Starting /dee2/code/volunteer_pipeline.sh SRR12060856
    current disk space = 344631692
    free memory = 65631352 
SRR12060856 SRAfilesize
97eec78653ee34f8c8ba6bec052934d7  SRR12060856.sra
SRR12060856.sra file validated
SRR12060856 is single end
SRR12060856 is conventional basespace
SRR12060856 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR12060856_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	47
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.51675	32.0	32.0	32.0	32.0	32.0
2	31.224	32.0	32.0	32.0	32.0	32.0
3	31.2885	32.0	32.0	32.0	32.0	32.0
4	31.47125	32.0	32.0	32.0	32.0	32.0
5	31.336	32.0	32.0	32.0	32.0	32.0
6	34.94125	36.0	36.0	36.0	36.0	36.0
7	34.9695	36.0	36.0	36.0	36.0	36.0
8	34.9895	36.0	36.0	36.0	36.0	36.0
9	34.92425	36.0	36.0	36.0	36.0	36.0
10	34.797	36.0	36.0	36.0	36.0	36.0
11	34.9695	36.0	36.0	36.0	36.0	36.0
12	34.84225	36.0	36.0	36.0	32.0	36.0
13	34.9435	36.0	36.0	36.0	32.0	36.0
14	34.937	36.0	36.0	36.0	32.0	36.0
15	34.851	36.0	36.0	36.0	36.0	36.0
16	35.043	36.0	36.0	36.0	36.0	36.0
17	35.0175	36.0	36.0	36.0	36.0	36.0
18	34.96125	36.0	36.0	36.0	36.0	36.0
19	34.90675	36.0	36.0	36.0	36.0	36.0
20	34.89875	36.0	36.0	36.0	36.0	36.0
21	34.83525	36.0	36.0	36.0	32.0	36.0
22	35.0185	36.0	36.0	36.0	36.0	36.0
23	34.92075	36.0	36.0	36.0	36.0	36.0
24	34.95175	36.0	36.0	36.0	36.0	36.0
25	34.9185	36.0	36.0	36.0	36.0	36.0
26	34.8085	36.0	36.0	36.0	32.0	36.0
27	34.6195	36.0	36.0	36.0	32.0	36.0
28	34.71925	36.0	36.0	36.0	32.0	36.0
29	34.6505	36.0	36.0	36.0	32.0	36.0
30	34.5845	36.0	36.0	36.0	32.0	36.0
31	34.7085	36.0	36.0	36.0	32.0	36.0
32	34.72825	36.0	36.0	36.0	32.0	36.0
33	34.801	36.0	36.0	36.0	32.0	36.0
34	34.5205	36.0	36.0	36.0	32.0	36.0
35	34.6145	36.0	36.0	36.0	32.0	36.0
36	34.38925	36.0	36.0	36.0	32.0	36.0
37	34.3785	36.0	36.0	36.0	32.0	36.0
38	34.40375	36.0	36.0	36.0	32.0	36.0
39	34.4675	36.0	36.0	36.0	32.0	36.0
40	34.3455	36.0	36.0	36.0	32.0	36.0
41	34.535	36.0	36.0	36.0	32.0	36.0
42	34.403	36.0	36.0	36.0	32.0	36.0
43	34.36375	36.0	36.0	36.0	32.0	36.0
44	34.4395	36.0	36.0	36.0	32.0	36.0
45	34.21875	36.0	36.0	36.0	32.0	36.0
46	34.27	36.0	36.0	36.0	32.0	36.0
47	34.0595	36.0	36.0	36.0	32.0	36.0
48	33.8745	36.0	36.0	36.0	32.0	36.0
49	33.93275	36.0	36.0	36.0	27.0	36.0
50	33.09875	36.0	32.0	36.0	27.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
22	3.0
23	6.0
24	9.0
25	12.0
26	30.0
27	44.0
28	58.0
29	89.0
30	105.0
31	137.0
32	193.0
33	317.0
34	642.0
35	2355.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	26.674999999999997	34.275	29.95	9.1
2	25.4	17.724999999999998	29.599999999999998	27.275
3	33.95	20.025000000000002	25.35	20.674999999999997
4	36.0	24.975	24.025	15.0
5	19.35	40.0	23.95	16.7
6	21.175	23.225	36.5	19.1
7	33.225	28.225	26.400000000000002	12.15
8	18.175	29.2	41.425	11.200000000000001
9	23.150000000000002	38.025	19.825	19.0
10	39.475	18.45	29.4	12.675
11	18.5	22.175	41.85	17.474999999999998
12	23.875	18.8	27.1	30.225
13	28.599999999999998	26.875	19.825	24.7
14	20.474999999999998	41.875	23.275000000000002	14.374999999999998
15	25.775	37.475	24.975	11.774999999999999
16	17.0	38.35	26.474999999999998	18.175
17	24.975	33.15	29.125	12.75
18	41.025	19.55	18.4	21.025
19	22.15	29.025000000000002	30.975	17.849999999999998
20	24.75	27.650000000000002	34.175	13.425
