Starting /dee2/code/volunteer_pipeline.sh SRR5030848
    current disk space = 160678363136
    free memory = 1054497080 
SRR5030848 SRAfilesize
0f75f47fa7ae06f1e62c98e879650237  SRR5030848.sra
SRR5030848.sra file validated
SRR5030848 is single end
SRR5030848 is conventional basespace
SRR5030848 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030848_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	32.37975	33.0	31.0	34.0	31.0	34.0
2	32.67975	34.0	31.0	34.0	31.0	34.0
3	32.69475	34.0	31.0	34.0	31.0	34.0
4	36.18475	37.0	37.0	37.0	35.0	37.0
5	36.25575	37.0	37.0	37.0	35.0	37.0
6	36.078	37.0	35.0	37.0	35.0	37.0
7	36.072	37.0	35.0	37.0	35.0	37.0
8	36.18775	37.0	36.0	37.0	35.0	37.0
9	37.857	39.0	38.0	39.0	35.0	39.0
10	37.879	39.0	38.0	39.0	35.0	39.0
11	37.869	39.0	38.0	39.0	35.0	39.0
12	37.7025	39.0	38.0	39.0	35.0	39.0
13	37.74375	39.0	38.0	39.0	35.0	39.0
14	39.089	40.0	39.0	41.0	36.0	41.0
15	39.05875	40.0	38.0	41.0	36.0	41.0
16	39.07325	40.0	38.0	41.0	36.0	41.0
17	39.2135	40.0	39.0	41.0	36.0	41.0
18	39.35125	41.0	39.0	41.0	36.0	41.0
19	39.225	41.0	39.0	41.0	36.0	41.0
20	39.018	40.0	39.0	41.0	35.0	41.0
21	39.0425	40.0	39.0	41.0	35.0	41.0
22	39.26375	41.0	39.0	41.0	36.0	41.0
23	39.2535	41.0	39.0	41.0	36.0	41.0
24	38.55325	40.0	38.0	41.0	34.0	41.0
25	38.72275	40.0	38.0	41.0	34.0	41.0
26	38.86275	41.0	38.0	41.0	35.0	41.0
27	39.0335	41.0	39.0	41.0	35.0	41.0
28	38.7005	40.0	38.0	41.0	34.0	41.0
29	38.2125	40.0	38.0	41.0	33.0	41.0
30	38.43675	40.0	38.0	41.0	34.0	41.0
31	38.8175	40.0	38.0	41.0	35.0	41.0
32	38.8125	40.0	38.0	41.0	35.0	41.0
33	37.6535	40.0	38.0	41.0	32.0	41.0
34	37.5285	40.0	37.0	41.0	31.0	41.0
35	37.455	39.0	37.0	41.0	32.0	41.0
36	33.50625	38.0	30.0	40.0	18.0	41.0
37	35.61425	38.0	34.0	40.0	30.0	41.0
38	37.02275	39.0	37.0	40.0	32.0	41.0
39	37.17375	39.0	37.0	40.0	32.0	41.0
40	37.092	39.0	37.0	41.0	31.0	41.0
41	36.90225	39.0	36.0	40.0	31.0	41.0
42	36.92575	39.0	36.0	40.0	31.0	41.0
43	36.93875	39.0	36.0	41.0	32.0	41.0
44	37.076	39.0	37.0	41.0	32.0	41.0
45	36.644	39.0	36.0	41.0	31.0	41.0
46	34.54175	38.0	33.0	40.0	25.0	41.0
47	35.483	38.0	34.0	40.0	28.0	41.0
48	35.581	39.0	35.0	40.0	29.0	41.0
49	34.89625	38.0	34.0	40.0	28.0	41.0
50	31.08475	34.0	29.0	38.0	15.0	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
13	1.0
14	0.0
15	2.0
16	0.0
17	1.0
18	3.0
19	2.0
20	7.0
21	5.0
22	5.0
23	11.0
24	11.0
25	25.0
26	23.0
27	22.0
28	35.0
29	43.0
30	52.0
31	66.0
32	70.0
33	118.0
34	168.0
35	204.0
36	298.0
37	549.0
38	1045.0
39	1234.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.882677362747556	26.67335171722236	45.29957382802707	16.144397092003008
2	22.0	27.625	20.8	29.575000000000003
3	23.280820205051263	20.230057514378593	25.006251562890725	31.48287071767942
4	30.7	28.7	16.875	23.724999999999998
5	21.3	38.2	26.5	14.000000000000002
6	34.449999999999996	17.775	33.650000000000006	14.124999999999998
7	21.3	18.85	23.775	36.075
8	25.275	29.7	15.7	29.325000000000003
9	21.325	33.725	27.675	17.275
10	24.175	21.224999999999998	27.825	26.775
11	31.65	12.6	17.8	37.95
12	17.150000000000002	19.900000000000002	29.275000000000002	33.675
13	31.2	18.375	30.425	20.0
14	32.775	29.625	21.325	16.275000000000002
15	34.075	22.225	28.625	15.075
16	18.825	18.475	25.7	37.0
17	24.625	21.425	37.175000000000004	16.775000000000002
18	25.55	18.65	28.725	27.075
