	41.825	13.100000000000001	27.675	17.4
20	50.4	10.95	27.025	11.625
21	22.225	17.974999999999998	28.799999999999997	31.0
22	27.325	9.15	52.449999999999996	11.075
23	28.475	10.075000000000001	48.775	12.675
24	56.599999999999994	10.8	24.3	8.3
25	54.25	26.224999999999998	13.375	6.15
26	26.724999999999998	51.949999999999996	12.950000000000001	8.375
27	14.025000000000002	52.2	24.925	8.85
28	8.7	24.275	53.349999999999994	13.675
29	8.9	9.950000000000001	60.675000000000004	20.474999999999998
30	6.825	4.8500000000000005	38.75	49.575
31	12.475	3.65	50.2	33.675
32	28.749999999999996	3.6999999999999997	19.8	47.75
33	60.199999999999996	6.7250000000000005	11.35	21.725
34	67.875	5.7250000000000005	14.2	12.2
35	70.3	4.9750000000000005	17.5	7.225
36	45.9	5.1499999999999995	37.724999999999994	11.225
37	49.45	7.7	18.425	24.425
38	21.875	14.799999999999999	10.45	52.87500000000001
39	13.0	25.3	7.95	53.75
40	13.200000000000001	54.275	7.375	25.15
41	24.975	53.625	5.925	15.475
42	53.65	30.55	8.15	7.6499999999999995
43	54.55	31.424999999999997	5.625	8.4
44	28.875	54.2	5.125	11.799999999999999
45	16.85	54.225	10.299999999999999	18.625
46	9.75	25.2	18.075	46.975
47	5.875	13.625000000000002	41.85	38.65
48	8.200000000000001	12.3	18.35	61.150000000000006
49	11.625	19.375	11.475	57.525000000000006
50	18.375	39.574999999999996	11.175	30.875000000000004
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.5
10	1.0
11	0.5
12	0.0
13	0.0
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	1.0
32	2.0
33	6.0
34	10.0
35	11.0
36	12.0
37	10.5
38	9.0
39	11.0
40	13.0
41	14.0
42	15.0
43	48.0
44	81.0
45	114.5
46	148.0
47	272.0
48	396.0
49	478.5
50	561.0
51	742.0
52	923.0
53	729.0
54	535.0
55	569.0
56	603.0
57	468.5
58	334.0
59	225.5
60	117.0
61	82.5
62	48.0
63	72.0
64	96.0
65	67.5
66	39.0
67	28.0
68	17.0
69	16.0
70	15.0
71	17.0
72	19.0
73	11.0
74	3.0
75	2.5
76	2.0
77	1.5
78	1.0
79	0.5
80	0.0
81	0.0
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	0.075
2	0.075
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	39.225
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.2906309751434	29.925
2	9.432759719566603	7.3999999999999995
3	4.461440407903123	5.25
4	2.2307202039515617	3.5000000000000004
5	1.8483110261312936	3.6249999999999996
6	0.5736137667304015	1.35
7	0.82855321861058	2.275
8	0.5098789037603569	1.6
9	0.19120458891013384	0.675
>10	2.995538559592097	20.674999999999997
>50	0.3824091778202677	9.950000000000001
>100	0.25493945188017847	13.775
>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	168	4.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	168	4.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	109	2.725	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	106	2.65	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	92	2.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	80	2.0	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	60	1.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	55	1.375	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	53	1.325	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	28	0.7000000000000001	RNA PCR Primer, Index 5 (100% over 35bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	26	0.65	RNA PCR Primer, Index 1 (96% over 30bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTC	15	0.375	RNA PCR Primer, Index 5 (100% over 44bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGC	14	0.35000000000000003	RNA PCR Primer, Index 5 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	13	0.325	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGACCCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTACCTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGACTCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGCCCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGACGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	10	0.25	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	8	0.2	No Hit
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	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)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCCTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTCGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATAAAGCTAGATAACCGAAAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTCGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGT	5	0.125	RNA PCR Primer, Index 5 (100% over 38bp)
CGCGACCTCAGATCAGCCGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	5	0.125	No Hit
AACCCGTAGATCCGCACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGCCCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTACCTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>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	0.5	0.0	0.0	0.0
2	0.0	0.525	0.0	0.0	0.0
3	0.0	0.6	0.0	0.0	0.0
4	0.0	0.625	0.0	0.0	0.0
5	0.0	0.7	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	1.475	0.0	0.0	0.0
9	0.0	1.525	0.0	0.0	0.0
10	0.0	1.65	0.0	0.0	0.0
11	0.0	1.725	0.0	0.0	0.0
12	0.0	1.85	0.0	0.0	0.0
13	0.0	2.125	0.0	0.0	0.0
14	0.0	2.325	0.0	0.0	0.0
15	0.0	2.575	0.0	0.0	0.0
16	0.0	3.5	0.0	0.0	0.0
17	0.0	4.15	0.0	0.0	0.0
18	0.0	4.95	0.0	0.0	0.0
19	0.0	5.175	0.0	0.0	0.0
20	0.0	5.95	0.0	0.0	0.0
21	0.0	11.05	0.0	0.0	0.0
22	0.0	24.925	0.0	0.0	0.0
23	0.0	59.925	0.0	0.0	0.0
24	0.0	73.975	0.0	0.0	0.0
25	0.0	79.8	0.0	0.0	0.0
26	0.0	81.3	0.0	0.0	0.0
27	0.0	81.85	0.0	0.0	0.0
28	0.0	82.25	0.0	0.0	0.0
29	0.0	82.7	0.0	0.0	0.0
30	0.0	83.125	0.0	0.0	0.0
31	0.0	83.775	0.0	0.0	0.0
32	0.0	84.15	0.0	0.0	0.0
33	0.0	84.85	0.0	0.0	0.0
34	0.0	87.7	0.0	0.0	0.0
35	0.0	88.525	0.0	0.0	0.0
36	0.0	89.175	0.0	0.0	0.0
37	0.0	89.925	0.0	0.0	0.0
38	0.0	90.225	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCTCG	20	6.952051E-4	44.000004	8
AACGCTG	40	5.315087E-9	44.000004	8
ACGCTGT	40	5.315087E-9	44.000004	9
TTCAACG	40	5.315087E-9	44.000004	5
CATCCTC	20	6.952051E-4	44.000004	7
TCGGTGA	40	5.315087E-9	44.000004	15
CATTCAA	40	5.315087E-9	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
ACATCCT	20	6.952051E-4	44.000004	6
ACATTCA	45	2.728484E-10	44.000004	2
GCTGTCG	45	2.728484E-10	44.000004	11
GACTGGA	20	6.952051E-4	44.000004	14
CTGTCGG	45	2.728484E-10	44.000004	12
TGGTGGA	20	6.952051E-4	44.000004	18
ACTGGAA	20	6.952051E-4	44.000004	15
ATTCAAC	40	5.315087E-9	44.000004	4
CGACTGG	20	6.952051E-4	44.000004	13
GTCGGTG	45	2.728484E-10	44.000004	14
AACATTC	45	2.728484E-10	44.000004	1
TGTCGGT	45	2.728484E-10	44.000004	13
>>END_MODULE
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111474 spots for SRR5031081.sra
Written 111474 spots for SRR5031081.sra
Read 111480 spots for SRR5031081.sra
Written 111480 spots for SRR5031081.sra
SRR ids: ['SRR5031081.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_yjmf6d3w
SRR5031081.sra spots: 1337694
blocks: [[1, 111474], [111475, 222948], [222949, 334422], [334423, 445896], [445897, 557370], [557371, 668844], [668845, 780318], [780319, 891792], [891793, 1003266], [1003267, 1114740], [1114741, 1226214], [1226215, 1337694]]
SRR5031081 file size 230788
SRR5031081 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031081 SRR5031081_1.fastq
Input file:	SRR5031081_1.fastq
trimmed:	SRR5031081-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 07:19:57 2020 >> started