21	23.35	37.075	17.474999999999998	22.1
22	26.474999999999998	36.425000000000004	20.674999999999997	16.425
23	35.025	36.425000000000004	18.275	10.274999999999999
24	23.35	39.025	25.924999999999997	11.700000000000001
25	22.025	42.825	21.825	13.325000000000001
26	36.3	25.124999999999996	19.975	18.6
27	25.924999999999997	40.35	14.274999999999999	19.45
28	30.075000000000003	21.825	29.599999999999998	18.5
29	25.575	27.700000000000003	10.95	35.775
30	42.975	31.2	7.074999999999999	18.75
31	43.974999999999994	29.425	9.700000000000001	16.900000000000002
32	25.25	49.05	10.925	14.774999999999999
33	30.132533133283324	43.16079019754939	7.576894223555889	19.129782445611404
34	39.2	27.6	10.475	22.725
35	24.10602650662666	40.93523380845212	11.10277569392348	23.85596399099775
36	31.424999999999997	32.800000000000004	7.75	28.025
37	17.375	33.675	10.25	38.7
38	23.055763940985248	40.235058764691175	7.751937984496124	28.95723930982746
39	22.95	26.924999999999997	11.625	38.5
40	19.625	41.05	14.374999999999998	24.95
41	22.400000000000002	20.025000000000002	15.575	42.0
42	31.424999999999997	22.475	21.9	24.2
43	23.925	19.25	34.425	22.400000000000002
44	19.32983245811453	24.33108277069267	17.57939484871218	38.759689922480625
45	18.95	31.1	27.975	21.975
46	32.175	28.275	12.825000000000001	26.724999999999998
47	14.075	41.525	17.95	26.450000000000003
48	12.6	38.525	14.475	34.4
49	13.275	26.75	13.025	46.949999999999996
50	11.38353765323993	25.11883912934701	29.146860145108832	34.35076307230423
>>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	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	1.0
28	1.0
29	1.0
30	1.0
31	4.0
32	7.0
33	19.0
34	31.0
35	45.5
36	60.0
37	77.5
38	95.0
39	127.5
40	160.0
41	249.5
42	339.0
43	494.0
44	649.0
45	562.5
46	476.0
47	486.5
48	497.0
49	474.0
50	451.0
51	460.0
52	469.0
53	440.0
54	411.0
55	280.5
56	150.0
57	129.5
58	109.0
59	84.0
60	59.0
61	37.0
62	15.0
63	11.5
64	8.0
65	7.0
66	6.0
67	3.0
68	0.0
69	0.0
70	0.0
71	0.0
72	0.0
73	0.0
74	0.0
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	1.5
100	3.0
>>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	0.0
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	0.025
34	0.0
35	0.025
36	0.0
37	0.0
38	0.025
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.025
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.075
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	68.30000000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	91.25183016105417	62.324999999999996
2	4.24597364568082	5.800000000000001
3	1.4641288433382138	3.0
4	0.5856515373352855	1.6
5	0.32942898975109813	1.125
6	0.43923865300146414	1.7999999999999998
7	0.18301610541727673	0.8750000000000001
8	0.18301610541727673	1.0
9	0.21961932650073207	1.35
>10	0.9882869692532943	13.275
>50	0.07320644216691069	4.875
>100	0.036603221083455345	2.9749999999999996
>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
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	119	2.9749999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAAGA	100	2.5	No Hit
