Starting /dee2/code/volunteer_pipeline.sh SRR6978711
    current disk space = 127851792
    free memory = 59495944 
SRR6978711 SRAfilesize
3b5876f8c8558f23a7afc479c26c1d9c  SRR6978711.sra
SRR6978711.sra file validated
SRR6978711 is single end
SRR6978711 is conventional basespace
SRR6978711 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR6978711_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	54
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.8715	33.0	33.0	33.0	33.0	33.0
2	31.9795	33.0	33.0	33.0	33.0	33.0
3	31.895	33.0	33.0	33.0	33.0	33.0
4	32.06875	33.0	33.0	33.0	33.0	33.0
5	32.18275	33.0	33.0	33.0	33.0	33.0
6	35.6945	37.0	37.0	37.0	33.0	37.0
7	35.88725	37.0	37.0	37.0	33.0	37.0
8	36.0885	37.0	37.0	37.0	37.0	37.0
9	36.15425	37.0	37.0	37.0	37.0	37.0
10	36.21925	37.0	37.0	37.0	37.0	37.0
11	36.0975	37.0	37.0	37.0	37.0	37.0
12	36.15275	37.0	37.0	37.0	37.0	37.0
13	36.1715	37.0	37.0	37.0	37.0	37.0
14	36.0895	37.0	37.0	37.0	37.0	37.0
15	36.187	37.0	37.0	37.0	37.0	37.0
16	36.161	37.0	37.0	37.0	37.0	37.0
17	36.128	37.0	37.0	37.0	37.0	37.0
18	36.0595	37.0	37.0	37.0	37.0	37.0
19	36.13925	37.0	37.0	37.0	37.0	37.0
20	36.08425	37.0	37.0	37.0	37.0	37.0
21	36.08175	37.0	37.0	37.0	37.0	37.0
22	36.06975	37.0	37.0	37.0	37.0	37.0
23	36.039	37.0	37.0	37.0	37.0	37.0
24	35.89	37.0	37.0	37.0	37.0	37.0
25	36.0125	37.0	37.0	37.0	37.0	37.0
26	36.021	37.0	37.0	37.0	37.0	37.0
27	36.03975	37.0	37.0	37.0	37.0	37.0
28	36.144	37.0	37.0	37.0	37.0	37.0
29	36.023	37.0	37.0	37.0	37.0	37.0
30	35.99225	37.0	37.0	37.0	37.0	37.0
31	36.0595	37.0	37.0	37.0	37.0	37.0
32	36.0265	37.0	37.0	37.0	37.0	37.0
33	36.0305	37.0	37.0	37.0	37.0	37.0
34	36.064	37.0	37.0	37.0	37.0	37.0
35	36.04725	37.0	37.0	37.0	37.0	37.0
36	35.971	37.0	37.0	37.0	37.0	37.0
37	35.93425	37.0	37.0	37.0	37.0	37.0
38	35.81925	37.0	37.0	37.0	37.0	37.0
39	36.0335	37.0	37.0	37.0	37.0	37.0
40	35.86825	37.0	37.0	37.0	37.0	37.0
41	35.92175	37.0	37.0	37.0	37.0	37.0
42	35.92875	37.0	37.0	37.0	37.0	37.0
43	35.8995	37.0	37.0	37.0	37.0	37.0
44	35.89725	37.0	37.0	37.0	37.0	37.0
45	35.91725	37.0	37.0	37.0	37.0	37.0
46	35.939	37.0	37.0	37.0	37.0	37.0
47	35.9125	37.0	37.0	37.0	37.0	37.0
48	35.7785	37.0	37.0	37.0	37.0	37.0
49	35.684	37.0	37.0	37.0	37.0	37.0
50	35.677	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
2	19.0
3	0.0
4	0.0
5	1.0
6	1.0
7	0.0
8	2.0
9	0.0
10	2.0
11	3.0
12	0.0
13	1.0
14	0.0
15	0.0
16	1.0
17	3.0
18	0.0
19	1.0
20	1.0
21	5.0
22	2.0
23	4.0
24	6.0
25	9.0
26	10.0
27	15.0
28	36.0
29	30.0
30	41.0
31	44.0
32	75.0
33	102.0
34	144.0
35	305.0
36	3137.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	30.625000000000004	21.349999999999998	26.650000000000002	21.375
2	24.725	19.950000000000003	20.175	35.15
3	32.4	20.05	18.525	29.025000000000002
4	39.45	20.125	19.75	20.674999999999997
5	25.2	30.0	21.25	23.549999999999997
6	23.730932733183295	20.080020005001252	34.133533383345835	22.05551387846962
7	42.05	20.525	18.75	18.675
8	24.075	21.85	35.425000000000004	18.65
9	24.95	31.075000000000003	19.6	24.375
10	42.0	19.55	19.025	19.425
11	25.6	18.575	31.55	24.275
12	25.650000000000002	21.475	24.099999999999998	28.775000000000002
13	22.650000000000002	19.55	24.6	33.2
14	23.45	36.7	18.55	21.3
15	37.275000000000006	24.925	18.9	18.9
16	26.900000000000002	19.35	24.474999999999998	29.275000000000002
17	40.8	17.575	22.125	19.5
18	41.525	17.424999999999997	20.474999999999998	20.575
19	26.674999999999997	18.55	35.475	19.3
20	29.25	21.95	31.15	17.65
21	30.099999999999998	34.2	18.525	17.175
