Starting /dee2/code/volunteer_pipeline.sh SRR13079627
    current disk space = 414457593856
    free memory = 73803956 
SRR13079627 SRAfilesize
a726fbedb409e86369e529615393707f  SRR13079627.sra
SRR13079627.sra file validated
SRR13079627 is paired end
SRR13079627 is conventional basespace
SRR13079627 read1 length is 38 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR13079627_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	38
%GC	54
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.2805	32.0	32.0	32.0	32.0	32.0
2	31.3835	32.0	32.0	32.0	32.0	32.0
3	31.4475	32.0	32.0	32.0	32.0	32.0
4	31.521	32.0	32.0	32.0	32.0	32.0
5	31.327	32.0	32.0	32.0	32.0	32.0
6	34.70625	36.0	36.0	36.0	32.0	36.0
7	34.629	36.0	36.0	36.0	32.0	36.0
8	34.82625	36.0	36.0	36.0	32.0	36.0
9	34.86475	36.0	36.0	36.0	32.0	36.0
10	34.838	36.0	36.0	36.0	32.0	36.0
11	34.78875	36.0	36.0	36.0	32.0	36.0
12	35.0255	36.0	36.0	36.0	36.0	36.0
13	34.95025	36.0	36.0	36.0	36.0	36.0
14	34.89475	36.0	36.0	36.0	32.0	36.0
15	34.825	36.0	36.0	36.0	32.0	36.0
16	34.84775	36.0	36.0	36.0	32.0	36.0
17	34.98875	36.0	36.0	36.0	36.0	36.0
18	34.91425	36.0	36.0	36.0	32.0	36.0
19	35.03	36.0	36.0	36.0	36.0	36.0
20	34.80675	36.0	36.0	36.0	32.0	36.0
21	34.983	36.0	36.0	36.0	36.0	36.0
22	34.79925	36.0	36.0	36.0	32.0	36.0
23	34.77725	36.0	36.0	36.0	32.0	36.0
24	34.88	36.0	36.0	36.0	32.0	36.0
25	34.56825	36.0	36.0	36.0	32.0	36.0
26	34.8085	36.0	36.0	36.0	32.0	36.0
27	34.667	36.0	36.0	36.0	32.0	36.0
28	34.809	36.0	36.0	36.0	32.0	36.0
29	34.6735	36.0	36.0	36.0	32.0	36.0
30	34.53075	36.0	36.0	36.0	32.0	36.0
31	34.74425	36.0	36.0	36.0	32.0	36.0
32	34.6225	36.0	36.0	36.0	32.0	36.0
33	34.66475	36.0	36.0	36.0	32.0	36.0
34	34.659	36.0	36.0	36.0	32.0	36.0
35	34.6115	36.0	36.0	36.0	32.0	36.0
36	34.6575	36.0	36.0	36.0	32.0	36.0
37	34.68475	36.0	36.0	36.0	32.0	36.0
38	34.54525	36.0	36.0	36.0	32.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
19	1.0
20	0.0
21	1.0
22	0.0
23	6.0
24	13.0
25	8.0
26	15.0
27	24.0
28	43.0
29	80.0
30	112.0
31	145.0
32	202.0
33	288.0
34	754.0
35	2308.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	16.85	19.775000000000002	31.825	31.55
2	32.2	32.375	13.450000000000001	21.975
3	25.63140785196299	20.130032508127034	25.581395348837212	28.657164291072768
4	30.5	20.825	26.55	22.125
5	34.175	33.975	14.899999999999999	16.950000000000003
6	23.331660812844955	18.088309081786253	22.553938785750123	36.026091319618665
7	23.45	27.125	23.3	26.125
8	18.224999999999998	17.525	26.724999999999998	37.525
9	15.85	16.400000000000002	33.925	33.825
10	29.575000000000003	18.4	24.375	27.650000000000002
11	53.974999999999994	15.9	15.425	14.7
12	28.599999999999998	25.8	31.025000000000002	14.575
13	34.475	15.125	25.85	24.55
14	26.700000000000003	17.424999999999997	26.25	29.625
15	27.825	28.599999999999998	20.625	22.95
16	41.65	16.5	22.425	19.425
17	31.85	25.775	20.375	22.0
18	21.575	23.175	18.55	36.7
19	26.375	25.05	19.650000000000002	28.925
20	26.75	15.725	44.7	12.825000000000001
21	42.5	12.925	22.225	22.35
22	29.725	23.275000000000002	25.4	21.6
23	23.425	18.45	32.75	25.374999999999996
24	47.199999999999996	10.35	20.674999999999997	21.775
25	40.725	24.425	20.25	14.6
26	29.725	27.075	15.725	27.474999999999998
27	25.224999999999998	29.875	19.675	25.224999999999998
28	18.275	26.174999999999997	35.0	20.549999999999997
29	35.55	17.275	32.975	14.2
30	17.575	12.925	31.175000000000004	38.324999999999996
31	16.475	11.05	41.025	31.45
32	27.125	20.925	22.975	28.975
33	33.324999999999996	23.25	20.849999999999998	22.575
34	41.725	22.7	22.525000000000002	13.05
35	54.325	11.575000000000001	22.925	11.175
36	40.725	15.2	32.550000000000004	11.525
37	37.9	21.275	20.325	20.5
38	23.225	29.15	16.1	31.525
>>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	0.0
12	0.5
13	1.0
14	0.5
15	0.0
16	0.0
17	0.5
18	1.0
19	1.0
20	0.5
21	0.0
22	0.0
23	0.0
24	0.0
25	2.0
26	4.0
27	4.0
28	7.0
29	10.0
30	10.5
31	11.0
32	11.0
33	21.0
34	31.0
35	31.0
36	36.0
37	41.0
38	61.0
39	81.0
40	81.0
41	135.0
42	189.0
43	189.0
44	189.0
45	189.0
46	255.5
47	322.0
48	322.0
49	343.0
50	364.0
51	516.0
52	668.0
53	668.0
54	580.0
55	492.0
56	492.0
57	431.0
58	370.0
59	488.5
60	607.0
61	607.0
62	508.0
63	409.0
64	246.0
65	83.0
66	83.0
67	69.0
68	55.0
69	55.0
70	42.0
71	29.0
72	27.0
73	25.0
74	25.0
75	14.5
76	4.0
77	4.0
78	4.0
79	4.0
80	2.5
81	1.0
82	1.0
83	2.0
84	3.0
85	3.0
86	2.0
87	1.0
88	2.5
89	4.0
90	4.0
91	2.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.5
97	1.0
98	1.0
99	0.5
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.0
