Starting /dee2/code/volunteer_pipeline.sh SRR5030893
    current disk space = 160665681920
    free memory = 73936332 
SRR5030893 SRAfilesize
4c227e3e270adf15e858adfc7561c520  SRR5030893.sra
SRR5030893.sra file validated
SRR5030893 is single end
SRR5030893 is conventional basespace
SRR5030893 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030893_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	32.532	34.0	31.0	34.0	31.0	34.0
2	32.84425	34.0	31.0	34.0	31.0	34.0
3	32.86275	34.0	31.0	34.0	31.0	34.0
4	36.32575	37.0	37.0	37.0	35.0	37.0
5	36.35725	37.0	37.0	37.0	35.0	37.0
6	36.185	37.0	36.0	37.0	35.0	37.0
7	36.1505	37.0	35.0	37.0	35.0	37.0
8	36.256	37.0	37.0	37.0	35.0	37.0
9	38.0675	39.0	38.0	39.0	35.0	39.0
10	37.99175	39.0	38.0	39.0	35.0	39.0
11	37.99825	39.0	38.0	39.0	35.0	39.0
12	37.899	39.0	38.0	39.0	35.0	39.0
13	37.88125	39.0	38.0	39.0	35.0	39.0
14	39.3305	41.0	39.0	41.0	36.0	41.0
15	39.24075	41.0	39.0	41.0	36.0	41.0
16	39.26725	41.0	39.0	41.0	36.0	41.0
17	39.24575	41.0	39.0	41.0	36.0	41.0
18	39.4055	41.0	39.0	41.0	36.0	41.0
19	39.455	41.0	39.0	41.0	37.0	41.0
20	39.34625	41.0	39.0	41.0	36.0	41.0
21	39.32	41.0	39.0	41.0	36.0	41.0
22	39.47775	41.0	39.0	41.0	36.0	41.0
23	39.46175	41.0	39.0	41.0	37.0	41.0
24	38.6215	40.0	38.0	41.0	34.0	41.0
25	38.9265	41.0	39.0	41.0	35.0	41.0
26	39.10975	41.0	39.0	41.0	36.0	41.0
27	39.1435	41.0	39.0	41.0	36.0	41.0
28	38.80325	40.0	38.0	41.0	35.0	41.0
29	38.405	40.0	38.0	41.0	33.0	41.0
30	38.44075	40.0	38.0	41.0	34.0	41.0
31	39.00225	41.0	39.0	41.0	35.0	41.0
32	39.04125	41.0	39.0	41.0	35.0	41.0
33	37.96275	40.0	38.0	41.0	33.0	41.0
34	37.973	40.0	38.0	41.0	33.0	41.0
35	37.61775	39.0	37.0	41.0	33.0	41.0
36	32.7895	38.0	30.0	40.0	15.0	41.0
37	35.33175	38.0	33.0	40.0	29.0	41.0
38	37.00125	39.0	37.0	40.0	31.0	41.0
39	37.0955	39.0	37.0	40.0	31.0	41.0
40	37.14675	39.0	37.0	40.0	32.0	41.0
41	36.799	39.0	36.0	40.0	31.0	41.0
42	36.84625	39.0	37.0	40.0	31.0	41.0
43	36.9275	39.0	37.0	40.0	31.0	41.0
44	37.22125	39.0	37.0	41.0	32.0	41.0
45	36.76525	39.0	36.0	40.0	31.0	41.0
46	34.33025	38.0	33.0	40.0	24.0	41.0
47	35.21675	38.0	34.0	40.0	26.0	41.0
48	35.50075	38.0	35.0	40.0	29.0	41.0
49	34.55775	38.0	34.0	40.0	26.0	41.0
50	30.95475	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
16	2.0
17	2.0
18	1.0
19	2.0
20	4.0
21	6.0
22	4.0
23	7.0
24	14.0
25	16.0
26	22.0
27	16.0
28	23.0
29	33.0
30	66.0
31	69.0
32	79.0
33	111.0
34	150.0
35	220.0
36	306.0
37	581.0
38	1044.0
39	1222.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.631473605203903	20.590442832124094	51.56367275456593	19.21441080810608
2	19.775000000000002	23.674999999999997	20.1	36.449999999999996
3	23.35	17.825	19.35	39.475
4	29.325000000000003	25.95	14.649999999999999	30.075000000000003
5	19.975	44.6	22.975	12.45
6	37.225	13.700000000000001	33.375	15.7
7	15.975	23.0	25.45	35.575
8	26.5	28.775000000000002	15.8	28.925
9	22.825	34.699999999999996	27.775	14.7
10	19.75	21.85	31.55	26.85
11	28.7	12.825000000000001	14.249999999999998	44.224999999999994
12	13.850000000000001	19.75	27.500000000000004	38.9
13	27.474999999999998	21.349999999999998	29.599999999999998	21.575
14	26.075	33.025	21.825	19.075
15	33.550000000000004	27.650000000000002	25.25	13.55
16	19.1	27.825	17.875	35.199999999999996
17	21.6	23.875	40.300000000000004	14.224999999999998
18	17.549999999999997	19.275000000000002	33.825	29.349999999999998
19	40.625	13.900000000000002	25.7	19.775000000000002
20	41.25	14.299999999999999	30.75	13.700000000000001
21	26.674999999999997	14.899999999999999	26.700000000000003	31.724999999999998
22	26.3	15.425	47.275	11.0
23	28.15	13.175	42.0	16.675
24	53.474999999999994	14.2	23.05	9.275
25	47.3	26.275	13.55	12.875
26	24.125	47.475	13.450000000000001	14.95
27	14.725	47.175	24.025	14.075
28	11.65	22.95	48.475	16.925
29	12.775	12.725	54.800000000000004	19.7
30	9.6	9.15	33.35	47.9
31	15.125	7.074999999999999	47.599999999999994	30.2
32	29.975	8.525	20.549999999999997	40.949999999999996
33	52.97500000000001	13.375	13.425	20.225
34	58.95	7.1499999999999995	18.95	14.95
35	61.4	8.025	18.425	12.15
36	45.800000000000004	9.25	31.275	13.675
37	44.074999999999996	12.325	19.1	24.5
38	23.1	16.525000000000002	12.7	47.675
39	16.150000000000002	23.825	12.225	47.8
40	15.950000000000001	46.800000000000004	15.8	21.45
41	25.55	47.0	10.100000000000001	17.349999999999998
42	50.675000000000004	27.224999999999998	13.775	8.325000000000001
43	49.65	29.275000000000002	10.075000000000001	11.0
44	30.275000000000002	49.2	8.7	11.825
45	19.35	51.2	11.975	17.474999999999998
46	14.875	25.6	20.7	38.824999999999996
47	10.15	15.5	41.375	32.975
48	14.424999999999999	12.975	19.1	53.5
49	15.1	19.25	14.000000000000002	51.65
50	19.575	36.675000000000004	14.374999999999998	29.375
>>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	0.5
12	1.0
13	0.5
14	0.0
15	0.5
16	1.0
17	0.5
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	0.0
26	0.0
27	1.5
28	3.0
29	4.5
30	6.0
31	17.5
32	29.0
33	31.0
34	33.0
35	35.0
36	37.0
37	47.0
38	57.0
39	52.0
40	47.0
41	54.5
42	62.0
43	82.5
44	103.0
45	147.0
46	191.0
47	286.0
48	381.0
49	449.5
50	518.0
51	689.0
52	860.0
53	675.5
54	491.0
55	498.5
56	506.0
57	395.0
58	284.0
59	176.5
60	69.0
61	62.0
62	55.0
63	111.5
64	168.0
65	113.0
66	58.0
67	35.0
68	12.0
69	7.0
70	2.0
71	5.5
72	9.0
73	6.5
74	4.0
75	2.5
76	1.0
77	2.5
78	4.0
79	4.5
80	5.0
81	3.5
82	2.0
83	1.0
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	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	38.074999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.18056467498359	28.625
2	9.12672357189757	6.950000000000001
3	5.121470781352593	5.8500000000000005
4	2.2324359816152333	3.4000000000000004
5	1.247537754432042	2.375
6	1.1818778726198294	2.7
7	0.6565988181221274	1.7500000000000002