19	31.75	14.575	34.075	19.6
20	39.1	18.3	26.625	15.975
21	22.2	21.875	27.675	28.249999999999996
22	30.15	13.725000000000001	42.175000000000004	13.950000000000001
23	28.175	15.275	39.65	16.900000000000002
24	48.325	15.125	25.75	10.8
25	47.25	23.5	15.775	13.475000000000001
26	29.15	41.199999999999996	15.950000000000001	13.700000000000001
27	17.424999999999997	42.699999999999996	24.9	14.975
28	14.05	24.349999999999998	43.925	17.675
29	13.125	14.224999999999998	51.949999999999996	20.7
30	12.075	9.0	35.4	43.525000000000006
31	17.75	7.35	40.725	34.175
32	28.925	8.075000000000001	22.6	40.400000000000006
33	49.6	10.625	14.725	25.05
34	55.474999999999994	8.975	18.775	16.775000000000002
35	59.025000000000006	8.55	19.75	12.675
36	43.525000000000006	9.4	32.025	15.049999999999999
37	40.6	12.575	21.4	25.424999999999997
38	24.75	17.8	14.399999999999999	43.05
39	18.475	24.275	12.3	44.95
40	18.35	43.875	13.775	24.0
41	27.175	44.2	12.65	15.975
42	44.675	29.125	13.15	13.05
43	47.55	29.7	10.7	12.049999999999999
44	31.175000000000004	43.7	10.299999999999999	14.825
45	19.0	45.525	15.775	19.7
46	15.2	26.400000000000002	20.599999999999998	37.8
47	12.075	15.85	35.825	36.25
48	13.075000000000001	13.975000000000001	23.674999999999997	49.275000000000006
49	16.3	20.3	16.775000000000002	46.625
50	20.65	33.875	15.9	29.575000000000003
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.5
2	1.0
3	0.5
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	0.0
16	0.0
17	0.5
18	1.0
19	1.0
20	1.0
21	1.0
22	1.0
23	1.0
24	1.0
25	0.5
26	0.0
27	1.5
28	3.0
29	5.5
30	8.0
31	16.5
32	25.0
33	23.0
34	21.0
35	32.5
36	44.0
37	59.5
38	75.0
39	69.5
40	64.0
41	61.5
42	59.0
43	92.5
44	126.0
45	193.5
46	261.0
47	319.0
48	377.0
49	508.0
50	639.0
51	718.5
52	798.0
53	592.0
54	386.0
55	382.5
56	379.0
57	302.0
58	225.0
59	152.0
60	79.0
61	67.5
62	56.0
63	82.5
64	109.0
65	69.5
66	30.0
67	24.5
68	19.0
69	34.0
70	49.0
71	93.5
72	138.0
73	73.0
74	8.0
75	7.0
76	6.0
77	4.0
78	2.0
79	5.0
80	8.0
81	4.0
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	0.27499999999999997
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	0.0
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	41.449999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.69360675512667	31.374999999999996
2	10.253317249698432	8.5
3	4.161640530759952	5.175
4	2.4728588661037394	4.1000000000000005
5	1.3872135102533172	2.875
6	1.0856453558504222	2.7
7	0.6031363088057901	1.7500000000000002
8	0.4221954161640531	1.4000000000000001
9	0.24125452352231602	0.8999999999999999
>10	3.1363088057901085	23.075000000000003
>50	0.4221954161640531	11.85
>100	0.12062726176115801	6.3
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	129	3.225	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	123	3.075	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	83	2.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	78	1.95	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	78	1.95	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	66	1.6500000000000001	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	51	1.275	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	48	1.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	35	0.8750000000000001	No Hit