3	0.025
4	0.0
5	0.0
6	0.35000000000000003
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
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
38	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	45.800000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	84.71615720524017	38.800000000000004
2	6.495633187772926	5.949999999999999
3	2.5109170305676853	3.45
4	1.2008733624454149	2.1999999999999997
5	0.7096069868995634	1.625
6	0.9825327510917031	2.7
7	0.49126637554585156	1.575
8	0.43668122270742354	1.6
9	0.21834061135371177	0.8999999999999999
>10	1.8013100436681224	16.275000000000002
>50	0.16375545851528384	5.7250000000000005
>100	0.2729257641921397	19.2
>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
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCA	219	5.475	RNA PCR Primer, Index 13 (100% over 38bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAA	165	4.125	No Hit
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAAC	161	4.025	RNA PCR Primer, Index 1 (100% over 24bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGA	118	2.9499999999999997	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGC	105	2.625	No Hit
TATTGCACTTGTCCCGGCCTGATGGAATTCTCGGGTGC	92	2.3	No Hit
GAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTGGA	83	2.075	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTG	54	1.35	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTA	37	0.9249999999999999	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGC	35	0.8750000000000001	No Hit
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACT	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 25bp)
TGCTTGGACTACATATGGTTGAGGGTTGTATGGAATTC	32	0.8	No Hit
AAAGTGCTACTACTTTTGAGTCTTGGAATTCTCGGGTG	30	0.75	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGC	29	0.7250000000000001	No Hit
TTTGGCAATGGTAGAACTCACACCTGGAATTCTCGGGT	26	0.65	No Hit
GGCAGAGGAGGGCTGTTCTTCCCTGGAATTCTCGGGTG	26	0.65	No Hit
ACTCAAACTGGGGGCTCTTTTTGGAATTCTCGGGTGCC	26	0.65	No Hit
TCTTAGATCGATGTGGTGCTCCGGATGGAATTCTCGGG	25	0.625	No Hit
CAAGACAGATGTTCTGATCAAGGCCCGAGATTTTGGAA	24	0.6	No Hit
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 23bp)
TATTGCACTTGTCCCGGCCTGTAATGGAATTCTCGGGT	21	0.525	No Hit
CTCTTAGATCGATGTGGTGCTCCGGATGGAATTCTCGG	21	0.525	No Hit
TTTGGCAATGGTAGAACTCACACTGGAATTCTCGGGTG	19	0.475	No Hit
GAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTTGG	17	0.42500000000000004	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTG	17	0.42500000000000004	No Hit
CATCAAAGTGGAGGCCCTCTCTTGGAATTCTCGGGTGC	17	0.42500000000000004	No Hit
AAAGTGCCGCCAGGTTTTGAGTGTTGGAATTCTCGGGT	17	0.42500000000000004	No Hit
CATCAAAGTGGAGGCCCTCTCTTTGGAATTCTCGGGTG	16	0.4	No Hit
CCTGCATGATGACGAACAAATACTGACTTGGAATTCTC	15	0.375	No Hit
AAGTGCCGCCAGGTTTTGAGTGTTGGAATTCTCGGGTG	15	0.375	No Hit
GGCAGAGGAGGGCTGTTCTTCCTGGAATTCTCGGGTGC	15	0.375	No Hit
TCTTAGATCGATGTGGTGCTCCGGAATGGAATTCTCGG	13	0.325	No Hit
TATTGCACTTGTCCCGGCCTGTGGAATTCTCGGGTGCC	12	0.3	No Hit
TGAGGGGCAGAGAGCGAGACTTTTGGAATTCTCGGGTG	12	0.3	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGC	12	0.3	No Hit
TTGTGGCAACAATGGCACGGCAAGGGGATCCAGTCCTT	12	0.3	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGA	12	0.3	No Hit
AAGACAGATGTTCTGATCAAGGCCCGAGATTTTGGAAT	11	0.27499999999999997	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGC	11	0.27499999999999997	No Hit
AAGACAGATGTTCTGATCAAGGCCCGAGATTTTTGGAA	10	0.25	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGC	10	0.25	No Hit
GGCAGAGGAGGGCTGTTCTTCTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TCTTAGATCGATGTGGTGCTCCGGTGGAATTCTCGGGT	9	0.22499999999999998	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTT	9	0.22499999999999998	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTTTGGAATTCTC	8	0.2	No Hit
CTGGACGCGAGCCGGGCCCTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGG	8	0.2	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGGAATTC	8	0.2	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTGGAATTCTCGG	8	0.2	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTGGAATTC	8	0.2	No Hit
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGA	8	0.2	No Hit
AAATCTACCTGCCTCTGCCTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTTGGAATTCTCG	7	0.17500000000000002	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
GAATGTTGCTCGGTGAACCCCTTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
AAGTGCTACTACTTTTGAGTCTTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATG	7	0.17500000000000002	No Hit
