Starting /dee2/code/volunteer_pipeline.sh ERR9744597
    current disk space = 294174228
    free memory = 65323708 
ERR9744597 SRAfilesize
a0e86e11fd0163de1bd575fe870f5c71  ERR9744597.sra
ERR9744597.sra file validated
ERR9744597 is single end
ERR9744597 is conventional basespace
ERR9744597 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	ERR9744597_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	76
%GC	47
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.8275	32.0	32.0	32.0	32.0	32.0
2	31.8015	32.0	32.0	32.0	32.0	32.0
3	31.839	32.0	32.0	32.0	32.0	32.0
4	31.785	32.0	32.0	32.0	32.0	32.0
5	31.80675	32.0	32.0	32.0	32.0	32.0
6	35.7315	36.0	36.0	36.0	36.0	36.0
7	35.68775	36.0	36.0	36.0	36.0	36.0
8	35.8105	36.0	36.0	36.0	36.0	36.0
9	35.749	36.0	36.0	36.0	36.0	36.0
10-11	35.742999999999995	36.0	36.0	36.0	36.0	36.0
12-13	35.7735	36.0	36.0	36.0	36.0	36.0
14-15	35.746375	36.0	36.0	36.0	36.0	36.0
16-17	35.697375	36.0	36.0	36.0	36.0	36.0
18-19	35.760875	36.0	36.0	36.0	36.0	36.0
20-21	35.685	36.0	36.0	36.0	36.0	36.0
22-23	35.772	36.0	36.0	36.0	36.0	36.0
24-25	35.71525	36.0	36.0	36.0	36.0	36.0
26-27	35.66225	36.0	36.0	36.0	36.0	36.0
28-29	35.665625000000006	36.0	36.0	36.0	36.0	36.0
30-31	35.69475	36.0	36.0	36.0	36.0	36.0
32-33	35.640625	36.0	36.0	36.0	36.0	36.0
34-35	35.687875	36.0	36.0	36.0	36.0	36.0
36-37	35.673625	36.0	36.0	36.0	36.0	36.0
38-39	35.661375	36.0	36.0	36.0	36.0	36.0
40-41	35.630375	36.0	36.0	36.0	36.0	36.0
42-43	35.514250000000004	36.0	36.0	36.0	36.0	36.0
44-45	35.587	36.0	36.0	36.0	36.0	36.0
46-47	35.618125	36.0	36.0	36.0	36.0	36.0
48-49	35.57225	36.0	36.0	36.0	36.0	36.0
50-51	35.512125	36.0	36.0	36.0	36.0	36.0
52-53	35.53975	36.0	36.0	36.0	36.0	36.0
54-55	35.461124999999996	36.0	36.0	36.0	36.0	36.0
56-57	35.352125	36.0	36.0	36.0	36.0	36.0
58-59	35.384625	36.0	36.0	36.0	36.0	36.0
60-61	35.510125	36.0	36.0	36.0	36.0	36.0
62-63	35.46575	36.0	36.0	36.0	36.0	36.0
64-65	35.43425	36.0	36.0	36.0	36.0	36.0
66-67	35.49325	36.0	36.0	36.0	36.0	36.0
68-69	35.528875	36.0	36.0	36.0	36.0	36.0
70-71	35.648125	36.0	36.0	36.0	36.0	36.0
72-73	35.616375000000005	36.0	36.0	36.0	36.0	36.0
74-75	35.46625	36.0	36.0	36.0	36.0	36.0
76	35.3295	36.0	36.0	36.0	36.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
23	6.0
24	18.0
25	18.0
26	23.0
27	14.0
28	7.0
29	5.0
30	11.0
31	15.0
32	17.0
33	38.0
34	92.0
35	3736.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	29.075	42.025	22.225	6.675000000000001
2	46.725	18.95	12.425	21.9
3	32.300000000000004	37.7	14.325	15.675
4	26.325	26.775	37.125	9.775
5	14.825	25.074999999999996	22.925	37.175000000000004
6	35.80895223805952	16.454113528382095	28.307076769192296	19.42985746436609
7	55.900000000000006	15.125	17.675	11.3
8	17.5	39.35	32.0	11.15
9	19.35	54.1	14.975	11.575000000000001
10-11	37.35	29.825000000000003	21.675	11.15
12-13	29.6625	20.4875	17.0875	32.7625
14-15	20.674999999999997	43.8875	11.799999999999999	23.6375
16-17	20.625	37.487500000000004	17.675	24.212500000000002
18-19	39.900000000000006	23.9	22.237499999999997	13.9625
20-21	22.7375	27.9125	25.85	23.5
22-23	38.337500000000006	40.1625	8.512500000000001	12.987499999999999
24-25	21.025	43.8125	8.6875	26.474999999999998
26-27	22.287499999999998	26.737499999999997	19.575	31.4
28-29	20.05	33.825	10.8875	35.2375
30-31	33.7625	24.125	21.6625	20.45
32-33	16.775000000000002	38.375	12.4	32.45
34-35	18.15	22.7	14.0375	45.1125
36-37	13.1375	46.300000000000004	12.6375	27.925
38-39	15.7625	45.85	13.5125	24.875
40-41	23.78094523630908	35.471367841960486	14.028507126781694	26.71917979494874
42-43	13.140785196299074	22.030507626906726	28.019504876219052	36.809202300575144
44-45	9.97624703087886	25.61570196274534	24.190523815476936	40.21752719089886
