Starting /dee2/code/volunteer_pipeline.sh SRR6235374
    current disk space = 2442736238592
    free memory = 1578611428 
SRR6235374 SRAfilesize
f360116785f529e698ec779bcd6dc32c  SRR6235374.sra
SRR6235374.sra file validated
SRR6235374 is single end
SRR6235374 is conventional basespace
SRR6235374 read1 length is 49 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR6235374_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	49
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.0415	34.0	31.0	34.0	31.0	34.0
2	32.73075	34.0	33.0	34.0	31.0	34.0
3	33.13675	34.0	33.0	34.0	31.0	34.0
4	36.379	37.0	37.0	37.0	35.0	37.0
5	36.3505	37.0	37.0	37.0	35.0	37.0
6	36.32125	37.0	37.0	37.0	35.0	37.0
7	36.37375	37.0	37.0	37.0	35.0	37.0
8	36.54875	37.0	37.0	37.0	35.0	37.0
9	38.411	39.0	39.0	39.0	37.0	39.0
10	38.57225	39.0	39.0	39.0	37.0	39.0
11	38.611	39.0	39.0	39.0	38.0	39.0
12	38.516	39.0	39.0	39.0	37.0	39.0
13	38.51025	39.0	39.0	39.0	37.0	39.0
14	40.17325	41.0	40.0	41.0	38.0	41.0
15	40.34225	41.0	41.0	41.0	39.0	41.0
16	40.094	41.0	40.0	41.0	38.0	41.0
17	40.3135	41.0	40.0	41.0	39.0	41.0
18	40.2895	41.0	41.0	41.0	39.0	41.0
19	40.28675	41.0	41.0	41.0	39.0	41.0
20	40.063	41.0	41.0	41.0	38.0	41.0
21	39.89025	41.0	40.0	41.0	38.0	41.0
22	39.49025	40.0	39.0	41.0	37.0	41.0
23	39.91075	41.0	40.0	41.0	38.0	41.0
24	39.9085	41.0	40.0	41.0	38.0	41.0
25	39.766	41.0	40.0	41.0	38.0	41.0
26	39.8355	40.0	40.0	41.0	38.0	41.0
27	40.083	41.0	40.0	41.0	38.0	41.0
28	39.3885	40.0	39.0	41.0	38.0	41.0
29	39.90975	41.0	40.0	41.0	38.0	41.0
30	39.9745	41.0	40.0	41.0	38.0	41.0
31	40.162	41.0	40.0	41.0	38.0	41.0
32	39.88375	41.0	40.0	41.0	38.0	41.0
33	39.80125	41.0	40.0	41.0	37.0	41.0
34	39.72875	41.0	40.0	41.0	37.0	41.0
35	39.01575	41.0	38.0	41.0	35.0	41.0
36	39.57075	41.0	40.0	41.0	37.0	41.0
37	39.92325	41.0	40.0	41.0	38.0	41.0
38	39.94275	41.0	40.0	41.0	38.0	41.0
39	39.7815	41.0	40.0	41.0	38.0	41.0
40	39.91	41.0	40.0	41.0	38.0	41.0
41	39.68675	41.0	40.0	41.0	37.0	41.0
42	39.773	41.0	40.0	41.0	38.0	41.0
43	39.90025	41.0	40.0	41.0	38.0	41.0
44	39.6295	41.0	39.0	41.0	38.0	41.0
45	39.52675	40.0	39.0	41.0	38.0	41.0
46	39.522	41.0	39.0	41.0	37.0	41.0
47	39.364	41.0	39.0	41.0	37.0	41.0
48	39.74425	41.0	40.0	41.0	38.0	41.0
49	39.71825	41.0	40.0	41.0	37.0	41.0
>>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
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
15	2.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	2.0
23	1.0
24	0.0
25	0.0
26	1.0
27	4.0
28	4.0
29	13.0
30	14.0
31	18.0
32	25.0
33	32.0
34	42.0
35	59.0
36	117.0
37	237.0
38	588.0
39	2841.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	40.9009009009009	10.81081081081081	10.99099099099099	37.2972972972973
2	51.2	19.175	12.25	17.375
3	54.37499999999999	20.05	10.2	15.375
4	33.95	27.075	14.325	24.65
5	26.325	22.725	26.85	24.099999999999998
6	17.474999999999998	23.95	42.3	16.275000000000002
7	23.65	16.900000000000002	49.625	9.825000000000001
8	57.125	12.975	11.700000000000001	18.2
9	8.85	5.5	78.875	6.775
10	80.0	7.249999999999999	7.5	5.25
11	81.05	5.525	7.55	5.875
12	9.950000000000001	80.05	5.55	4.45
13	8.55	79.07499999999999	6.550000000000001	5.825
14	6.8500000000000005	7.1499999999999995	79.425	6.575
15	6.4	8.649999999999999	79.125	5.825
16	5.875	6.625	8.924999999999999	78.57499999999999
17	5.949999999999999	5.475	80.175	8.4
18	7.025	5.949999999999999	9.15	77.875
19	79.825	5.8500000000000005	7.35	6.9750000000000005
20	81.925	2.775	8.7	6.6000000000000005
21	83.76688344172086	3.376688344172086	8.30415207603802	4.552276138069034
22	14.825	3.925	76.3	4.95
23	81.575	7.000000000000001	5.075	6.35
24	8.649999999999999	7.7	5.925	77.725
25	7.675	6.825	8.175	77.325
26	6.3	78.05	8.425	7.225
27	8.325000000000001	78.0	4.875	8.799999999999999
28	78.875	8.7	6.575	5.8500000000000005
29	78.55	8.95	4.675	7.825
30	10.525	79.475	5.050000000000001	4.95
31	9.725	78.10000000000001	5.475	6.7
32	9.25	7.85	6.5	76.4
33	6.65	6.05	78.8	8.5
34	8.475000000000001	5.65	6.625	79.25
35	6.9	7.9	5.65	79.55
36	6.4750000000000005	75.6	6.25	11.675
37	74.7	8.425	8.875	8.0
38	5.7250000000000005	7.85	77.275	9.15
39	8.0	7.324999999999999	7.75	76.925
40	8.649999999999999	75.55	5.3	10.5
41	6.625	10.85	6.5	76.02499999999999
42	8.450000000000001	78.875	4.875	7.8
43	77.425	6.7250000000000005	7.324999999999999	8.525
44	8.05	5.800000000000001	79.80000000000001	6.35
45	7.75	5.25	76.825	10.174999999999999
46	4.5249999999999995	4.9750000000000005	8.85	81.65
47	5.5	9.8	6.75	77.95
48	6.05	75.14999999999999	8.85	9.950000000000001
49	4.625	5.75	78.27499999999999	11.35
>>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	0.0
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	0.5
33	1.0
34	0.5
35	0.0
36	1.5
37	3.0
38	4.0
39	5.0
40	9.0
41	13.0
42	19.5
43	26.0