CTCTTAGATCGATGTGGTGCTCCGGAATGGAATTCTCG	7	0.17500000000000002	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATT	7	0.17500000000000002	No Hit
ATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTTGGAAT	6	0.15	No Hit
CTCTTAGATCGATGTGGTGCTCCGGTGGAATTCTCGGG	6	0.15	No Hit
CGAATGTTGCTCGGTGAACCCCTTGGAATTCTCGGGTG	6	0.15	No Hit
GATCGATGTGGTGCTCCGGATGGAATTCTCGGGTGCCA	6	0.15	No Hit
CGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTAGTGGAATTCTCGGGT	6	0.15	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCC	6	0.15	No Hit
CGGTGGATCACTCGGCTCGTGCGTCGATTGGAATTCTC	6	0.15	No Hit
AGTGCCGCAGAGTTTGTAGTGTTGGAATTCTCGGGTGC	6	0.15	No Hit
AAATCTACCTGCCTCTGCCTCCTGGAATTCTCGGGTGC	6	0.15	No Hit
TATTGCACTTGTCCCGGCCTGTATGGAATTCTCGGGTG	6	0.15	No Hit
CAAGACAGATGTTCTGATCAAGGCCCGAGATTTTTGGA	6	0.15	No Hit
TATGGCACTGGTAGAATTCACTGTGGAATTCTCGGGTG	6	0.15	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGAT	6	0.15	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCC	6	0.15	No Hit
CCTGCATGATGACGAACAAATACTGACTACCTGAAGTG	6	0.15	No Hit
GTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGG	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGGTGGAA	5	0.125	No Hit
TATTGCACTTGTCCCGGCCTGATTGGAATTCTCGGGTG	5	0.125	No Hit
ATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGC	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACACTCTGGAATTCTCGG	5	0.125	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGT	5	0.125	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTGGAATT	5	0.125	No Hit
AGGTCAGAGGTCGATCCTGGGCTGGAATTCTCGGGTGC	5	0.125	No Hit
AGCAGTGATGACAGATTGGATCTGACTTGGAATTCTCG	5	0.125	No Hit
AATCTACCTGCCTCTGCCTCCTGGAATTCTCGGGTGCC	5	0.125	No Hit
CTCTTAGATCGATGTGGTGCTCCGGAAATGGAATTCTC	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAAT	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	5.7	0.0	0.0	0.0
2	0.0	5.7	0.0	0.0	0.0
3	0.0	5.7	0.0	0.0	0.0
4	0.0	5.725	0.0	0.0	0.0
5	0.0	5.825	0.0	0.0	0.0
6	0.0	6.05	0.0	0.0	0.0
7	0.0	6.25	0.0	0.0	0.0
8	0.0	6.425	0.0	0.0	0.0
9	0.0	6.575	0.0	0.0	0.0
10	0.0	7.05	0.0	0.0	0.0
11	0.0	7.575	0.0	0.0	0.0
12	0.0	8.05	0.0	0.0	0.0
13	0.0	8.6	0.0	0.0	0.0
14	0.0	10.075	0.0	0.0	0.0
15	0.0	14.7	0.0	0.0	0.0
16	0.0	16.025	0.0	0.0	0.0
17	0.0	16.925	0.0	0.0	0.0
18	0.0	17.7	0.0	0.0	0.0
19	0.0	18.7	0.0	0.0	0.0
20	0.0	19.65	0.0	0.0	0.0
21	0.0	21.275	0.0	0.0	0.0
22	0.0	25.775	0.0	0.0	0.0
23	0.0	39.55	0.0	0.0	0.0
24	0.0	47.375	0.0	0.0	0.0
25	0.0	51.925	0.0	0.0	0.0
26	0.0	54.825	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCGACC	40	8.843199E-8	32.0	1
CGCTGAT	25	2.4147211E-4	32.0	28
TGCACTT	20	0.0033271667	32.0	4
TTGTCCC	20	0.0033271667	32.0	9
TTGCACT	25	2.4147211E-4	32.0	3
ACTTGTC	20	0.0033271667	32.0	7
GCGACCT	40	8.843199E-8	32.0	2
GCGACCC	35	1.2459041E-6	32.0	22
TGTCCCG	20	0.0033271667	32.0	10
CCCGGCC	25	2.4147211E-4	32.0	13
CCGCTGA	30	1.7408885E-5	32.0	27
GGCGACC	35	1.2459041E-6	32.0	21
ACCCGCT	35	1.2459041E-6	32.0	25
TATTGCA	25	2.4147211E-4	32.0	1
CCCGCTG	30	1.7408885E-5	32.0	26
CGTGGCG	35	1.2459041E-6	32.0	18
ATCAGAC	40	8.843199E-8	32.0	12
GTCCCGG	25	2.4147211E-4	32.0	11
GCTGTGG	20	0.0033271667	32.0	20
AGACGTG	40	8.843199E-8	32.0	15
>>END_MODULE
SRR13079627 read2 length is 38 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR13079627_2.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	38
%GC	54
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.9165	32.0	32.0	32.0	32.0	32.0
2	30.89825	32.0	32.0	32.0	32.0	32.0
3	30.90125	32.0	32.0	32.0	32.0	32.0
4	30.98875	32.0	32.0	32.0	32.0	32.0
5	31.0065	32.0	32.0	32.0	32.0	32.0
6	34.45375	36.0	36.0	36.0	32.0	36.0
7	34.39175	36.0	36.0	36.0	32.0	36.0
8	34.30375	36.0	36.0	36.0	32.0	36.0
9	34.158	36.0	36.0	36.0	32.0	36.0
10	34.22575	36.0	36.0	36.0	32.0	36.0
11	34.19975	36.0	36.0	36.0	32.0	36.0
12	33.97025	36.0	36.0	36.0	32.0	36.0
13	34.112	36.0	36.0	36.0	32.0	36.0
14	34.13	36.0	36.0	36.0	32.0	36.0
15	34.3075	36.0	36.0	36.0	32.0	36.0
16	34.24125	36.0	36.0	36.0	32.0	36.0
17	34.16975	36.0	36.0	36.0	32.0	36.0
18	34.028	36.0	36.0	36.0	32.0	36.0
19	34.3545	36.0	36.0	36.0	32.0	36.0
20	34.2195	36.0	36.0	36.0	32.0	36.0
21	34.15025	36.0	36.0	36.0	32.0	36.0
22	34.1045	36.0	36.0	36.0	32.0	36.0
23	34.01525	36.0	36.0	36.0	32.0	36.0
24	33.9645	36.0	36.0	36.0	32.0	36.0
25	33.984	36.0	36.0	36.0	32.0	36.0
26	34.0885	36.0	36.0	36.0	32.0	36.0
27	34.21	36.0	36.0	36.0	32.0	36.0
28	33.86525	36.0	36.0	36.0	32.0	36.0
29	34.13325	36.0	36.0	36.0	32.0	36.0
30	33.98675	36.0	36.0	36.0	32.0	36.0
31	33.82475	36.0	36.0	36.0	32.0	36.0
32	33.70525	36.0	36.0	36.0	27.0	36.0
33	33.93925	36.0	36.0	36.0	32.0	36.0
34	34.04725	36.0	36.0	36.0	32.0	36.0