46-47	23.1125	29.9375	21.8	25.15
48-49	9.0125	43.0	21.6625	26.325
50-51	21.1875	30.7125	12.8	35.3
52-53	21.8875	30.8	13.525	33.7875
54-55	11.9375	28.349999999999998	27.375	32.337500000000006
56-57	11.837499999999999	25.374999999999996	40.2625	22.525000000000002
58-59	12.225	22.975	31.075000000000003	33.725
60-61	24.875	22.35	20.7625	32.0125
62-63	17.4875	18.512500000000003	44.237500000000004	19.7625
64-65	25.090636329541194	26.490811351418923	24.36554569321165	24.05300662582823
66-67	15.625	33.95	25.912499999999998	24.5125
68-69	14.080280105039389	34.3878954607978	26.897586594973117	24.634237839189694
70-71	14.4161040260065	34.03350837709427	30.620155038759687	20.930232558139537
72-73	15.143178692009505	35.913467550331376	29.336001000375138	19.607352757283984
74-75	26.069017254313575	28.19454863715929	25.143785946486624	20.59264816204051
76	39.00425318989242	19.5896922692019	25.894420815611706	15.511633725293972
>>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	0.5
12	1.0
13	0.5
14	1.0
15	1.5
16	1.5
17	2.0
18	3.5
19	5.0
20	4.5
21	4.0
22	4.5
23	6.0
24	9.0
25	11.0
26	8.5
27	6.0
28	5.5
29	5.0
30	4.0
31	4.5
32	4.0
33	2.0
34	2.0
35	2.5
36	2.5
37	2.0
38	7.0
39	9.5
40	11.5
41	23.0
42	30.0
43	84.0
44	595.5
45	716.5
46	380.0
47	400.5
48	498.0
49	506.5
50	438.0
51	425.5
52	299.5
53	150.0
54	114.0
55	106.5
56	62.5
57	18.0
58	10.0
59	6.0
60	1.5
61	1.0
62	1.0
63	0.5
64	0.0
65	0.0
66	0.0
67	0.0
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	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
10-11	0.0
12-13	0.0
14-15	0.0
16-17	0.0
18-19	0.0
20-21	0.0
22-23	0.0
24-25	0.0
26-27	0.0
28-29	0.0
30-31	0.0
32-33	0.0
34-35	0.0
36-37	0.0
38-39	0.0
40-41	0.025
42-43	0.025
44-45	0.0125
46-47	0.0
48-49	0.0
50-51	0.0
52-53	0.0
54-55	0.0
56-57	0.0
58-59	0.0
60-61	0.0
62-63	0.0
64-65	0.0125
66-67	0.0
68-69	0.0375
70-71	0.025
72-73	0.0375
74-75	0.025
76	0.075
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
76	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	48.775
#Duplication Level	Percentage of deduplicated	Percentage of total
1	83.75192209123526	40.849999999999994
2	7.227063044592516	7.049999999999999
3	3.0240902101486418	4.425
4	1.7939518195797026	3.5000000000000004
5	0.9738595592004101	2.375
6	0.7175807278318811	2.1
7	0.4613018964633521	1.575
8	0.3075345976422348	1.2
9	0.2562788313685289	1.125
>10	1.3839056893900563	12.950000000000001
>50	0.05125576627370579	2.0500000000000003
>100	0.0	0.0
>500	0.05125576627370579	20.8
>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
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTATG	832	20.8	TruSeq Adapter, Index 7 (97% over 37bp)
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	82	2.0500000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGATTGTAGTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA	39	0.975	TruSeq Adapter, Index 2 (97% over 36bp)
GGGATTGTAGTTCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	37	0.9249999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	31	0.775	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCCGTTGTAGTCTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGGAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGA	28	0.7000000000000001	TruSeq Adapter, Index 7 (97% over 37bp)
TCCCAAATGTAGACAAAGCAAGATCGGAAGAGCACACGTCTGAACTCCAG	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	23	0.575	TruSeq Adapter, Index 7 (100% over 35bp)
TATTCTGGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGA	22	0.5499999999999999	TruSeq Adapter, Index 7 (97% over 37bp)
AACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA	22	0.5499999999999999	TruSeq Adapter, Index 2 (97% over 36bp)
GCGGAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAG	22	0.5499999999999999	TruSeq Adapter, Index 7 (97% over 37bp)
GGGATTGTAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAA	21	0.525	TruSeq Adapter, Index 7 (97% over 37bp)
GGGATTGTAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAA	20	0.5	TruSeq Adapter, Index 7 (97% over 37bp)
GCGGCGACGTGGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA	19	0.475	TruSeq Adapter, Index 2 (97% over 36bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTAT	19	0.475	TruSeq Adapter, Index 7 (97% over 37bp)
GCATGCCTGTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAA	16	0.4	TruSeq Adapter, Index 7 (97% over 37bp)
TCCCAAATGTAGACAAAGCAGATCGGAAGAGCACACGTCTGAACTCCAGT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCGGACTGCTCGAGCTGCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TTGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGAT	13	0.325	TruSeq Adapter, Index 7 (97% over 37bp)
ATATTCTGGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAG	12	0.3	TruSeq Adapter, Index 7 (97% over 37bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AGTTACTAATTCATGATCTGGCATAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCG	10	0.25	TruSeq Adapter, Index 7 (97% over 37bp)
AACGACTCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGA	10	0.25	TruSeq Adapter, Index 7 (97% over 37bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	10	0.25	No Hit
GCGGGTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATC	10	0.25	TruSeq Adapter, Index 7 (97% over 37bp)
GAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTAT	10	0.25	TruSeq Adapter, Index 7 (97% over 37bp)
TTTGGATTGAAGGGAGCTCTAAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACGACTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATC	9	0.22499999999999998	TruSeq Adapter, Index 7 (97% over 37bp)
AGTTACTAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGGATATGATGAAATGGCAATAAGATCGGAAGAGCACACGTCTGAACTCC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCTTGACTCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAG	9	0.22499999999999998	TruSeq Adapter, Index 7 (97% over 37bp)
TCGGACCAGGCTTCATTCCCCAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAAAACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCTGCCGTGATCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA	8	0.2	TruSeq Adapter, Index 2 (97% over 36bp)
TAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTAT	8	0.2	TruSeq Adapter, Index 7 (97% over 37bp)
ATTGTATCATTAACTATTTCTTTATAGATCGGAAGAGCACACGTCTGAAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	8	0.2	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
TCCCAAATGTAGACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAA	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 37bp)
GGGATTGTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGA	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 37bp)
TTTGGATTGAAGGGAGCTCTTAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AAAACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGATCGGAAGAGCACACGTCTAAACTCCAGTCACCAAAAGATCTCGTATG	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 35bp)
GCGGCGAGAGCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAA	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 37bp)
TGAAGCTGCCAGCATGATCTAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGACTCTCGGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	6	0.15	TruSeq Adapter, Index 7 (100% over 35bp)
GGTGGCTGTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAG	6	0.15	TruSeq Adapter, Index 7 (97% over 37bp)
TACCGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAA	6	0.15	TruSeq Adapter, Index 7 (97% over 37bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGGACTGCTCGAGCTGCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TACCTGGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGAT	6	0.15	TruSeq Adapter, Index 7 (97% over 37bp)
GTGGACGTGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	6	0.15	TruSeq Adapter, Index 7 (100% over 35bp)
TGACAGAAGAGAGTGAGCACAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATGGGTCGGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	6	0.15	TruSeq Adapter, Index 7 (100% over 35bp)
AAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTAT	6	0.15	TruSeq Adapter, Index 7 (97% over 37bp)
AACGACTCTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAA	6	0.15	TruSeq Adapter, Index 7 (97% over 37bp)
TCGATACCTGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAA	6	0.15	TruSeq Adapter, Index 7 (97% over 37bp)
TTTGGATTGAAGGGAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAAAACGACTCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAA	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTTACTAATTCATGATCTGGCAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATTGGTCAGAAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CGCGGCGACGTGGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	5	0.125	TruSeq Adapter, Index 7 (100% over 35bp)
GGATGGGTCGGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA	5	0.125	TruSeq Adapter, Index 2 (97% over 36bp)
TATTCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGA	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
GGCGGATGTAGCCAAGTGGAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGCTGTAGCACACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AAGGAAGCTATAAGTAATGCAACTATGAAAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	5	0.125	No Hit
AACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAGGGACGACGATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	5	0.125	TruSeq Adapter, Index 7 (100% over 35bp)
GCGGACTGCTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAA	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
GCGGAACGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGA	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAAGATCGGAAGA	5	0.125	No Hit
TATTCTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATC	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
TTCATGGACGTTGATAAGATCTTTAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TATTCTGGTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAG	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
>>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	22.225	0.0	0.0	0.0	0.0
2	23.375	0.0	0.0	0.0	0.0
3	23.775	0.0	0.0	0.0	0.0
4	24.025	0.0	0.0	0.0	0.0
5	24.425	0.0	0.0	0.0	0.0
6	24.75	0.0	0.0	0.0	0.0
7	25.275	0.0	0.0	0.0	0.0
8	26.75	0.0	0.0	0.0	0.0
9	28.85	0.0	0.0	0.0	0.0
10	32.7	0.0	0.0	0.0	0.0
11	35.725	0.0	0.0	0.0	0.0
12	39.025	0.0	0.0	0.0	0.0
13	42.925	0.0	0.0	0.0	0.0
14	47.675	0.0	0.0	0.0	0.0
15	51.5	0.0	0.0	0.0	0.0
16	54.025	0.0	0.0	0.0	0.0
17	59.375	0.0	0.0	0.0	0.0
18	63.7	0.0	0.0	0.0	0.0
19	65.65	0.0	0.0	0.0	0.0
20	68.125	0.0	0.0	0.0	0.0
21	70.875	0.0	0.0	0.0	0.0
22	74.325	0.0	0.0	0.0	0.0
23	77.275	0.0	0.0	0.0	0.0
24	79.275	0.0	0.0	0.0	0.0
25	83.2	0.0	0.0	0.0	0.0
26	84.425	0.0	0.0	0.0	0.0
27	85.925	0.0	0.0	0.0	0.0
28	86.5	0.0	0.0	0.0	0.0
29	87.075	0.0	0.0	0.0	0.0
30	88.125	0.0	0.0	0.0	0.0
31	89.0	0.0	0.0	0.0	0.0
32	89.6	0.0	0.0	0.0	0.0
33	90.525	0.0	0.0	0.0	0.0
34	91.075	0.0	0.0	0.0	0.0
35	91.9	0.0	0.0	0.0	0.0
36	92.25	0.0	0.0	0.0	0.0
37	92.525	0.0	0.0	0.0	0.0
38	92.975	0.0	0.0	0.0	0.0
39	93.175	0.0	0.0	0.0	0.0
40	93.7	0.0	0.0	0.0	0.0
41	93.875	0.0	0.0	0.0	0.0
42	94.0	0.0	0.0	0.0	0.0
43	94.05	0.0	0.0	0.0	0.0
44	94.1	0.0	0.0	0.0	0.0