22	40.525	23.575	21.4	14.499999999999998
23	37.824999999999996	24.975	23.974999999999998	13.225000000000001
24	25.650000000000002	34.475	25.650000000000002	14.224999999999998
25	23.3	22.6	41.0	13.100000000000001
26	21.3	29.15	33.050000000000004	16.5
27	20.9	20.549999999999997	37.025000000000006	21.525
28	21.9	16.45	32.925	28.725
29	26.05	15.75	33.975	24.224999999999998
30	39.825	13.925	28.999999999999996	17.25
31	37.55	11.65	25.8	25.0
32	33.85	12.775	26.375	27.0
33	32.35	11.200000000000001	37.05	19.400000000000002
34	37.525	9.9	30.5	22.075
35	38.1	11.700000000000001	24.55	25.650000000000002
36	36.5	20.25	17.849999999999998	25.4
37	30.349999999999998	27.200000000000003	16.35	26.1
38	32.125	23.799999999999997	19.775000000000002	24.3
39	34.75	23.474999999999998	21.775	20.0
40	33.475	25.275	15.525	25.724999999999998
41	31.175000000000004	25.525	15.825	27.474999999999998
42	28.775000000000002	26.75	15.950000000000001	28.525
43	29.675	27.775	11.675	30.875000000000004
44	32.550000000000004	28.525	10.45	28.475
45	31.225	26.8	10.625	31.35
46	25.25	28.525	18.4	27.825
47	24.349999999999998	28.749999999999996	17.4	29.5
48	24.6	26.1	13.825000000000001	35.475
49	18.54454203262233	27.578419071518194	14.68005018820577	39.1969887076537
50	16.225	30.225	14.35	39.2
>>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	0.5
22	1.0
23	0.5
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.5
30	1.0
31	1.0
32	1.0
33	1.5
34	2.0
35	1.5
36	1.0
37	2.5
38	4.0
39	10.0
40	16.0
41	24.5
42	33.0
43	63.0
44	93.0
45	119.0
46	145.0
47	207.0
48	269.0
49	399.5
50	530.0
51	557.5
52	585.0
53	542.0
54	499.0
55	566.0
56	633.0
57	569.0
58	505.0
59	419.0
60	333.0
61	252.5
62	172.0
63	144.0
64	116.0
65	81.0
66	46.0
67	28.0
68	10.0
69	7.0
70	4.0
71	2.0
72	0.0
73	0.5
74	1.0
75	0.5
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	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.025
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	0.375
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	65.85
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.35763097949885	57.525000000000006
2	6.454062262718299	8.5
3	1.9362186788154898	3.8249999999999997
4	1.1769172361427487	3.1
5	0.7972665148063782	2.625
6	0.3416856492027335	1.35
7	0.22779043280182232	1.05
8	0.26575550493545935	1.4000000000000001
9	0.22779043280182232	1.35
>10	1.1009870918754745	13.55
>50	0.11389521640091116	5.7250000000000005
>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	fail
#Sequence	Count	Percentage	Possible Source
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTGGAATTCTCGGGTGCCA	90	2.25	No Hit
GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC	72	1.7999999999999998	No Hit
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTTGGAATTCTCGGGTGCC	67	1.675	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTGGAATTCTCGGGTGCC	46	1.15	No Hit
GCGCCTGTAGCTCAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTC	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 31bp)
TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	43	1.075	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGGAATTCTCGGGTGCCA	36	0.8999999999999999	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTGGAATTCTCGGGTGCCA	28	0.7000000000000001	No Hit
TTTGTCGCTAAGATTCGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 32bp)
GGCTGTCAGCGGACTGCTCGAGCTGCTTGGAATTCTCGGGTGCCAAGGAA	20	0.5	RNA PCR Primer, Index 1 (100% over 23bp)
GGGGATGTAGCTCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	18	0.44999999999999996	RNA PCR Primer, Index 2 (100% over 34bp)
CCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
GCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 22bp)
TAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
CGGCTGTCAGCGGACTGCTCGAGCTGCTTGGAATTCTCGGGTGCCAAGGA	16	0.4	RNA PCR Primer, Index 1 (100% over 22bp)
AGGGATGTAGCGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
TCCGTTATCGTCCAGCGGTTAGGATATCTGGCTGGAATTCTCGGGTGCCA	16	0.4	No Hit
AGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGT	15	0.375	RNA PCR Primer, Index 30 (100% over 46bp)
GGCGGATGTAGCCAAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
CAGCGGACTGCTCGAGCTGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
AACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACT	13	0.325	RNA PCR Primer, Index 1 (100% over 25bp)
CTTTGTCGCTAAGATTCGATGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
ACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCAGCGGACTGCTCGAGCTGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 32bp)
TCCGTTATCGTCCAGCGGTTAGGATATCTGGCTTGGAATTCTCGGGTGCC	11	0.27499999999999997	No Hit
TCGGCTGTCAGCGGACTGCTCGAGCTGCTTGGAATTCTCGGGTGCCAAGG	11	0.27499999999999997	Illumina Small RNA Adapter 2 (100% over 21bp)
CAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 31bp)
TCGGACCAGGCTTCATCCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGGAATTCTCGGGTGCCAA	10	0.25	No Hit
AATAACAATACCGGGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
ACGCATTTATTAGATAAAAGGTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TCCGTTGTCGTCCAGCGGTTAGGATATCTGGCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
GCTAAGTCCGTTCGGCGGAAGCGTCGTTCTGGAATTCTCGGGTGCCAAGG	9	0.22499999999999998	Illumina Small RNA Adapter 2 (100% over 21bp)
TCGGTCGGCGATACGCTCCTGGTCTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
GGCTAAGTCCGTTCGGCGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGC	8	0.2	RNA PCR Primer, Index 30 (100% over 50bp)
CTGTCAGCGGACTGCTCGAGCTGCTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCAAATGTAGACAAAGCATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
GGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTTGGAATTCTCGGGTGC	8	0.2	No Hit
GCGGACTGCTCGAGCTGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
TCCGTTGTCGTCCAGCGGTTAGGATATCTGGCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
AACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CAGCGGACTGCTCGAGCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
GACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 33bp)
GGGGATGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	7	0.17500000000000002	RNA PCR Primer, Index 2 (100% over 34bp)
TGTCAGCGGACTGCTCGAGCTGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TAAATAACAATACCGGGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCGGTCGGCGATACGCTCCTGGTCTTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
GGGGGTGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	6	0.15	RNA PCR Primer, Index 2 (100% over 34bp)
CCTTTGTCGCTAAGATTCGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GCGTCTGTAGTCCAACGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
ACCCCTGTTTTTGGTCCCAAGGCTCTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
GGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGT	6	0.15	RNA PCR Primer, Index 30 (100% over 46bp)
CGGTCGGCGATACGCTCCTGGTCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CCTTGGGATGGGTCGGCCGGTCCGCCTTGGAATTCTCGGGTGCCAAGGAA	6	0.15	RNA PCR Primer, Index 1 (100% over 23bp)
CGGACTGCTCGAGCTGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
GGGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCG	5	0.125	RNA PCR Primer, Index 30 (100% over 45bp)
GAGCCTATAGCTCAGTGGTAGAGCAATTGACTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCCATTGTCGTCCAGCGGTTAGGATATCTGGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCGGCGATACGCTCCTGGTCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGGATTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCG	5	0.125	RNA PCR Primer, Index 30 (100% over 45bp)
CCCTTTGTCGCTAAGATTCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
GACTCTGGCCCAATGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GGCTGTCAGCGGACTGCTCGAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTGACATGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGG	5	0.125	RNA PCR Primer, Index 30 (100% over 39bp)
GTCGGGGGCATTCGTATTTCATAGTCATGGAATTCTCGGGTGCCAAGGAA	5	0.125	RNA PCR Primer, Index 1 (100% over 23bp)
TAAAACGACTCTCGGCAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
GTCGTTGTAGTATAGTGGTAAGTATTCCCGCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
ATAAATAACAATACCGGGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGATGTAGCTCAAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
GGTCCCAGTTCCGAACCCGTCGGCTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CCGTAGTAATTCTAGAGCTATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAGCCCTTTGTCGCTAAGATTCGATGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
CTTCGGTCGGCGATACGCTCCTGGTCTTGGAATTCTCGGGTGCCAAGGAA	5	0.125	RNA PCR Primer, Index 1 (100% over 23bp)
>>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	0.225	0.0	0.0	0.0
2	0.0	0.225	0.0	0.0	0.0
3	0.0	0.25	0.0	0.0	0.0
4	0.0	0.275	0.0	0.0	0.0
5	0.0	1.225	0.0	0.0	0.0
6	0.0	2.025	0.0	0.0	0.0
7	0.0	2.375	0.0	0.0	0.0
8	0.0	2.55	0.0	0.0	0.0
9	0.0	2.75	0.0	0.0	0.0
10	0.0	3.0	0.0	0.0	0.0
11	0.0	3.175	0.0	0.0	0.0
12	0.0	3.55	0.0	0.0	0.0
13	0.0	3.7	0.0	0.0	0.0
14	0.0	3.95	0.0	0.0	0.0
15	0.0	4.325	0.0	0.0	0.0
16	0.0	4.55	0.0	0.0	0.0
17	0.0	6.65	0.0	0.0	0.0
18	0.0	10.3	0.0	0.0	0.0
19	0.0	15.525	0.0	0.0	0.0
20	0.0	22.55	0.0	0.0	0.0
21	0.0	28.725	0.0	0.0	0.0
22	0.0	36.9	0.0	0.0	0.0
23	0.0	42.475	0.0	0.0	0.0
24	0.0	48.175	0.0	0.0	0.0
25	0.0	54.325	0.0	0.0	0.0
26	0.0	59.975	0.0	0.0	0.0
27	0.0	65.0	0.0	0.0	0.0
28	0.0	69.875	0.0	0.0	0.0
29	0.0	74.675	0.0	0.0	0.0
30	0.0	78.4	0.0	0.0	0.0
31	0.0	80.65	0.0	0.0	0.0
32	0.0	82.975	0.0	0.0	0.0
33	0.0	89.375	0.0	0.0	0.0
34	0.0	95.6	0.0	0.0	0.0
35	0.0	96.65	0.0	0.0	0.0
36	0.0	96.925	0.0	0.0	0.0
37	0.0	97.375	0.0	0.0	0.0
38	0.0	97.5	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TAGGATA	25	3.7082697E-5	43.975002	20
CCAGCGG	25	3.7082697E-5	43.975002	12
AGGATAT	25	3.7082697E-5	43.975002	21
GTCGTCC	25	3.7082697E-5	43.975002	7
GCGGTTA	25	3.7082697E-5	43.975002	15
TCCAGCG	25	3.7082697E-5	43.975002	11
GGTTAGG	25	3.7082697E-5	43.975002	17
AGCGGTT	25	3.7082697E-5	43.975002	14
GTCCAGC	25	3.7082697E-5	43.975002	10
TCGTCCA	25	3.7082697E-5	43.975002	8
GTTAGGA	25	3.7082697E-5	43.975002	18
TTAGGAT	25	3.7082697E-5	43.975002	19
CAGCGGT	25	3.7082697E-5	43.975002	13
CGGTTAG	25	3.7082697E-5	43.975002	16
CGTCCAG	25	3.7082697E-5	43.975002	9
TCTGGCT	20	6.971556E-4	43.975	27
ATCTGGC	20	6.971556E-4	43.975	26
TGTCGTC	20	6.971556E-4	43.975	6
GATATCT	25	0.0020901307	35.18	23
GGATATC	25	0.0020901307	35.18	22
>>END_MODULE
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
Rejected 3928459 READS because READLEN < 1
Read 3928459 spots for SRR6978711.sra
Written 3928459 spots for SRR6978711.sra