8	0.8535784635587657	2.6
9	0.6565988181221274	2.25
>10	3.217334208798424	24.3
>50	0.2626395272488509	7.175
>100	0.2626395272488509	12.025
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	125	3.125	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	122	3.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	102	2.55	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	80	2.0	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	79	1.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	62	1.55	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	47	1.175	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	44	1.0999999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	39	0.975	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	34	0.8500000000000001	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	32	0.8	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGC	16	0.4	RNA PCR Primer, Index 23 (100% over 50bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	16	0.4	RNA PCR Primer, Index 1 (100% over 25bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	15	0.375	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	14	0.35000000000000003	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	14	0.35000000000000003	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTTCTATGATGAATCAAACTAGCTCACTATGACTGCTAATGAAAACACAG	11	0.27499999999999997	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	11	0.27499999999999997	No Hit
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	10	0.25	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	10	0.25	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	9	0.22499999999999998	No Hit
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	9	0.22499999999999998	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 33bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	9	0.22499999999999998	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	9	0.22499999999999998	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	9	0.22499999999999998	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	9	0.22499999999999998	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGATCTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	8	0.2	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCTC	7	0.17500000000000002	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTC	7	0.17500000000000002	RNA PCR Primer, Index 23 (100% over 44bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 33bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
CAACGGAATCCCAAAAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAATA	6	0.15	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	6	0.15	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCT	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATGGAAT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	6	0.15	RNA PCR Primer, Index 7 (97% over 35bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TACCATGATGATAACATAGTTCAGCAGACTTAACTCTGATGAACAATCAT	5	0.125	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAG	5	0.125	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCTTGGAATT	5	0.125	No Hit
AAGCTGCCAGTTGAAGAACTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.475	0.0	0.0	0.0
2	0.0	0.5	0.0	0.0	0.0
3	0.0	0.575	0.0	0.0	0.0
4	0.0	0.65	0.0	0.0	0.0
5	0.0	0.725	0.0	0.0	0.0
6	0.0	0.75	0.0	0.0	0.0
7	0.0	0.925	0.0	0.0	0.0
8	0.0	1.025	0.0	0.0	0.0
9	0.0	1.1	0.0	0.0	0.0
10	0.0	1.225	0.0	0.0	0.0
11	0.0	1.45	0.0	0.0	0.0
12	0.0	1.6	0.0	0.0	0.0
13	0.0	1.675	0.0	0.0	0.0
14	0.0	1.925	0.0	0.0	0.0
15	0.0	2.05	0.0	0.0	0.0
16	0.0	2.45	0.0	0.0	0.0
17	0.0	2.675	0.0	0.0	0.0
18	0.0	3.35	0.0	0.0	0.0
19	0.0	4.0	0.0	0.0	0.0
20	0.0	4.825	0.0	0.0	0.0
21	0.0	9.85	0.0	0.0	0.0
22	0.0	21.05	0.0	0.0	0.0
23	0.0	50.05	0.0	0.0	0.0
24	0.0	61.125	0.0	0.0	0.0
25	0.0	66.15	0.0	0.0	0.0
26	0.0	67.55	0.0	0.0	0.0
27	0.0	68.1	0.0	0.0	0.0
28	0.0	68.55	0.0	0.0	0.0
29	0.0	68.925	0.0	0.0	0.0
30	0.0	69.375	0.0	0.0	0.0
31	0.0	69.9	0.0	0.0	0.0
32	0.0	70.675	0.0	0.0	0.0
33	0.0	71.65	0.0	0.0	0.0
34	0.0	76.325	0.0	0.0	0.0
35	0.0	76.925	0.0	0.0	0.0
36	0.0	77.85	0.0	0.0	0.0
37	0.0	78.55	0.0	0.0	0.0
38	0.0	79.175	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACGCTGT	40	5.315087E-9	44.000004	9
GTGAGTT	20	6.952051E-4	44.000004	18
GAGTTGG	20	6.952051E-4	44.000004	20
GGGGGCC	20	6.952051E-4	44.000004	33
GGCTTGG	40	5.315087E-9	44.000004	19
GGCCAAG	20	6.952051E-4	44.000004	36
GGGGCCA	20	6.952051E-4	44.000004	34
TGAGTTG	20	6.952051E-4	44.000004	19
CGCTGTC	40	5.315087E-9	44.000004	10
GGGCCAA	20	6.952051E-4	44.000004	35
TGAGACC	25	3.6958358E-5	44.0	5
AACGCTG	35	1.02281774E-7	44.0	8
GGTGAGT	30	1.9515464E-6	44.0	17
CTGAGAC	25	3.6958358E-5	44.0	4
CTTTAAC	25	3.6958358E-5	44.0	12
TTCAACG	35	1.02281774E-7	44.0	5
TCGGTGA	35	1.02281774E-7	44.0	15
CCTGAGA	25	3.6958358E-5	44.0	3
AACCTGT	25	3.6958358E-5	44.0	16
CATTCAA	35	1.02281774E-7	44.0	3
>>END_MODULE
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152512 spots for SRR5030893.sra
Written 152512 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
Read 152508 spots for SRR5030893.sra
Written 152508 spots for SRR5030893.sra
SRR ids: ['SRR5030893.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_3jm899ih
SRR5030893.sra spots: 1830100
blocks: [[1, 152508], [152509, 305016], [305017, 457524], [457525, 610032], [610033, 762540], [762541, 915048], [915049, 1067556], [1067557, 1220064], [1220065, 1372572], [1372573, 1525080], [1525081, 1677588], [1677589, 1830100]]
SRR5030893 file size 316116
SRR5030893 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030893 SRR5030893_1.fastq
Input file:	SRR5030893_1.fastq
trimmed:	SRR5030893-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 06:38:38 2020 >> started