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	21	0.525	RNA PCR Primer, Index 7 (97% over 35bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	21	0.525	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	20	0.5	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	19	0.475	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	18	0.44999999999999996	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGC	18	0.44999999999999996	RNA PCR Primer, Index 44 (100% over 50bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTC	14	0.35000000000000003	RNA PCR Primer, Index 44 (100% over 44bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	13	0.325	RNA PCR Primer, Index 1 (100% over 33bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	13	0.325	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	12	0.3	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 25bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	11	0.27499999999999997	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	11	0.27499999999999997	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	10	0.25	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	10	0.25	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	8	0.2	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	8	0.2	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	8	0.2	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	7	0.17500000000000002	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
GACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	6	0.15	RNA PCR Primer, Index 7 (97% over 35bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	6	0.15	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	5	0.125	RNA PCR Primer, Index 3 (100% over 34bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	5	0.125	No Hit
TTGTGCTTGATCTAACCATGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	5	0.125	No Hit
GGTCCATGATGAAGCCCATTATCAGTGGACATCTATGGATGAGAAATGCG	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	0.475	0.0	0.0	0.0
2	0.0	0.475	0.0	0.0	0.0
3	0.0	0.55	0.0	0.0	0.0
4	0.0	0.55	0.0	0.0	0.0
5	0.0	0.55	0.0	0.0	0.0
6	0.0	0.575	0.0	0.0	0.0
7	0.0	0.925	0.0	0.0	0.0
8	0.0	1.075	0.0	0.0	0.0
9	0.0	1.125	0.0	0.0	0.0
10	0.0	1.275	0.0	0.0	0.0
11	0.0	1.375	0.0	0.0	0.0
12	0.0	1.625	0.0	0.0	0.0
13	0.0	1.9	0.0	0.0	0.0
14	0.0	2.075	0.0	0.0	0.0
15	0.0	2.45	0.0	0.0	0.0
16	0.0	3.675	0.0	0.0	0.0
17	0.0	4.275	0.0	0.0	0.0
18	0.0	5.175	0.0	0.0	0.0
19	0.0	5.8	0.0	0.0	0.0
20	0.0	6.65	0.0	0.0	0.0
21	0.0	12.0	0.0	0.0	0.0
22	0.0	22.15	0.0	0.0	0.0
23	0.0	46.025	0.0	0.0	0.0
24	0.0	58.1	0.0	0.0	0.0
25	0.0	62.95	0.0	0.0	0.0
26	0.0	64.3	0.0	0.0	0.0
27	0.0	64.975	0.0	0.0	0.0
28	0.0	65.75	0.0	0.0	0.0
29	0.0	66.175	0.0	0.0	0.0
30	0.0	66.75	0.0	0.0	0.0
31	0.0	67.525	0.0	0.0	0.0
32	0.0	68.475	0.0	0.0	0.0
33	0.0	69.55	0.0	0.0	0.0
34	0.0	72.225	0.0	0.0	0.0
35	0.0	73.675	0.0	0.0	0.0
36	0.0	74.625	0.0	0.0	0.0
37	0.0	75.65	0.0	0.0	0.0
38	0.0	76.175	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	20	6.952051E-4	44.000004	8
GGTGAGT	20	6.952051E-4	44.000004	17
ACGCTGT	20	6.952051E-4	44.000004	9
CTGAGCT	20	6.952051E-4	44.000004	11
TTCAACG	20	6.952051E-4	44.000004	5
TCGGTGA	20	6.952051E-4	44.000004	15
GAGCTTG	20	6.952051E-4	44.000004	13
GGATCCG	20	6.952051E-4	44.000004	3
CCGTCTG	20	6.952051E-4	44.000004	7
TCGGATC	20	6.952051E-4	44.000004	1
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