35	33.975	36.0	36.0	36.0	32.0	36.0
36	33.908	36.0	36.0	36.0	32.0	36.0
37	33.97725	36.0	36.0	36.0	32.0	36.0
38	33.19225	36.0	36.0	36.0	21.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
5	1.0
6	4.0
7	1.0
8	3.0
9	2.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	1.0
17	1.0
18	1.0
19	8.0
20	6.0
21	8.0
22	13.0
23	9.0
24	21.0
25	31.0
26	37.0
27	60.0
28	80.0
29	101.0
30	151.0
31	172.0
32	242.0
33	369.0
34	830.0
35	1848.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	21.696696696696698	32.98298298298298	25.925925925925924	19.394394394394393
2	25.6064016004001	27.406851712928233	14.47861965491373	32.50812703175794
3	21.525	36.125	20.625	21.725
4	30.45	17.825	12.7	39.025
5	41.6	19.3	14.924999999999999	24.175
6	33.45	16.7	20.25	29.599999999999998
7	34.79349186483104	20.275344180225282	12.7909887359199	32.14017521902378
8	37.81007266349286	24.630418441493358	13.05437233775996	24.50513655725382
9	33.516896120150186	26.25782227784731	21.176470588235293	19.048811013767207
10	27.368421052631582	20.100250626566414	17.61904761904762	34.91228070175438
11	29.062186559679038	21.840521564694082	14.69408224674022	34.403209628886664
12	21.233391827525697	19.05239408373026	24.442216094259212	35.271997994484835
13	27.525695663073453	24.141388819252946	13.311606919027325	35.02130859864628
14	27.345709984947312	25.062719518314097	19.16708479678876	28.424485699949827
15	27.63982944569852	28.86882367695009	17.33132681213945	26.160020065211935
16	32.55580637070479	20.792575871582645	23.5766240280913	23.07499372962127
17	31.115017579105974	22.25012556504269	28.80462079357107	17.83023606228026
18	18.70142892955628	20.105289546252195	25.495111556781147	35.69816996741038
19	22.729553437029605	24.636226793778224	23.95885599598595	28.675363773206218
20	22.50125565042692	22.75238573581115	33.92767453540934	20.818684078352586
21	18.826773627475557	22.536976685886188	31.23589872148408	27.400350965154175
22	21.88518425670594	28.95462521935322	30.308347956881427	18.851842567059414
23	36.98217424052222	19.708762239517952	19.28194828019081	24.027115239769017
24	20.35597894209075	37.8290298320381	18.901980446227125	22.913010779644022
25	20.260782347041122	28.46038114343029	30.115346038114343	21.163490471414242
26	23.640010027575833	21.509150162948107	21.38380546502883	33.46703434444723
27	44.148669010547465	17.55399296835761	19.53792064289302	18.75941737820191
28	33.484049233860844	11.379050489826676	35.34287867370007	19.794021602612407
29	33.961316252197946	14.56920371765888	24.315498618437577	27.1539814117056
30	37.67897513187641	13.740266264757597	24.315498618437577	24.265259984928413
31	41.55778894472362	23.668341708542716	16.105527638190956	18.668341708542712
32	32.9984932194877	28.578603716725265	14.339527875439478	24.083375188347564
33	25.251256281407038	22.763819095477388	19.34673366834171	32.63819095477387
34	28.460185882943982	14.770158251695554	34.011554885707106	22.758100979653353
35	33.75219904498618	17.592359889419452	24.252324704699674	24.403116360894696
36	22.833458929917107	19.844260236121578	43.55689525244914	13.765385581512183
37	26.14264188849824	25.715720743345056	24.786539427423403	23.355097940733298
38	40.94448630997237	26.6767143933685	16.4531524742527	15.925646822406431
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	1.0
1	0.5
2	0.0
3	0.0
4	0.5
5	1.0
6	1.0
7	1.0
8	1.0
9	3.0
10	5.0
11	5.0
12	4.0
13	3.0
14	4.0
15	5.0
16	5.0
17	2.5
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	1.0
28	1.5
29	2.0
30	6.5
31	11.0
32	11.0
33	11.5
34	12.0
35	12.0
36	16.5
37	21.0
38	42.0
39	63.0
40	63.0
41	92.5
42	122.0
43	137.5
44	153.0
45	153.0
46	245.5
47	338.0
48	338.0
49	467.5
50	597.0
51	526.5
52	456.0
53	456.0
54	581.5
55	707.0
56	707.0
57	576.5
58	446.0
59	412.0
60	378.0
61	378.0
62	314.5
63	251.0
64	259.5
65	268.0
66	268.0
67	164.5
68	61.0
69	61.0
70	47.5
71	34.0
72	28.5
73	23.0
74	23.0
75	16.5
76	10.0
77	10.0
78	10.0
79	10.0
80	6.5
81	3.0
82	3.0
83	3.0
84	3.0
85	3.0
86	4.0
87	5.0
88	2.5
89	0.0
90	0.0
91	1.0
92	2.0
93	1.0
94	0.0
95	0.0
96	1.0
97	2.0
98	2.0
99	3.5
100	5.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.1
2	0.025
3	0.0
4	0.0
5	0.0
6	0.0
7	0.125
8	0.22499999999999998
9	0.125
10	0.25
11	0.3
12	0.27499999999999997
13	0.27499999999999997
14	0.35000000000000003
15	0.325
16	0.325
17	0.44999999999999996
18	0.27499999999999997
19	0.35000000000000003
20	0.44999999999999996
21	0.27499999999999997
22	0.27499999999999997
23	0.42500000000000004
24	0.27499999999999997
25	0.3
26	0.27499999999999997
27	0.44999999999999996