Wed Mar  4 06:38:39 2020 >> done (1.322s)
1830100 reads processed; of these:
     59 ( 0.00%) short reads filtered out after trimming by size control
      2 ( 0.00%) empty reads filtered out after trimming by size control
1830039 (100.00%) reads available; of these:
 140598 ( 7.68%) trimmed reads available after processing
1689441 (92.32%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     22	  0.00%
 19	     26	  0.00%
 20	     72	  0.00%
 21	     70	  0.00%
 22	    128	  0.01%
 23	    179	  0.01%
 24	    185	  0.01%
 25	    233	  0.01%
 26	    197	  0.01%
 27	    300	  0.02%
 28	    347	  0.02%
 29	    465	  0.03%
 30	    391	  0.02%
 31	    621	  0.03%
 32	    737	  0.04%
 33	   1536	  0.08%
 34	   5053	  0.28%
 35	   2489	  0.14%
 36	   1810	  0.10%
 37	   1686	  0.09%
 38	   2649	  0.14%
 39	   2324	  0.13%
 40	   3853	  0.21%
 41	   2667	  0.15%
 42	   4626	  0.25%
 43	   3573	  0.20%
 44	  10752	  0.59%
 45	  10238	  0.56%
 46	   9650	  0.53%
 47	  11066	  0.60%
 48	  27039	  1.48%
 49	  35614	  1.95%
 50	1689441	 92.32%
1830039 reads passed initial QC