Wed Mar  4 07:19:58 2020 >> done (1.037s)
1337694 reads processed; of these:
     78 ( 0.01%) short reads filtered out after trimming by size control
      3 ( 0.00%) empty reads filtered out after trimming by size control
1337613 (99.99%) reads available; of these:
 118095 ( 8.83%) trimmed reads available after processing
1219518 (91.17%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     29	  0.00%
 19	     44	  0.00%
 20	     68	  0.01%
 21	     98	  0.01%
 22	    173	  0.01%
 23	    230	  0.02%
 24	    222	  0.02%
 25	    322	  0.02%
 26	    226	  0.02%
 27	    304	  0.02%
 28	    313	  0.02%
 29	    514	  0.04%
 30	    313	  0.02%
 31	    403	  0.03%
 32	    564	  0.04%
 33	   1073	  0.08%
 34	   1540	  0.12%
 35	   4262	  0.32%
 36	   2210	  0.17%
 37	   2081	  0.16%
 38	   1833	  0.14%
 39	   1950	  0.15%
 40	   2300	  0.17%
 41	   2718	  0.20%
 42	   3300	  0.25%
 43	   5737	  0.43%
 44	   5756	  0.43%
 45	   7992	  0.60%
 46	  11083	  0.83%
 47	   8506	  0.64%
 48	  26000	  1.94%
 49	  25931	  1.94%
 50	1219518	 91.17%
1337613 reads passed initial QC