28	0.475
29	0.475
30	0.475
31	0.5
32	0.44999999999999996
33	0.5
34	0.475
35	0.525
36	0.475
37	0.44999999999999996
38	0.475
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
38	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	47.099999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	85.08492569002122	40.075
2	6.210191082802548	5.8500000000000005
3	2.335456475583864	3.3000000000000003
4	1.48619957537155	2.8000000000000003
5	0.6369426751592357	1.5
6	0.9023354564755839	2.55
7	0.5307855626326964	1.7500000000000002
8	0.3715498938428875	1.4000000000000001
9	0.3184713375796179	1.35
>10	1.7515923566878981	16.3
>50	0.10615711252653928	4.324999999999999
>100	0.2653927813163482	18.8
>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
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCG	218	5.45	Illumina RNA PCR Primer (100% over 33bp)
TCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCG	165	4.125	No Hit
CCACGGGAACGTGGGATCGTCGGACTGTAGAACTCTGA	157	3.925	Illumina DpnII expression Sequencing Primer (100% over 24bp)
TTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATC	111	2.775	No Hit
ACAGGCCGGGACAAGTGCAATAGATCGTCGGACTGTAG	101	2.5250000000000004	No Hit
TCAGGCCGGGACAAGTGCAATAGATCGTCGGACTGTAG	92	2.3	No Hit
AAGCCTACAGCACCCGGTATTCCCAGGCGGTCTCGATC	81	2.025	No Hit
CAGCTGCTTTTGGGATTCCGTTGGATCGTCGGACTGTA	50	1.25	No Hit
TACAACCCTCAACCATATGTAGTCCAAGCAGATCGTCG	33	0.8250000000000001	No Hit
ACAGTTCTTCAACTGGCAGCTTGATCGTCGGACTGTAG	33	0.8250000000000001	No Hit
CCACGGGAACGTGGATCGTCGGACTGTAGAACTCTGAA	32	0.8	Illumina DpnII expression Sequencing Primer (100% over 25bp)
AGACTCAAAAGTAGTAGCACTTTGATCGTCGGACTGTA	30	0.75	No Hit
GGAGGCCGGGACGAGTGCAATAGATCGTCGGACTGTAG	30	0.75	No Hit
TTAAATTCAGCGGGTCGCCACGTCTGATCTGAGGTCGC	25	0.625	No Hit
GGGAAGAACAGCCCTCCTCTGCCGATCGTCGGACTGTA	24	0.6	No Hit
AAAAGAGCCCCCAGTTTGAGTGATCGTCGGACTGTAGA	24	0.6	No Hit
GGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGT	24	0.6	No Hit
AAATCTCGGGCCTTGATCAGAACATCTGTCTTGGATCG	23	0.575	No Hit
TCCGGAGCACCACATCGATCTAAGAGATCGTCGGACTG	23	0.575	No Hit
TTACAGGCCGGGACAAGTGCAATAGATCGTCGGACTGT	21	0.525	No Hit
CCACGGGAACGTGGTGATCGTCGGACTGTAGAACTCTG	21	0.525	Illumina DpnII expression Sequencing Primer (100% over 23bp)
TCCGGAGCACCACATCGATCTAAGAGGATCGTCGGACT	20	0.5	No Hit
GTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTA	19	0.475	No Hit
AATTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGA	18	0.44999999999999996	No Hit
AAAGCCTACAGCACCCGGTATTCCCAGGCGGTCTCGAT	17	0.42500000000000004	No Hit
AGTCAGTATTTGTTCGTCATCATGCAGGGATCGTCGGA	15	0.375	No Hit
GGAAGAACAGCCCTCCTCTGCCGATCGTCGGACTGTAG	15	0.375	No Hit
AGAGAGGGCCTCCACTTTGATGGATCGTCGGACTGTAG	15	0.375	No Hit
ACACTCAAAACCTGGCGGCACTTGATCGTCGGACTGTA	13	0.325	No Hit
AGCCTATCCTGGATTACTTGAAGATCGTCGGACTGTAG	13	0.325	No Hit
TTCCGGAGCACCACATCGATCTAAGAGATCGTCGGACT	12	0.3	No Hit
AAGAGAGGGCCTCCACTTTGATGGATCGTCGGACTGTA	12	0.3	No Hit
AGGAGTCGAGTGATGGTTCAAAGATCGTCGGACTGTAG	12	0.3	No Hit
ACACTCAAAACCTGGCGGCACTTTGATCGTCGGACTGT	12	0.3	No Hit
TCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGGATC	12	0.3	No Hit
CAGGCCGGGACAAGTGCAATAGATCGTCGGACTGTAGA	12	0.3	No Hit
AAAGTCTCGCTCTCTGCCCCTCAGATCGTCGGACTGTA	11	0.27499999999999997	No Hit
AGGCCAACAACACGCGGTGTTCCCAAGCGGTCCCCCAT	11	0.27499999999999997	No Hit
AAATCTCGGGCCTTGATCAGAACATCTGTCTTGATCGT	10	0.25	No Hit
CGCAAGGTCGGTTCTACGGGTGGATCGTCGGACTGTAG	10	0.25	No Hit
GCAAGGTCGGTTCTACGGGTGGATCGTCGGACTGTAGA	9	0.22499999999999998	No Hit
AAAGGACTGGATCCCCTTGCCGTGCCATTGTTGCCACA	9	0.22499999999999998	No Hit
CCGGAGCACCACATCGATCTAAGAGATCGTCGGACTGT	9	0.22499999999999998	No Hit
AAATTCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGG	9	0.22499999999999998	No Hit
AAAATCTCGGGCCTTGATCAGAACATCTGTCTTGATCG	9	0.22499999999999998	No Hit
AAGCCTACAGCACCCGGTATTCCCAGGCGGTCTCCCAT	9	0.22499999999999998	No Hit
GAAGAACAGCCCTCCTCTGCCGATCGTCGGACTGTAGA	8	0.2	No Hit
CTCCGGAGCACCACATCGATCTAAGAGATCGTCGGACT	8	0.2	No Hit
AGGCAGAGGCAGGTAGATTTGATCGTCGGACTGTAGAA	8	0.2	No Hit
GCGAGAATTCTACCACTGAACCACCAATGCGATCGTCG	8	0.2	No Hit
GAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCGATC	8	0.2	No Hit
AGTGTGACCAACATCAGAATCCCTTGATCGTCGGACTG	8	0.2	No Hit
AACTCCGGAGCACCACATCGATCTAAGAGATCGTCGGA	8	0.2	No Hit
GGCGAGAATTCTACCACTGAACCACCAATGCGATCGTC	7	0.17500000000000002	No Hit
AGCCAAGCTCAGACGGATCCGAGATCGTCGGACTGTAG	7	0.17500000000000002	No Hit
CCTCAAGGAGCCTCAGTCTAGGATCGTCGGACTGTAGA	7	0.17500000000000002	No Hit
AGACTCAAAAGTAGTAGCACTTGATCGTCGGACTGTAG	7	0.17500000000000002	No Hit
GCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCGTCG	7	0.17500000000000002	No Hit