TTCATGGACGTTGATAAGATCTTTCAGATCGGAAGAGCACACGTCTGAAC	95	2.375	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCCAAATGTAGACAAAGCAAGATCGGAAGAGCACACGTCTGAACTCCAG	40	1.0	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	39	0.975	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	30	0.75	TruSeq Adapter, Index 9 (100% over 36bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AGTTACTAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCC	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTAGGGAAGTACTTTAAGAAACATATGTATAAGATCGGAAGAGCACACGT	25	0.625	No Hit
TTCATGGACGTTGATAAGATCTTTCCAGATCGGAAGAGCACACGTCTGAA	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AGTTACTAATTCATGATCTGGCATAGATCGGAAGAGCACACGTCTGAACT	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	19	0.475	No Hit
TTGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT	18	0.44999999999999996	TruSeq Adapter, Index 9 (100% over 41bp)
TCCCAAATGTAGACAAAGCAGATCGGAAGAGCACACGTCTGAACTCCAGT	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGGATATGGCGGAATTGGTAGACGCTACGGACTTAGATCGGAAGAGCAC	18	0.44999999999999996	No Hit
GGGTTGATATGAGAACACACGAGATCGGAAGAGCACACGTCTGAACTCCA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTTGGATTGAAGGGAGCTCTTAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTTGGATTGAAGGGAGCTCTAAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATTGTATCATTAACTATTTCTTTATAGATCGGAAGAGCACACGTCTGAAC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCGGACTGCTCGAGCTGCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCAGATCGGA	16	0.4	No Hit
TTCATGGACGTTGATAAGATCTTTAGATCGGAAGAGCACACGTCTGAACT	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCGGACCAGGCTTCATTCCCCAGATCGGAAGAGCACACGTCTGAACTCCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	13	0.325	TruSeq Adapter, Index 9 (100% over 36bp)
GGGGATATAGCTCAGTTGGTAGAGCTCCGCTCTTGCAAAGATCGGAAGAG	13	0.325	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	13	0.325	No Hit
TCGGTGGATCTTAGAAAATTAAGATCGGAAGAGCACACGTCTGAACTCCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAAGATCGGAAG	12	0.3	No Hit
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCAGATCGGAAGAGCACACG	12	0.3	No Hit
TGAAAGTGACTACATCGGGGTAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTAGGGAAGTACTTTAAGAAACATATGTAAGATCGGAAGAGCACACGTCT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TTAAGTGTCACGGAAATCCCTAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CTTCGTGATTGATTTGCCATATTTTCTGATCAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
ATGATATTTGTAGTAATGGCGAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGAAGATCGGAAGAGCACA	8	0.2	No Hit
TGTGTTCTCAGGTCACCCCTGAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAGATCGGAAGAGCAC	8	0.2	No Hit
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTAGATCGGAAGAGCACAC	8	0.2	No Hit
GCGGACTGCTCGAGCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGAAGATCGGAAGA	7	0.17500000000000002	No Hit
TTCATGGACGTTGATAAGATCTTTAAGATCGGAAGAGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATG	7	0.17500000000000002	TruSeq Adapter, Index 9 (100% over 49bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
TCCCAAATGTAGACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTAGGGAAGTACTTTAAGAAACATATGTAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
AAACAAGAATTCTTGAACAGCGAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTTGGATTGAAGGGAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GTGGACGTGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	6	0.15	TruSeq Adapter, Index 7 (97% over 35bp)
TCCGCTGTAGCACACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCCAAATGTAGACAAAGCTAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AAGGAAGCTATAAGTAATGCAACTATGAAAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	6	0.15	No Hit
TCCGCTTTTATGTTAGTTCGTACTATAAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TTTGGATTGAAGGGAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTAGATCGGAAGAGCACAC	6	0.15	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TTCATGGACGTTGATAAGATCTTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGTTACTAATTCATGATCTGGAAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGGACTGCTCGAGCTGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TTCATGGACGTTGATAAGATCTTTCAAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TGACAGAAGAGAGTGAGCACAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTAACAGACCGGTAGACTTGAACAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TTAGGGAAGTACTTTAAGAAACAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACCGGTAGACTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
>>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	0.225	0.0	0.0	0.0	0.0
2	0.225	0.0	0.0	0.0	0.0
3	0.225	0.0	0.0	0.0	0.0
4	0.225	0.0	0.0	0.0	0.0
5	0.25	0.0	0.0	0.0	0.0
6	0.325	0.0	0.0	0.0	0.0
7	0.4	0.0	0.0	0.0	0.0
8	0.625	0.0	0.0	0.0	0.0
9	1.35	0.0	0.0	0.0	0.0
10	1.55	0.0	0.0	0.0	0.0
11	1.8	0.0	0.0	0.0	0.0
12	2.225	0.0	0.0	0.0	0.0
13	2.9	0.0	0.0	0.0	0.0
14	5.325	0.0	0.0	0.0	0.0
15	7.0	0.0	0.0	0.0	0.0
16	8.525	0.0	0.0	0.0	0.0
17	12.925	0.0	0.0	0.0	0.0
18	15.0	0.0	0.0	0.0	0.0
19	16.95	0.0	0.0	0.0	0.0
20	19.425	0.0	0.0	0.0	0.0
21	23.25	0.0	0.0	0.0	0.0
22	31.8	0.0	0.0	0.0	0.0
23	40.225	0.0	0.0	0.0	0.0
24	46.85	0.0	0.0	0.0	0.0
25	65.825	0.0	0.0	0.0	0.0
26	70.575	0.0	0.0	0.0	0.0
27	73.3	0.0	0.0	0.0	0.0
28	74.575	0.0	0.0	0.0	0.0
29	75.85	0.0	0.0	0.0	0.0
30	77.475	0.0	0.0	0.0	0.0
31	78.9	0.0	0.0	0.0	0.0
32	81.475	0.0	0.0	0.0	0.0
33	83.475	0.0	0.0	0.0	0.0
34	85.775	0.0	0.0	0.0	0.0
35	87.275	0.0	0.0	0.0	0.0
36	89.3	0.0	0.0	0.0	0.0
37	89.9	0.0	0.0	0.0	0.0
38	90.475	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTCATGG	30	1.10034984E-4	36.572914	1
ATAAGAT	30	1.10034984E-4	36.572914	14
ACGTTGA	30	1.10034984E-4	36.572914	8
GATAAGA	30	1.10034984E-4	36.572914	13
TGATAAG	30	1.10034984E-4	36.572914	12
ATGGACG	30	1.10034984E-4	36.572914	4
GACGTTG	30	1.10034984E-4	36.572914	7
TCATGGA	30	1.10034984E-4	36.572914	2
TGGACGT	30	1.10034984E-4	36.572914	5
TTGATAA	30	1.10034984E-4	36.572914	11
CATGGAC	30	1.10034984E-4	36.572914	3
CGTTGAT	30	1.10034984E-4	36.572914	9
GGACGTT	30	1.10034984E-4	36.572914	6
GTTGATA	35	2.7250365E-4	31.348213	10
AAGATCT	35	2.7250365E-4	31.348213	16
GATCTTT	35	2.7250365E-4	31.348213	18
AGATCTT	35	2.7250365E-4	31.348213	17
CAGTCAC	40	5.963292E-4	27.429688	44
TAAGATC	40	5.963292E-4	27.429688	15
CCAGTCA	50	0.0021941867	21.94375	43
>>END_MODULE
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407263 READS because READLEN < 1
Read 1407263 spots for SRR12060856.sra
Written 1407263 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
Rejected 1407255 READS because READLEN < 1
Read 1407255 spots for SRR12060856.sra
Written 1407255 spots for SRR12060856.sra
SRR ids: ['SRR12060856.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ybjz_y1i