45	94.225	0.0	0.0	0.0	0.0
46	94.3	0.0	0.0	0.0	0.0
47	94.325	0.0	0.0	0.0	0.0
48	94.325	0.0	0.0	0.0	0.0
49	94.35	0.0	0.0	0.0	0.0
50	94.35	0.0	0.0	0.0	0.0
51	94.35	0.0	0.0	0.0	0.0
52	94.425	0.0	0.0	0.0	0.0
53	94.45	0.0	0.0	0.0	0.0
54	94.525	0.0	0.0	0.0	0.0
55	94.525	0.0	0.0	0.0	0.0
56	94.525	0.0	0.0	0.0	0.0
57	94.55	0.0	0.0	0.0	0.0
58	94.55	0.0	0.0	0.0	0.0
59	94.55	0.0	0.0	0.0	0.0
60	94.55	0.0	0.0	0.0	0.0
61	94.55	0.0	0.0	0.0	0.0
62	94.55	0.0	0.0	0.0	0.0
63	94.55	0.0	0.0	0.0	0.0
64	94.6	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TAGGATA	15	0.0020658788	70.00001	20
GGATTGT	30	7.878043E-8	70.00001	2
GTTCAAT	15	0.0020658788	70.00001	10
GATTGTA	30	7.878043E-8	70.00001	3
GGTTAGG	15	0.0020658788	70.00001	17
ATTGTAG	30	7.878043E-8	70.00001	4
GGGATTG	30	7.878043E-8	70.00001	1
GTTAGGA	15	0.0020658788	70.00001	18
TTAGGAT	15	0.0020658788	70.00001	19
CGGTTAG	15	0.0020658788	70.00001	16
AGTTCAA	15	0.0020658788	70.00001	9
TTGTAGT	25	2.3570374E-6	70.0	5
TAGTTCA	20	7.003785E-5	70.0	8
TGTAGTT	20	7.003785E-5	70.0	6
AAAAAGG	80	0.0	70.0	70
GTAGTTC	20	7.003785E-5	70.0	7
AAAAAAG	85	0.0	65.88235	69
GAAAAAA	95	0.0	58.947372	64
TGAAAAA	105	0.0	53.333336	63
TTGAAAA	110	0.0	50.90909	62
>>END_MODULE
Rejected 1638838 READS because READLEN < 1
Read 1638838 spots for ERR9744597.sra
Written 1638838 spots for ERR9744597.sra
Rejected 1638838 READS because READLEN < 1
Read 1638838 spots for ERR9744597.sra
Written 1638838 spots for ERR9744597.sra
Rejected 1638838 READS because READLEN < 1
Read 1638838 spots for ERR9744597.sra
Written 1638838 spots for ERR9744597.sra
Rejected 1638838 READS because READLEN < 1
Read 1638838 spots for ERR9744597.sra
Written 1638838 spots for ERR9744597.sra
Rejected 1638843 READS because READLEN < 1
Read 1638843 spots for ERR9744597.sra
Written 1638843 spots for ERR9744597.sra
Rejected 1638838 READS because READLEN < 1
Read 1638838 spots for ERR9744597.sra
Written 1638838 spots for ERR9744597.sra
Rejected 1638838 READS because READLEN < 1
Read 1638838 spots for ERR9744597.sra
Written 1638838 spots for ERR9744597.sra
Rejected 1638838 READS because READLEN < 1
Read 1638838 spots for ERR9744597.sra
Written 1638838 spots for ERR9744597.sra
SRR ids: ['ERR9744597.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_12p78ovv
ERR9744597.sra spots: 13110709
blocks: [[1, 1638838], [1638839, 3277676], [3277677, 4916514], [4916515, 6555352], [6555353, 8194190], [8194191, 9833028], [9833029, 11471866], [11471867, 13110709]]
ERR9744597 file size 2487776
ERR9744597 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -q 10 -k inf -t 8 -o ERR9744597 ERR9744597_1.fastq
Input file:	ERR9744597_1.fastq
trimmed:	ERR9744597-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):	8
Sat Feb  8 00:38:46 2025 >> started

Sat Feb  8 00:38:59 2025 >> done (13.423s)
13110709 reads processed; of these:
 5652746 (43.12%) short reads filtered out after trimming by size control
 2816393 (21.48%) empty reads filtered out after trimming by size control
 4641570 (35.40%) reads available; of these:
 4392278 (94.63%) trimmed reads available after processing
  249292 ( 5.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 281117	  6.06%
 19	 363616	  7.83%
 20	 411396	  8.86%
 21	 513243	 11.06%
 22	 444804	  9.58%
 23	 277661	  5.98%
 24	 586316	 12.63%
 25	 172985	  3.73%
 26	 184086	  3.97%
 27	 100401	  2.16%
 28	  84396	  1.82%
 29	 123124	  2.65%
 30	  89194	  1.92%
 31	 126970	  2.74%
 32	 117534	  2.53%
 33	 112830	  2.43%
 34	  97913	  2.11%
 35	  68046	  1.47%
 36	  40466	  0.87%
 37	  54609	  1.18%
 38	  34771	  0.75%
 39	  40517	  0.87%
 40	  24350	  0.52%
 41	  15172	  0.33%
 42	  13092	  0.28%
 43	   7331	  0.16%
 44	   6194	  0.13%