AGCTTCCAGTCGGGGATGTTTACAGATCGTCGGACTGT	7	0.17500000000000002	No Hit
ACTCCGGAGCACCACATCGATCTAAGAGATCGTCGGAC	7	0.17500000000000002	No Hit
AGGGGTTCACCGAGCAACATTCGATCGTCGGACTGTAG	7	0.17500000000000002	No Hit
AGGGGTTCACCGAGCAACATTCGGATCGTCGGACTGTA	7	0.17500000000000002	No Hit
AGGGCCCGGCTCGCGTCCAGGATCGTCGGACTGTAGAA	7	0.17500000000000002	No Hit
CTACAGGCCGGGACAAGTGCAATAGATCGTCGGACTGT	6	0.15	No Hit
AAAATCTCGGGCCTTGATCAGAACATCTGTCTTGGATC	6	0.15	No Hit
CTTCAGGTAGTCAGTATTTGTTCGTCATCATGCAGGGA	6	0.15	No Hit
CAGTGAATTCTACCAGTGCCATAGATCGTCGGACTGTA	6	0.15	No Hit
GGAGGCAGAGGCAGGTAGATTTGATCGTCGGACTGTAG	6	0.15	No Hit
ATCGACGCACGAGCCGAGTGATCCACCGGATCGTCGGA	6	0.15	No Hit
CGTACGCTATACGGTCTACTAGATCGTCGGACTGTAGA	6	0.15	No Hit
CCACGGGAACGGATCGTCGGACTGTAGAACTCTGAACG	6	0.15	Illumina DpnII expression Sequencing Primer (96% over 26bp)
CCACGGGAACGATCGTCGGACTGTAGAACTCTGAACGT	6	0.15	Illumina DpnII expression Sequencing Primer (96% over 28bp)
TCCGGAGCACCACATCGATCGATCGTCGGACTGTAGAA	6	0.15	No Hit
AGGAGCGAGCGACCAAAGGAACCATAACTGATGATCGT	6	0.15	No Hit
CCGGAGCACCACATCGATCTAAGAGGATCGTCGGACTG	6	0.15	No Hit
AGCGACGCTCAGACAGGCGATCGTCGGACTGTAGAACT	6	0.15	No Hit
ACAGGCCATCTGTGTTATATTGATCGTCGGACTGTAGA	6	0.15	No Hit
ACACTACAAACTCTGCGGCACTGATCGTCGGACTGTAG	6	0.15	No Hit
TTCCGGAGCACCACATCGATCTAAGAGGATCGTCGGAC	6	0.15	No Hit
TGTGAGTTCTACCATTGCCAAAGATCGTCGGACTGTAG	6	0.15	No Hit
GAGTGTGACCAACATCAGAATCCCTTGATCGTCGGACT	5	0.125	No Hit
TCGACGCACGAGCCGAGTGATCCACCGCTAAGAGTCGA	5	0.125	No Hit
ACTGAGGGGCCTCAGACCGAGCTGATCGTCGGACTGTA	5	0.125	No Hit
CGGTGTGAGTTCTACCATTGCCAAAGATCGTCGGACTG	5	0.125	No Hit
AGGCGAGAATTCTACCACTGAACCACCAATGCGATCGT	5	0.125	No Hit
CCAGCGGGTCGCCACGTCTGATCTGAGGTCGCGGATCG	5	0.125	No Hit
ATCAGGCCGGGACAAGTGCAATAGATCGTCGGACTGTA	5	0.125	No Hit
GAGAACTCCGGAGCACCACATCGATCTAAGAGATCGTC	5	0.125	No Hit
CTTAAATTCAGCGGGTCGCCACGTCTGATCTGAGGTCG	5	0.125	No Hit
GCCCAGGATCGACCTCTGACCTGATCGTCGGACTGTAG	5	0.125	No Hit
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	5	0.125	No Hit
GGAGGCAGAGGCAGGTAGATTGATCGTCGGACTGTAGA	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	0.0	5.625	0.0	0.0
2	0.0	0.0	5.625	0.0	0.0
3	0.0	0.0	5.625	0.0	0.0
4	0.0	0.0	5.65	0.0	0.0
5	0.0	0.0	5.75	0.0	0.0
6	0.0	0.0	5.975	0.0	0.0
7	0.0	0.0	6.2	0.0	0.0
8	0.0	0.0	6.375	0.0	0.0
9	0.0	0.0	6.525	0.0	0.0
10	0.0	0.0	7.0	0.0	0.0
11	0.0	0.0	7.475	0.0	0.0
12	0.0	0.0	7.925	0.0	0.0
13	0.0	0.0	8.35	0.0	0.0
14	0.0	0.0	9.725	0.0	0.0
15	0.0	0.0	14.25	0.0	0.0
16	0.0	0.0	15.525	0.0	0.0
17	0.0	0.0	16.325	0.0	0.0
18	0.0	0.0	17.075	0.0	0.0
19	0.0	0.0	18.05	0.0	0.0
20	0.0	0.0	18.9	0.0	0.0
21	0.0	0.0	20.425	0.0	0.0
22	0.0	0.0	24.75	0.0	0.0
23	0.0	0.0	38.275	0.0	0.0
24	0.0	0.0	45.95	0.0	0.0
25	0.0	0.0	50.375	0.0	0.0
26	0.0	0.0	53.15	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTGCAAT	30	1.7408885E-5	32.0	15
TGCAATA	30	1.7408885E-5	32.0	16
CCACGGG	60	1.8189894E-12	32.0	1
GGCCGGG	30	1.7408885E-5	32.0	4
GGACAAG	25	2.4147211E-4	32.0	9
GCAATAG	30	1.7408885E-5	32.0	17
CAATAGA	30	1.7408885E-5	32.0	18
CGTGGGA	45	6.2191248E-9	32.0	10
GCCGGGA	30	1.7408885E-5	32.0	5
AATAGAT	30	1.7408885E-5	32.0	19
GTGGGAT	45	6.2191248E-9	32.0	11
AGTGCAA	30	1.7408885E-5	32.0	14
GACAAGT	25	2.4147211E-4	32.0	10
AGGCCGG	30	1.7408885E-5	32.0	3
CGGGACA	25	2.4147211E-4	32.0	7
CGGGAAC	60	1.8189894E-12	32.0	4
ATAGATC	30	1.7408885E-5	32.0	20
ACGGGAA	60	1.8189894E-12	32.0	3
GGGATCG	45	6.2191248E-9	32.0	13
GGGACAA	25	2.4147211E-4	32.0	8
>>END_MODULE
Read 738196 spots for SRR13079627.sra
Written 738196 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
Read 738194 spots for SRR13079627.sra
Written 738194 spots for SRR13079627.sra
SRR ids: ['SRR13079627.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_j6mh6tl7
SRR13079627.sra spots: 8858330
blocks: [[1, 738194], [738195, 1476388], [1476389, 2214582], [2214583, 2952776], [2952777, 3690970], [3690971, 4429164], [4429165, 5167358], [5167359, 5905552], [5905553, 6643746], [6643747, 7381940], [7381941, 8120134], [8120135, 8858330]]
SRR13079627 file size 1027265
SRR13079627 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR13079627 SRR13079627_1.fastq SRR13079627_2.fastq
Input file:	SRR13079627_1.fastq
Paired file:	SRR13079627_2.fastq
trimmed:	SRR13079627-trimmed-pair1.fastq, SRR13079627-trimmed-pair2.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- paired 3' end adapter sequence (-y):	AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
-- 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)
-- number of concurrent threads (-t):	12
Tue Apr 20 16:25:38 2021 >> started