SRR12060856.sra spots: 22516088
blocks: [[1, 1407255], [1407256, 2814510], [2814511, 4221765], [4221766, 5629020], [5629021, 7036275], [7036276, 8443530], [8443531, 9850785], [9850786, 11258040], [11258041, 12665295], [12665296, 14072550], [14072551, 15479805], [15479806, 16887060], [16887061, 18294315], [18294316, 19701570], [19701571, 21108825], [21108826, 22516088]]
SRR12060856 file size 3166612
SRR12060856 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -q 10 -k inf -t 16 -o SRR12060856 SRR12060856_1.fastq
Input file:	SRR12060856_1.fastq
trimmed:	SRR12060856-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):	16
Fri Apr 26 15:29:21 2024 >> started

Fri Apr 26 15:29:36 2024 >> done (14.730s)
22516088 reads processed; of these:
 4268328 (18.96%) short reads filtered out after trimming by size control
   86769 ( 0.39%) empty reads filtered out after trimming by size control
18160991 (80.66%) reads available; of these:
  587054 ( 3.23%) trimmed reads available after processing
17573937 (96.77%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  583999	  3.22%
 19	       0	  0.00%
 20	       0	  0.00%
 21	       0	  0.00%
 22	       0	  0.00%
 23	       0	  0.00%
 24	       0	  0.00%
 25	       0	  0.00%
 26	       0	  0.00%
 27	       0	  0.00%
 28	       0	  0.00%
 29	       0	  0.00%
 30	       0	  0.00%
 31	       0	  0.00%
 32	       0	  0.00%
 33	       0	  0.00%
 34	       0	  0.00%
 35	       0	  0.00%
 36	       0	  0.00%
 37	       0	  0.00%
 38	       0	  0.00%
 39	       0	  0.00%
 40	       0	  0.00%
 41	       0	  0.00%
 42	       6	  0.00%
 43	       2	  0.00%
 44	       4	  0.00%
 45	      31	  0.00%
 46	      24	  0.00%
 47	      45	  0.00%
 48	     439	  0.00%
 49	    2504	  0.01%
 50	17573937	 96.77%
18160991 reads passed initial QC


criterion=sequence-density
sequence-density=85.61
sequence-density-rank=1
fanout-score=47.57
fanout-score-rank=1
prefix-density=91.81
prefix-fanout=44.4
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT


criterion=fanout-score
sequence-density=85.61
sequence-density-rank=1
fanout-score=47.57
fanout-score-rank=1
prefix-density=91.81
prefix-fanout=44.4
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT
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 16 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT -o SRR12060856 -
Input file:	STDIN
trimmed:	SRR12060856-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT
-- 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):	16
Fri Apr 26 15:30:06 2024 >> started

Fri Apr 26 15:30:25 2024 >> done (18.948s)
17738642 reads processed; of these:
   12518 ( 0.07%) short reads filtered out after trimming by size control
     109 ( 0.00%) empty reads filtered out after trimming by size control
17726015 (99.93%) reads available; of these:
17001367 (95.91%) trimmed reads available after processing
  724648 ( 4.09%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  583229	  3.29%
 19	  672138	  3.79%
 20	  921308	  5.20%
 21	 1927405	 10.87%
 22	 1738270	  9.81%
 23	 1431237	  8.07%
 24	 3821570	 21.56%
 25	 1041396	  5.87%
 26	  617684	  3.48%
 27	  234801	  1.32%
 28	  219898	  1.24%
 29	  261613	  1.48%
 30	  274623	  1.55%
 31	  548380	  3.09%