44	41.5
45	57.0
46	105.0
47	153.0
48	273.0
49	393.0
50	662.0
51	931.0
52	1074.0
53	1217.0
54	1001.0
55	785.0
56	519.5
57	254.0
58	168.0
59	82.0
60	59.5
61	37.0
62	27.0
63	17.0
64	15.5
65	14.0
66	11.0
67	8.0
68	5.0
69	2.0
70	1.5
71	1.0
72	1.0
73	1.0
74	0.5
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
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	2.875
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	0.05
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
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
49	4000.0
>>END_MODULE
>>Sequence Duplication Levels	pass
#Total Deduplicated Percentage	74.225
#Duplication Level	Percentage of deduplicated	Percentage of total
1	84.94442573256988	63.05
2	7.645671943415292	11.35
3	3.3681374200067364	7.5
4	1.5493432132030986	4.6
5	0.8083529808016167	3.0
6	0.5052206130010104	2.25
7	0.370495116200741	1.925
8	0.30313236780060626	1.7999999999999998
9	0.10104412260020208	0.675
>10	0.40417649040080833	3.85
>50	0.0	0.0
>100	0.0	0.0
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	warn
#Sequence	Count	Percentage	Possible Source
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATG	22	0.5499999999999999	RNA PCR Primer, Index 14 (100% over 49bp)
GGGCGTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	20	0.5	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCTATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	13	0.325	RNA PCR Primer, Index 14 (100% over 41bp)
CAGGGTACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	13	0.325	RNA PCR Primer, Index 14 (100% over 41bp)
CAGAGTTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	12	0.3	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCTTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	12	0.3	RNA PCR Primer, Index 14 (100% over 41bp)
GCGGAATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	11	0.27499999999999997	RNA PCR Primer, Index 14 (100% over 41bp)
GGAATGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	11	0.27499999999999997	RNA PCR Primer, Index 14 (100% over 41bp)
GGAATCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	10	0.25	RNA PCR Primer, Index 14 (100% over 41bp)
CAGTGTACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	10	0.25	RNA PCR Primer, Index 14 (100% over 41bp)
CAGCGTGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	10	0.25	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	10	0.25	RNA PCR Primer, Index 14 (100% over 41bp)
CGGAATTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	9	0.22499999999999998	RNA PCR Primer, Index 14 (100% over 41bp)
CGGACTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	9	0.22499999999999998	RNA PCR Primer, Index 14 (100% over 41bp)
CGGATCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	9	0.22499999999999998	RNA PCR Primer, Index 14 (100% over 41bp)
GGACGTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	8	0.2	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	8	0.2	RNA PCR Primer, Index 14 (100% over 41bp)
GCGGGTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	8	0.2	RNA PCR Primer, Index 14 (100% over 41bp)
CGGATATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	8	0.2	RNA PCR Primer, Index 14 (100% over 41bp)
GCGGATTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	8	0.2	RNA PCR Primer, Index 14 (100% over 41bp)
GGAAGTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	8	0.2	RNA PCR Primer, Index 14 (100% over 41bp)
GGAAGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	8	0.2	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCGATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	8	0.2	RNA PCR Primer, Index 14 (100% over 41bp)
CGGATGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	8	0.2	RNA PCR Primer, Index 14 (100% over 41bp)
GGGTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
GGGAGTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
CACAGATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
GGAATATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
CAGGCATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
GCGGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
CGGACATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
GGACTATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
CGGCTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
GGGTGTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
CGGACTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 41bp)
CAGGTATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
GGGACATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
CGGAGTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
GGAACTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
CACGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCATTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCATGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
GGGAAGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
CACACGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
CGAGGTTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
CAGGCTTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
CACACATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
GCGGCTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCAATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
CACAGTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	6	0.15	RNA PCR Primer, Index 14 (100% over 41bp)
CAGTAATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CGGGCTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CGGGTTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGGATGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CGGGTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CACGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGTCTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGAAAGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CACGCGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGGATTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCTTAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGGATATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CGGAAATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GCGGGATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGTCTATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGAACGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CGGGATTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CGGACAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
AGGAGTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CAGTGTGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CACATATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
CGGATTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
GGGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCAT	5	0.125	RNA PCR Primer, Index 14 (100% over 41bp)
>>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	0.575	0.0	0.0	0.0
2	0.0	0.8	0.0	0.0	0.0
3	0.0	0.875	0.0	0.0	0.0
4	0.0	0.95	0.0	0.0	0.0
5	0.0	1.1	0.0	0.0	0.0
6	0.0	1.425	0.0	0.0	0.0
7	0.0	1.85	0.0	0.0	0.0
8	0.0	3.375	0.0	0.0	0.0
9	0.0	76.125	0.0	0.0	0.0
10	0.0	78.025	0.0	0.0	0.0
11	0.0	79.8	0.0	0.0	0.0
12	0.0	80.725	0.0	0.0	0.0
13	0.0	81.875	0.0	0.0	0.0
14	0.0	82.35	0.0	0.0	0.0
15	0.0	82.4	0.0	0.0	0.0
16	0.0	82.425	0.0	0.0	0.0
17	0.0	82.45	0.0	0.0	0.0
18	0.0	82.525	0.0	0.0	0.0
19	0.0	82.65	0.0	0.0	0.0
20	0.0	85.35	0.0	0.0	0.0
21	0.0	86.475	0.0	0.0	0.0
22	0.0	86.8	0.0	0.0	0.0
23	0.0	87.225	0.0	0.0	0.0
24	0.0	87.575	0.0	0.0	0.0
25	0.0	88.1	0.0	0.0	0.0
26	0.0	88.55	0.0	0.0	0.0
27	0.0	88.975	0.0	0.0	0.0
28	0.0	89.6	0.0	0.0	0.0
29	0.0	90.05	0.0	0.0	0.0
30	0.0	90.6	0.0	0.0	0.0
31	0.0	91.375	0.0	0.0	0.0
32	0.0	92.1	0.0	0.0	0.0
33	0.0	93.975	0.0	0.0	0.0
34	0.0	94.475	0.0	0.0	0.0
35	0.0	94.8	0.0	0.0	0.0
36	0.0	95.15	0.0	0.0	0.0
37	0.0	95.425	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATGGTGG	20	7.7972177E-4	42.987503	5
CTGGTGG	20	7.7972177E-4	42.987503	5
TTGTGGA	40	6.531991E-9	42.987503	6
TGGTGGA	40	6.531991E-9	42.987503	6
GTTGTGG	20	7.7972177E-4	42.987503	5
GTTCCAT	285	0.0	39.216667	43
AGTTCCA	295	0.0	37.887287	42
GGTGGAA	80	0.0	37.614063	7
CAGTTCC	300	0.0	37.255833	41
CCAGTCA	305	0.0	36.64508	34
TCCAGTC	305	0.0	36.64508	33
CAGTCAC	310	0.0	36.05403	35
GTCACAG	310	0.0	36.05403	37
TCACAGT	310	0.0	36.05403	38
AGTCACA	310	0.0	36.05403	36
ACAGTTC	310	0.0	36.05403	40
CACAGTT	315	0.0	35.481747	39
TGTGGAA	110	0.0	35.17159	7
CTCCAGT	320	0.0	34.927345	32
ACTCCAG	325	0.0	34.39	31
>>END_MODULE
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384946 spots for SRR6235374.sra
Written 384946 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
Read 384927 spots for SRR6235374.sra
Written 384927 spots for SRR6235374.sra
SRR ids: ['SRR6235374.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_3z6v913x
SRR6235374.sra spots: 7698559
blocks: [[1, 384927], [384928, 769854], [769855, 1154781], [1154782, 1539708], [1539709, 1924635], [1924636, 2309562], [2309563, 2694489], [2694490, 3079416], [3079417, 3464343], [3464344, 3849270], [3849271, 4234197], [4234198, 4619124], [4619125, 5004051], [5004052, 5388978], [5388979, 5773905], [5773906, 6158832], [6158833, 6543759], [6543760, 6928686], [6928687, 7313613], [7313614, 7698559]]
SRR6235374 file size 1220540
SRR6235374 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR6235374 SRR6235374_1.fastq
Input file:	SRR6235374_1.fastq
trimmed:	SRR6235374-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 
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	20
Thu Jun 26 12:17:40 2025 >> started