Rejected 3928454 READS because READLEN < 1
Read 3928454 spots for SRR6978711.sra
Written 3928454 spots for SRR6978711.sra
SRR ids: ['SRR6978711.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ofx7tvdt
SRR6978711.sra spots: 62855269
blocks: [[1, 3928454], [3928455, 7856908], [7856909, 11785362], [11785363, 15713816], [15713817, 19642270], [19642271, 23570724], [23570725, 27499178], [27499179, 31427632], [31427633, 35356086], [35356087, 39284540], [39284541, 43212994], [43212995, 47141448], [47141449, 51069902], [51069903, 54998356], [54998357, 58926810], [58926811, 62855269]]
SRR6978711 file size 8817328
SRR6978711 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 16 -o SRR6978711 SRR6978711_1.fastq
Input file:	SRR6978711_1.fastq
trimmed:	SRR6978711-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):	16
Wed Nov 11 20:25:06 2020 >> started

Wed Nov 11 20:26:32 2020 >> done (85.237s)
62855269 reads processed; of these:
   94517 ( 0.15%) short reads filtered out after trimming by size control
  208236 ( 0.33%) empty reads filtered out after trimming by size control
62552516 (99.52%) reads available; of these:
 1697238 ( 2.71%) trimmed reads available after processing
60855278 (97.29%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    6027	  0.01%
 19	    7119	  0.01%
 20	    7341	  0.01%
 21	    8297	  0.01%
 22	    8731	  0.01%
 23	    9808	  0.02%
 24	   10479	  0.02%
 25	   13469	  0.02%
 26	   12704	  0.02%
 27	   13563	  0.02%
 28	   12298	  0.02%
 29	   13239	  0.02%
 30	   12530	  0.02%
 31	   14787	  0.02%
 32	   10992	  0.02%
 33	   13236	  0.02%
 34	   16379	  0.03%
 35	   18658	  0.03%
 36	   18193	  0.03%
 37	   20693	  0.03%
 38	   20814	  0.03%
 39	   26476	  0.04%
 40	   23131	  0.04%
 41	   25262	  0.04%
 42	   32214	  0.05%
 43	   42692	  0.07%
 44	   54983	  0.09%
 45	   71880	  0.11%
 46	   98711	  0.16%
 47	  162183	  0.26%
 48	  309707	  0.50%
 49	  580642	  0.93%
 50	60855278	 97.29%
62552516 reads passed initial QC


criterion=sequence-density
sequence-density=97.43
sequence-density-rank=1
fanout-score=27.55
fanout-score-rank=2
prefix-density=98.17
prefix-fanout=27.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC


criterion=fanout-score
sequence-density=3.07
sequence-density-rank=4
fanout-score=34.02
fanout-score-rank=1
prefix-density=3.08
prefix-fanout=33.9
sequence=GTTGGAATTCTC
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 16 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC -o SRR6978711 -
Input file:	STDIN
trimmed:	SRR6978711-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC
-- 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):	16
Wed Nov 11 20:29:07 2020 >> started

Wed Nov 11 20:30:54 2020 >> done (106.844s)
61275934 reads processed; of these:
 6528660 (10.65%) short reads filtered out after trimming by size control
  107544 ( 0.18%) empty reads filtered out after trimming by size control
54639730 (89.17%) reads available; of these:
54398776 (99.56%) trimmed reads available after processing
  240954 ( 0.44%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 3109731	  5.69%
 19	 4313552	  7.89%
 20	 3919647	  7.17%
 21	 5197816	  9.51%
 22	 3734149	  6.83%
 23	 3685436	  6.74%
 24	 3712562	  6.79%
 25	 3336307	  6.11%
 26	 3004959	  5.50%
 27	 3253921	  5.96%
 28	 2966418	  5.43%
 29	 2268620	  4.15%
 30	 1391457	  2.55%
 31	 1522228	  2.79%
 32	 3753411	  6.87%
 33	 4054477	  7.42%
 34	  540964	  0.99%
 35	  241909	  0.44%
 36	  148946	  0.27%