 32	  505485	  2.85%
 33	  461471	  2.60%
 34	  341724	  1.93%
 35	  394419	  2.23%
 36	  158737	  0.90%
 37	  118949	  0.67%
 38	  130629	  0.74%
 39	  631102	  3.56%
 40	  166704	  0.94%
 41	  104032	  0.59%
 42	  116261	  0.66%
 43	   49678	  0.28%
 44	   29724	  0.17%
 45	   25561	  0.14%
 46	   15372	  0.09%
 47	   18982	  0.11%
 48	      49	  0.00%
 49	     118	  0.00%
 50	  163466	  0.92%


criterion=sequence-density
sequence-density=4.94
sequence-density-rank=1
fanout-score=1.90
fanout-score-rank=3
prefix-density=0.02
prefix-fanout=1.9
sequence=AGTTACTAATTCATGATCTGGCAT


criterion=fanout-score
sequence-density=0.30
sequence-density-rank=19
fanout-score=11.05
fanout-score-rank=1
prefix-density=3.18
prefix-fanout=1.0
sequence=GTAGACAAAGCTTTTT
                                 Started job on |	Apr 26 15:30:56
                             Started mapping on |	Apr 26 15:30:57
                                    Finished on |	Apr 26 15:32:50
       Mapping speed, Million of reads per hour |	578.18

                          Number of input reads |	18148364
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	8245879
                        Uniquely mapped reads % |	45.44%
                          Average mapped length |	25.88
                       Number of splices: Total |	79898
            Number of splices: Annotated (sjdb) |	13990
                       Number of splices: GT/AG |	72992
                       Number of splices: GC/AG |	709
                       Number of splices: AT/AC |	147
               Number of splices: Non-canonical |	6050
                      Mismatch rate per base, % |	0.33%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.16
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	7915084
             % of reads mapped to multiple loci |	43.61%
        Number of reads mapped to too many loci |	1148721
             % of reads mapped to too many loci |	6.33%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.14%
                     % of reads unmapped: other |	0.48%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1987401	1987401	1987401
N_multimapping	7915084	7915084	7915084
N_noFeature	4051440	4456836	7622202
N_ambiguous	350314	128078	6696
UnstrandedReadsAssigned:3844125 PositiveStrandReadsAssigned:3660965 NegativeStrandReadsAssigned:616981
Dataset is classified positive stranded
MeadianReadLen=24 20thPercentileLength=21 echo kmer=19
SRR12060856 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: SRR12060856-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 18,148,364 reads, 781,193 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 791 rounds

  48360 SRR12060856.ke.tsv
  32833 SRR12060856.se.tsv
  81193 total
==> SRR12060856.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	311	106.452
AT1G18320.1	699	600	0	0
AT5G11100.1	1709	1610	1	0.512371
AT4G35335.1	1280	1181	6	4.19095
AT1G60930.1	3876	3777	1	0.218406
AT1G17000.1	2351	2252	0	0
AT3G55270.1	3130	3031	9	2.44944
AT4G16150.1	3181	3082	8	2.14125
AT3G18150.1	1370	1271	4	2.59612

==> SRR12060856.se.tsv <==
AT1G01010	1
AT1G01020	2
AT1G03987	0
AT1G01030	2
AT1G01040	42
AT1G03993	1
AT1G01046	38
AT1G01050	5
AT1G03997	0
AT1G01060	10
SRR12060856 completed mapping pipeline successfully