 45	      2	  0.00%
 46	      0	  0.00%
 47	      0	  0.00%
 48	      0	  0.00%
 49	      0	  0.00%
 50	      0	  0.00%
 51	      0	  0.00%
 52	      0	  0.00%
 53	      0	  0.00%
 54	      0	  0.00%
 55	      0	  0.00%
 56	      2	  0.00%
 57	      1	  0.00%
 58	      4	  0.00%
 59	      1	  0.00%
 60	      5	  0.00%
 61	      4	  0.00%
 62	      2	  0.00%
 63	      3	  0.00%
 64	      6	  0.00%
 65	      5	  0.00%
 66	      6	  0.00%
 67	      7	  0.00%
 68	      5	  0.00%
 69	     10	  0.00%
 70	     12	  0.00%
 71	     12	  0.00%
 72	      4	  0.00%
 73	      9	  0.00%
 74	      9	  0.00%
 75	     35	  0.00%
 76	 249292	  5.37%
4641570 reads passed initial QC


criterion=sequence-density
sequence-density=6.30
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=8
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG


criterion=fanout-score
sequence-density=1.21
sequence-density-rank=4
fanout-score=34.59
fanout-score-rank=1
prefix-density=1.28
prefix-fanout=32.7
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTCTGCTTGAAAAA
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:
    0 (0.00%) aligned 0 times
    1 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
Potential adapter found in reference sequence. Continuing without clipping.
                                 Started job on |	Feb 08 00:39:22
                             Started mapping on |	Feb 08 00:39:22
                                    Finished on |	Feb 08 00:40:23
       Mapping speed, Million of reads per hour |	273.93

                          Number of input reads |	4641570
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1762852
                        Uniquely mapped reads % |	37.98%
                          Average mapped length |	25.86
                       Number of splices: Total |	16045
            Number of splices: Annotated (sjdb) |	3082
                       Number of splices: GT/AG |	14850
                       Number of splices: GC/AG |	103
                       Number of splices: AT/AC |	24
               Number of splices: Non-canonical |	1068
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.07
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	2426587
             % of reads mapped to multiple loci |	52.28%
        Number of reads mapped to too many loci |	256533
             % of reads mapped to too many loci |	5.53%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	3.77%
                     % of reads unmapped: other |	0.44%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	452131	452131	452131
N_multimapping	2426587	2426587	2426587
N_noFeature	571015	628295	1610383
N_ambiguous	136011	42971	1230
UnstrandedReadsAssigned:1055826 PositiveStrandReadsAssigned:1091586 NegativeStrandReadsAssigned:151239
Dataset is classified positive stranded
MeadianReadLen=24 20thPercentileLength=20 echo kmer=19
ERR9744597 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: ERR9744597-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,641,570 reads, 181,138 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 912 rounds

  48360 ERR9744597.ke.tsv
  32833 ERR9744597.se.tsv
  81193 total
==> ERR9744597.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	30	34.8037
AT1G18320.1	699	600	0	0
AT5G11100.1	1709	1610	1	1.73658
AT4G35335.1	1280	1181	0	0
AT1G60930.1	3876	3777	0	0
AT1G17000.1	2351	2252	0	0
AT3G55270.1	3130	3031	1	0.922435
AT4G16150.1	3181	3082	2	1.81434
AT3G18150.1	1370	1271	1	2.19976

==> ERR9744597.se.tsv <==
AT1G01010	1
AT1G01020	0
AT1G03987	0
AT1G01030	0
AT1G01040	4
AT1G03993	1
AT1G01046	29
AT1G01050	2
AT1G03997	0
AT1G01060	0
ERR9744597 completed mapping pipeline successfully