CGGATCC	20	6.952051E-4	44.000004	2
ACATTCA	20	6.952051E-4	44.000004	2
GCTGTCG	20	6.952051E-4	44.000004	11
GATCCGT	20	6.952051E-4	44.000004	4
CGGTGAG	20	6.952051E-4	44.000004	16
TCCGTCT	20	6.952051E-4	44.000004	6
ATCCGTC	20	6.952051E-4	44.000004	5
CTGTCGG	20	6.952051E-4	44.000004	12
>>END_MODULE
Read 67971 spots for SRR5030848.sra
Written 67971 spots for SRR5030848.sra
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SRR ids: ['SRR5030848.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_gvp7cd44
SRR5030848.sra spots: 3262608
blocks: [[1, 67971], [67972, 135942], [135943, 203913], [203914, 271884], [271885, 339855], [339856, 407826], [407827, 475797], [475798, 543768], [543769, 611739], [611740, 679710], [679711, 747681], [747682, 815652], [815653, 883623], [883624, 951594], [951595, 1019565], [1019566, 1087536], [1087537, 1155507], [1155508, 1223478], [1223479, 1291449], [1291450, 1359420], [1359421, 1427391], [1427392, 1495362], [1495363, 1563333], [1563334, 1631304], [1631305, 1699275], [1699276, 1767246], [1767247, 1835217], [1835218, 1903188], [1903189, 1971159], [1971160, 2039130], [2039131, 2107101], [2107102, 2175072], [2175073, 2243043], [2243044, 2311014], [2311015, 2378985], [2378986, 2446956], [2446957, 2514927], [2514928, 2582898], [2582899, 2650869], [2650870, 2718840], [2718841, 2786811], [2786812, 2854782], [2854783, 2922753], [2922754, 2990724], [2990725, 3058695], [3058696, 3126666], [3126667, 3194637], [3194638, 3262608]]
SRR5030848 file size 564408
SRR5030848 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5030848 SRR5030848_1.fastq
Input file:	SRR5030848_1.fastq
trimmed:	SRR5030848-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):	32
Wed Mar  4 06:26:56 2020 >> started

Wed Mar  4 06:26:58 2020 >> done (2.059s)
3262608 reads processed; of these:
    170 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3262432 (99.99%) reads available; of these:
 231328 ( 7.09%) trimmed reads available after processing
3031104 (92.91%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     61	  0.00%
 19	     66	  0.00%
 20	    181	  0.01%
 21	    180	  0.01%
 22	    318	  0.01%
 23	    377	  0.01%
 24	    413	  0.01%
 25	    526	  0.02%
 26	    452	  0.01%
 27	    598	  0.02%
 28	    724	  0.02%
 29	   1166	  0.04%
 30	    833	  0.03%
 31	   1107	  0.03%
 32	   1445	  0.04%
 33	   2722	  0.08%
 34	   7758	  0.24%
 35	   4062	  0.12%
 36	   2891	  0.09%
 37	   3034	  0.09%
 38	   4277	  0.13%
 39	   4203	  0.13%
 40	   6431	  0.20%
 41	   4852	  0.15%
 42	   8101	  0.25%
 43	   6474	  0.20%
 44	  16715	  0.51%
 45	  15855	  0.49%
 46	  15467	  0.47%
 47	  18835	  0.58%
 48	  43720	  1.34%
 49	  57484	  1.76%
 50	3031104	 92.91%
3262432 reads passed initial QC


criterion=sequence-density
sequence-density=76.63
sequence-density-rank=1
fanout-score=22.13
fanout-score-rank=2
prefix-density=78.85
prefix-fanout=21.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCCG


criterion=fanout-score
sequence-density=1.52
sequence-density-rank=4
fanout-score=159.84
fanout-score-rank=1
prefix-density=78.94
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCCG -o SRR5030848 -
Input file:	STDIN
trimmed:	SRR5030848-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCCG
-- 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):	32