Thu Jun 26 12:17:43 2025 >> done (2.987s)
7698559 reads processed; of these:
    110 ( 0.00%) short reads filtered out after trimming by size control
     19 ( 0.00%) empty reads filtered out after trimming by size control
7698430 (100.00%) reads available; of these:
  51332 ( 0.67%) trimmed reads available after processing
7647098 (99.33%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     19	  0.00%
 19	     35	  0.00%
 20	     44	  0.00%
 21	     65	  0.00%
 22	    347	  0.00%
 23	    278	  0.00%
 24	    142	  0.00%
 25	    784	  0.01%
 26	    241	  0.00%
 27	    341	  0.00%
 28	    210	  0.00%
 29	    297	  0.00%
 30	    664	  0.01%
 31	    372	  0.00%
 32	    387	  0.01%
 33	    312	  0.00%
 34	    956	  0.01%
 35	   1757	  0.02%
 36	   1624	  0.02%
 37	   1002	  0.01%
 38	   1080	  0.01%
 39	    845	  0.01%
 40	    995	  0.01%
 41	   2648	  0.03%
 42	   1561	  0.02%
 43	   2338	  0.03%
 44	   1964	  0.03%
 45	   6471	  0.08%
 46	   6671	  0.09%
 47	   6308	  0.08%
 48	  10574	  0.14%
 49	7647098	 99.33%
7698430 reads passed initial QC