criterion=sequence-density
sequence-density=91.10
sequence-density-rank=1
fanout-score=18.10
fanout-score-rank=2
prefix-density=92.32
prefix-fanout=17.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC


criterion=fanout-score
sequence-density=4.02
sequence-density-rank=4
fanout-score=65.58
fanout-score-rank=1
prefix-density=92.17
prefix-fanout=2.9
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC -o SRR5031081 -
Input file:	STDIN
trimmed:	SRR5031081-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC
-- 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 07:20:08 2020 >> started

Wed Mar  4 07:20:10 2020 >> done (2.094s)
1308535 reads processed; of these:
  71106 ( 5.43%) short reads filtered out after trimming by size control
   6475 ( 0.49%) empty reads filtered out after trimming by size control
1230954 (94.07%) reads available; of these:
1197307 (97.27%) trimmed reads available after processing
  33647 ( 2.73%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   6618	  0.54%
 19	  13119	  1.07%
 20	  79330	  6.44%
 21	 170312	 13.84%
 22	 463190	 37.63%
 23	 192898	 15.67%
 24	  82942	  6.74%
 25	  21355	  1.73%
 26	   9645	  0.78%
 27	   7813	  0.63%
 28	   7951	  0.65%
 29	   5523	  0.45%
 30	   8010	  0.65%
 31	   8889	  0.72%
 32	   9764	  0.79%
 33	  39758	  3.23%
 34	  10740	  0.87%
 35	   7661	  0.62%
 36	   9155	  0.74%
 37	   4141	  0.34%
 38	   4035	  0.33%
 39	   3852	  0.31%
 40	   5509	  0.45%
 41	   6569	  0.53%
 42	   6842	  0.56%
 43	   4707	  0.38%
 44	   3489	  0.28%
 45	   4044	  0.33%
 46	   2838	  0.23%
 47	   2243	  0.18%
 48	    458	  0.04%
 49	    748	  0.06%
 50	  26806	  2.18%


criterion=sequence-density
sequence-density=7.57
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=10
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=0.45
sequence-density-rank=31
fanout-score=30.45
fanout-score-rank=1
prefix-density=13.61
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:20:28
                             Started mapping on |	Mar 04 07:20:29
                                    Finished on |	Mar 04 07:20:55
       Mapping speed, Million of reads per hour |	174.47

                          Number of input reads |	1260032
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	685002
                        Uniquely mapped reads % |	54.36%
                          Average mapped length |	23.42
                       Number of splices: Total |	2632
            Number of splices: Annotated (sjdb) |	845
                       Number of splices: GT/AG |	2594
                       Number of splices: GC/AG |	24
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	12
                      Mismatch rate per base, % |	0.31%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.59
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.18
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	456936
             % of reads mapped to multiple loci |	36.26%
        Number of reads mapped to too many loci |	17336
             % of reads mapped to too many loci |	1.38%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.61%
                     % of reads unmapped: other |	0.39%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	118094	118094	118094
N_multimapping	456936	456936	456936
N_noFeature	31602	37041	442099
N_ambiguous	410157	195684	3865
UnstrandedReadsAssigned:243243 PositiveStrandReadsAssigned:452277 NegativeStrandReadsAssigned:239038
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031081 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: SRR5031081-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,260,032 reads, 356,725 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,054 rounds

 109283 SRR5031081.ke.tsv
  52636 SRR5031081.se.tsv
 161919 total
==> SRR5031081.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

==> SRR5031081.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031081 completed mapping pipeline successfully