Wed Mar  4 06:27:15 2020 >> started

Wed Mar  4 06:27:20 2020 >> done (4.886s)
3177694 reads processed; of these:
 149972 ( 4.72%) short reads filtered out after trimming by size control
  13225 ( 0.42%) empty reads filtered out after trimming by size control
3014497 (94.86%) reads available; of these:
2607397 (86.50%) trimmed reads available after processing
 407100 (13.50%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16332	  0.54%
 19	  30643	  1.02%
 20	 160433	  5.32%
 21	 339186	 11.25%
 22	 808887	 26.83%
 23	 379337	 12.58%
 24	 175343	  5.82%
 25	  45517	  1.51%
 26	  23878	  0.79%
 27	  18128	  0.60%
 28	  18906	  0.63%
 29	  16379	  0.54%
 30	  25751	  0.85%
 31	  35185	  1.17%
 32	  34234	  1.14%
 33	  84795	  2.81%
 34	  35666	  1.18%
 35	  30290	  1.00%
 36	  36119	  1.20%
 37	  16705	  0.55%
 38	  20824	  0.69%
 39	  18974	  0.63%
 40	  27867	  0.92%
 41	  37504	  1.24%
 42	  46821	  1.55%
 43	  33073	  1.10%
 44	  25666	  0.85%
 45	  41329	  1.37%
 46	  30813	  1.02%
 47	  24087	  0.80%
 48	   3884	  0.13%
 49	   9711	  0.32%
 50	 362230	 12.02%


criterion=sequence-density
sequence-density=6.38
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.03
sequence-density-rank=38
fanout-score=53.62
fanout-score-rank=1
prefix-density=1.48
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:28:01
                             Started mapping on |	Mar 04 06:28:01
                                    Finished on |	Mar 04 06:28:30
       Mapping speed, Million of reads per hour |	384.73

                          Number of input reads |	3099235
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1631235
                        Uniquely mapped reads % |	52.63%
                          Average mapped length |	27.29
                       Number of splices: Total |	1694
            Number of splices: Annotated (sjdb) |	232
                       Number of splices: GT/AG |	1551
                       Number of splices: GC/AG |	36
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	106
                      Mismatch rate per base, % |	0.25%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.71
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	970839
             % of reads mapped to multiple loci |	31.33%
        Number of reads mapped to too many loci |	73044
             % of reads mapped to too many loci |	2.36%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.19%
                     % of reads unmapped: other |	0.50%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	497161	497161	497161
N_multimapping	970839	970839	970839
N_noFeature	88664	111051	1163738
N_ambiguous	875281	473748	22562
UnstrandedReadsAssigned:667290 PositiveStrandReadsAssigned:1046436 NegativeStrandReadsAssigned:444935
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030848 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: SRR5030848-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,099,235 reads, 738,688 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,141 rounds

 109283 SRR5030848.ke.tsv
  52636 SRR5030848.se.tsv
 161919 total
==> SRR5030848.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

==> SRR5030848.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030848 completed mapping pipeline successfully