criterion=sequence-density
sequence-density=78.07
sequence-density-rank=1
fanout-score=19.35
fanout-score-rank=3
prefix-density=80.40
prefix-fanout=18.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCG


criterion=fanout-score
sequence-density=2.24
sequence-density-rank=3
fanout-score=110.63
fanout-score-rank=1
prefix-density=79.66
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCG -o SRR5030893 -
Input file:	STDIN
trimmed:	SRR5030893-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCG
-- 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 06:38:52 2020 >> started

Wed Mar  4 06:38:55 2020 >> done (2.800s)
1783709 reads processed; of these:
  52845 ( 2.96%) short reads filtered out after trimming by size control
  10272 ( 0.58%) empty reads filtered out after trimming by size control
1720592 (96.46%) reads available; of these:
1506262 (87.54%) trimmed reads available after processing
 214330 (12.46%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  10598	  0.62%
 19	  14255	  0.83%
 20	  98481	  5.72%
 21	 200492	 11.65%
 22	 513541	 29.85%
 23	 186630	 10.85%
 24	  92144	  5.36%
 25	  26933	  1.57%
 26	  12430	  0.72%
 27	   9195	  0.53%
 28	  10360	  0.60%
 29	   7988	  0.46%
 30	  10843	  0.63%
 31	  15399	  0.89%
 32	  16105	  0.94%
 33	  81277	  4.72%
 34	  18301	  1.06%
 35	  15346	  0.89%
 36	  15077	  0.88%
 37	   8560	  0.50%
 38	   9482	  0.55%
 39	  11534	  0.67%
 40	  18059	  1.05%
 41	  21390	  1.24%
 42	  22637	  1.32%
 43	  15916	  0.93%
 44	  14809	  0.86%
 45	  17208	  1.00%
 46	  14809	  0.86%
 47	  11914	  0.69%
 48	   2596	  0.15%
 49	   9423	  0.55%
 50	 186860	 10.86%


criterion=sequence-density
sequence-density=2.96
sequence-density-rank=1
fanout-score=1.79
fanout-score-rank=6
prefix-density=0.03
prefix-fanout=1.8
sequence=CCTGAGACCCTAACTTGTGAAA


criterion=fanout-score
sequence-density=0.43
sequence-density-rank=26
fanout-score=26.04
fanout-score-rank=1
prefix-density=11.27
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 06:39:57
                             Started mapping on |	Mar 04 06:39:57
                                    Finished on |	Mar 04 06:40:20
       Mapping speed, Million of reads per hour |	276.56

                          Number of input reads |	1766922
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1041600
                        Uniquely mapped reads % |	58.95%
                          Average mapped length |	28.01
                       Number of splices: Total |	656
            Number of splices: Annotated (sjdb) |	182
                       Number of splices: GT/AG |	597
                       Number of splices: GC/AG |	12
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	47
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.36
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	483244
             % of reads mapped to multiple loci |	27.35%
        Number of reads mapped to too many loci |	42769
             % of reads mapped to too many loci |	2.42%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.93%
                     % of reads unmapped: other |	0.35%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	242078	242078	242078
N_multimapping	483244	483244	483244
N_noFeature	43593	55800	732937
N_ambiguous	592107	336795	9831
UnstrandedReadsAssigned:405900 PositiveStrandReadsAssigned:649005 NegativeStrandReadsAssigned:298832
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030893 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: SRR5030893-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,766,922 reads, 495,378 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 932 rounds

 109283 SRR5030893.ke.tsv
  52636 SRR5030893.se.tsv
 161919 total
==> SRR5030893.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

==> SRR5030893.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030893 completed mapping pipeline successfully