criterion=sequence-density
sequence-density=34.85
sequence-density-rank=1
fanout-score=44.33
fanout-score-rank=1
prefix-density=35.11
prefix-fanout=44.0
sequence=TGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC


criterion=fanout-score
sequence-density=34.85
sequence-density-rank=1
fanout-score=44.33
fanout-score-rank=1
prefix-density=35.11
prefix-fanout=44.0
sequence=TGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC
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 -f sanger -l 18 -t 20 -x TGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC -o SRR6235374 -
Input file:	STDIN
trimmed:	SRR6235374-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC
-- 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):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	20
Thu Jun 26 12:17:55 2025 >> started

Thu Jun 26 12:17:59 2025 >> done (3.914s)
7258520 reads processed; of these:
6027650 (83.04%) short reads filtered out after trimming by size control
  56504 ( 0.78%) empty reads filtered out after trimming by size control
1174366 (16.18%) reads available; of these:
 453257 (38.60%) trimmed reads available after processing
 721109 (61.40%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  45007	  3.83%
 19	  17233	  1.47%
 20	  16755	  1.43%
 21	  24072	  2.05%
 22	  22897	  1.95%
 23	  20856	  1.78%
 24	  24030	  2.05%
 25	  25379	  2.16%
 26	  24191	  2.06%
 27	  31528	  2.68%
 28	  40613	  3.46%
 29	  36821	  3.14%
 30	  70768	  6.03%
 31	  20676	  1.76%
 32	   5351	  0.46%
 33	   4621	  0.39%
 34	   3332	  0.28%
 35	   4358	  0.37%
 36	   5949	  0.51%
 37	   3346	  0.28%
 38	   3881	  0.33%
 39	   2497	  0.21%
 40	   2204	  0.19%
 41	   1424	  0.12%
 42	   1312	  0.11%
 43	   1187	  0.10%
 44	   1137	  0.10%
 45	   1306	  0.11%
 46	   1285	  0.11%
 47	   1325	  0.11%
 48	   1883	  0.16%
 49	 707142	 60.21%


criterion=sequence-density
sequence-density=54.92
sequence-density-rank=1
fanout-score=41.04
fanout-score-rank=3
prefix-density=61.45
prefix-fanout=36.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=12
fanout-score=48.19
fanout-score-rank=1
prefix-density=0.95
prefix-fanout=1.2
sequence=CGACGATCCCATTCTTGACACCA
                                 Started job on |	Jun 26 12:18:13
                             Started mapping on |	Jun 26 12:18:14
                                    Finished on |	Jun 26 12:18:34
       Mapping speed, Million of reads per hour |	290.57

                          Number of input reads |	1614276
                      Average input read length |	42
                                    UNIQUE READS:
                   Uniquely mapped reads number |	137047
                        Uniquely mapped reads % |	8.49%
                          Average mapped length |	26.03
                       Number of splices: Total |	7616
            Number of splices: Annotated (sjdb) |	713
                       Number of splices: GT/AG |	7211
                       Number of splices: GC/AG |	214
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	190
                      Mismatch rate per base, % |	2.07%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.55
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.90
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	162228
             % of reads mapped to multiple loci |	10.05%
        Number of reads mapped to too many loci |	76110
             % of reads mapped to too many loci |	4.71%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	76.49%
                     % of reads unmapped: other |	0.26%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1315001	1315001	1315001
N_multimapping	162228	162228	162228
N_noFeature	125375	129458	132498
N_ambiguous	485	12	12
UnstrandedReadsAssigned:11187 PositiveStrandReadsAssigned:7577 NegativeStrandReadsAssigned:4537
Dataset is classified unstranded
MeadianReadLen=49 20thPercentileLength=27 echo kmer=23
SRR6235374 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=23

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[index] k-mer length: 23
[index] number of targets: 72,539
[index] number of k-mers: 57,809,627
[index] number of equivalence classes: 250,891
[quant] running in single-end mode
[quant] will process file 1: SRR6235374-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,614,276 reads, 111,967 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 763 rounds

  72540 SRR6235374.ke.tsv
  44303 SRR6235374.se.tsv
 116843 total
==> SRR6235374.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	0	0
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	0	0
Zm00001eb080260_T001	3529	3430	0	0
Zm00001eb026490_T001	2433	2334	0	0
Zm00001eb026490_T002	2229	2130	0.0378693	0.131501
Zm00001eb026490_T003	2220	2121	0.962131	3.35517
Zm00001eb281360_T001	2412	2313	0	0

==> SRR6235374.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR6235374 completed mapping pipeline successfully