Tue Apr 20 16:25:46 2021 >> done (8.683s)
8858330 read pairs processed; of these:
   4544 ( 0.05%) short read pairs filtered out after trimming by size control
      0 ( 0.00%) empty read pairs filtered out after trimming by size control
8853786 (99.95%) read pairs available; of these:
   5480 ( 0.06%) trimmed read pairs available after processing
8848306 (99.94%) untrimmed read pairs available after processing

Length distribution of reads after trimming:
length	count	percentage
 26	      1	  0.00%
 27	      9	  0.00%
 28	    154	  0.00%
 29	    576	  0.01%
 30	    206	  0.00%
 31	    528	  0.01%
 32	    482	  0.01%
 33	    151	  0.00%
 34	    369	  0.00%
 35	    131	  0.00%
 36	    977	  0.01%
 37	   1896	  0.02%
 38	8848306	 99.94%
8853786 reads passed initial QC


criterion=sequence-density
sequence-density=55.47
sequence-density-rank=1
fanout-score=23.46
fanout-score-rank=1
prefix-density=56.54
prefix-fanout=23.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAA


criterion=fanout-score
sequence-density=55.47
sequence-density-rank=1
fanout-score=23.46
fanout-score-rank=1
prefix-density=56.54
prefix-fanout=23.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAA


criterion=sequence-density
sequence-density=53.68
sequence-density-rank=1
fanout-score=22.68
fanout-score-rank=1
prefix-density=54.86
prefix-fanout=22.2
sequence=GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCG


criterion=fanout-score
sequence-density=53.68
sequence-density-rank=1
fanout-score=22.68
fanout-score-rank=1
prefix-density=54.86
prefix-fanout=22.2
sequence=GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCG
Potential 3prime adapter identified. Now checking if in reference sequence
/dee2/code/volunteer_pipeline.sh: line 802: -f: command not found
/dee2/code/volunteer_pipeline.sh: line 803: -f: command not found
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAA -y GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCG -o SRR13079627 SRR13079627_1.fastq SRR13079627_2.fastq
Input file:	SRR13079627_1.fastq
Paired file:	SRR13079627_2.fastq
trimmed:	SRR13079627-trimmed-pair1.fastq, SRR13079627-trimmed-pair2.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAA
-- paired 3' end adapter sequence (-y):	GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCG
-- 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 (auto detected)
-- number of concurrent threads (-t):	12
Tue Apr 20 16:26:37 2021 >> started

Tue Apr 20 16:26:45 2021 >> done (7.246s)
8531830 read pairs processed; of these:
1029210 (12.06%) short read pairs filtered out after trimming by size control
 502200 ( 5.89%) empty read pairs filtered out after trimming by size control
7000420 (82.05%) read pairs available; of these:
6097997 (87.11%) trimmed read pairs available after processing
 902423 (12.89%) untrimmed read pairs available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  89246	  1.27%
 19	  76634	  1.09%
 20	 145765	  2.08%
 21	 364540	  5.21%
 22	1237903	 17.68%
 23	 653995	  9.34%
 24	 383757	  5.48%
 25	 248258	  3.55%
 26	 203891	  2.91%
 27	 170056	  2.43%
 28	 176629	  2.52%
 29	 122643	  1.75%
 30	 227734	  3.25%
 31	 139665	  2.00%
 32	 202818	  2.90%
 33	 598223	  8.55%
 34	 609577	  8.71%
 35	 160049	  2.29%
 36	 162616	  2.32%
 37	 125995	  1.80%
 38	 900426	 12.86%


criterion=sequence-density
sequence-density=8.12
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=9
prefix-density=0.00
prefix-fanout=1.0
sequence=TATTGCACTTGTCCCGGCCTG


criterion=fanout-score
sequence-density=1.29
sequence-density-rank=6
fanout-score=29.70
fanout-score-rank=1
prefix-density=1.58
prefix-fanout=24.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGT


criterion=sequence-density
sequence-density=7.84
sequence-density-rank=1
fanout-score=2.63
fanout-score-rank=7
prefix-density=1.17
prefix-fanout=2.6
sequence=CAGGCCGGGACAAGTGCAATAGATCGTCGGA


criterion=fanout-score
sequence-density=0.33
sequence-density-rank=12
fanout-score=13.02
fanout-score-rank=1
prefix-density=0.29
prefix-fanout=13.0
sequence=GATCGTCGGACTGTAGAACTCTGAACGTGTAGA
SRR13079627 testing PE reads STAR mapping to Ensembl genome
                                 Started job on |	Apr 20 16:27:47
                             Started mapping on |	Apr 20 16:27:48
                                    Finished on |	Apr 20 16:28:34
       Mapping speed, Million of reads per hour |	573.06

                          Number of input reads |	7322376
                      Average input read length |	57
                                    UNIQUE READS:
                   Uniquely mapped reads number |	3746205
                        Uniquely mapped reads % |	51.16%
                          Average mapped length |	48.89
                       Number of splices: Total |	23155
            Number of splices: Annotated (sjdb) |	8969
                       Number of splices: GT/AG |	18695
                       Number of splices: GC/AG |	1751
                       Number of splices: AT/AC |	6
               Number of splices: Non-canonical |	2703
                      Mismatch rate per base, % |	0.40%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.35
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	594173
             % of reads mapped to multiple loci |	8.11%
        Number of reads mapped to too many loci |	103045
             % of reads mapped to too many loci |	1.41%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	34.75%
                     % of reads unmapped: other |	4.57%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2982001	2982001	2982001
N_multimapping	594173	594173	594173
N_noFeature	682593	736438	2844965
N_ambiguous	1530974	814813	178315
UnstrandedReadsAssigned:1532638 PositiveStrandReadsAssigned:2194954 NegativeStrandReadsAssigned:722925
Dataset is classified unstranded
MeadianReadLen=27 20thPercentileLength=22 echo kmer=19
SRR13079627 Starting Kallisto paired end mapping to ensembl reference transcriptome

[quant] fragment length distribution will be estimated from the data
[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 paired-end mode
[quant] will process pair 1: SRR13079627-trimmed-pair1.fastq
                             SRR13079627-trimmed-pair2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 7,322,376 reads, 1,487,186 reads pseudoaligned
[quant] estimated average fragment length: 29.8201
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,314 rounds

 109283 SRR13079627.ke.tsv
  52636 SRR13079627.se.tsv
 161919 total
==> SRR13079627.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSMUST00000177564.1	16	17	0	0
ENSMUST00000196221.1	9	10	0	0
ENSMUST00000179664.1	11	12	0	0
ENSMUST00000178537.1	12	13	0	0
ENSMUST00000178862.1	14	15	0	0
ENSMUST00000179520.1	11	12	0	0
ENSMUST00000179883.1	16	17	0	0
ENSMUST00000195858.1	10	11	0	0
ENSMUST00000179932.1	12	13	0	0

==> SRR13079627.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR13079627 completed mapping pipeline successfully