 37	  111029	  0.20%
 38	   71778	  0.13%
 39	   53574	  0.10%
 40	   51872	  0.09%
 41	   28688	  0.05%
 42	   16764	  0.03%
 43	   12057	  0.02%
 44	    6595	  0.01%
 45	    5180	  0.01%
 46	    3626	  0.01%
 47	    3259	  0.01%
 48	    1262	  0.00%
 49	    1850	  0.00%
 50	  115686	  0.21%


criterion=sequence-density
sequence-density=4.45
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTTTCACCCAGGA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=27
fanout-score=7.66
fanout-score-rank=1
prefix-density=0.03
prefix-fanout=1.6
sequence=TGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTACGTGGAGGCATCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCGTTTAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTTCACACCTTGGCC
                                 Started job on |	Nov 11 20:32:37
                             Started mapping on |	Nov 11 20:32:39
                                    Finished on |	Nov 11 20:38:21
       Mapping speed, Million of reads per hour |	588.59

                          Number of input reads |	55916312
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	5790327
                        Uniquely mapped reads % |	10.36%
                          Average mapped length |	24.62
                       Number of splices: Total |	204130
            Number of splices: Annotated (sjdb) |	31091
                       Number of splices: GT/AG |	197229
                       Number of splices: GC/AG |	4144
                       Number of splices: AT/AC |	193
               Number of splices: Non-canonical |	2564
                      Mismatch rate per base, % |	0.38%
                         Deletion rate per base |	0.02%
                        Deletion average length |	1.15
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.01
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	43662474
             % of reads mapped to multiple loci |	78.09%
        Number of reads mapped to too many loci |	4265923
             % of reads mapped to too many loci |	7.63%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	2.81%
                     % of reads unmapped: other |	1.12%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	6463511	6463511	6463511
N_multimapping	43662474	43662474	43662474
N_noFeature	1228180	1450339	5204647
N_ambiguous	455513	90536	5200
UnstrandedReadsAssigned:4106634 PositiveStrandReadsAssigned:4249452 NegativeStrandReadsAssigned:580480
Dataset is classified positive stranded
MeadianReadLen=24 20thPercentileLength=20 echo kmer=19
SRR6978711 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: 48,359
[index] number of k-mers: 44,957,248
[index] number of equivalence classes: 195,259
[quant] running in single-end mode
[quant] will process file 1: SRR6978711-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 55,916,312 reads, 1,319,560 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,165 rounds

  48360 SRR6978711.ke.tsv
  32833 SRR6978711.se.tsv
  81193 total
==> SRR6978711.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	63	7.66929
AT1G18320.1	699	600	0	0
AT5G11100.1	1709	1610	0	0
AT4G35335.1	1280	1181	6	1.4905
AT1G60930.1	3876	3777	1	0.0776756
AT1G17000.1	2351	2252	0	0
AT3G55270.1	3130	3031	48	4.64608
AT4G16150.1	3181	3082	120.7	11.4896
AT3G18150.1	1370	1271	0	0

==> SRR6978711.se.tsv <==
AT1G01010	17
AT1G01020	9
AT1G03987	0
AT1G01030	26
AT1G01040	44
AT1G03993	0
AT1G01046	4
AT1G01050	13
AT1G03997	0
AT1G01060	587
SRR6978711 completed mapping pipeline successfully
