Starting /dee2/code/volunteer_pipeline.sh SRR9060556
    current disk space = 759597080
    free memory = 128124300 
SRR9060556 SRAfilesize
0470c6a1f8a61983a92a2cc5095a6b47  SRR9060556.sra
SRR9060556.sra file validated
SRR9060556 is single end
SRR9060556 is conventional basespace
SRR9060556 read1 length is 49-51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR9060556_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	49-51
%GC	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.199	32.0	32.0	32.0	32.0	32.0
2	31.58425	32.0	32.0	32.0	32.0	32.0
3	31.71525	32.0	32.0	32.0	32.0	32.0
4	31.79225	32.0	32.0	32.0	32.0	32.0
5	31.69075	32.0	32.0	32.0	32.0	32.0
6	34.72425	36.0	36.0	36.0	36.0	36.0
7	35.30675	36.0	36.0	36.0	36.0	36.0
8	35.342	36.0	36.0	36.0	36.0	36.0
9	35.3395	36.0	36.0	36.0	36.0	36.0
10	35.46	36.0	36.0	36.0	36.0	36.0
11	35.4525	36.0	36.0	36.0	36.0	36.0
12	35.3245	36.0	36.0	36.0	36.0	36.0
13	35.42125	36.0	36.0	36.0	36.0	36.0
14	35.4815	36.0	36.0	36.0	36.0	36.0
15	35.446	36.0	36.0	36.0	36.0	36.0
16	35.43075	36.0	36.0	36.0	36.0	36.0
17	35.432	36.0	36.0	36.0	36.0	36.0
18	35.3855	36.0	36.0	36.0	36.0	36.0
19	35.3635	36.0	36.0	36.0	36.0	36.0
20	35.37	36.0	36.0	36.0	36.0	36.0
21	35.48775	36.0	36.0	36.0	36.0	36.0
22	35.416	36.0	36.0	36.0	36.0	36.0
23	35.506	36.0	36.0	36.0	36.0	36.0
24	35.367	36.0	36.0	36.0	36.0	36.0
25	35.189	36.0	36.0	36.0	36.0	36.0
26	35.346	36.0	36.0	36.0	36.0	36.0
27	35.328	36.0	36.0	36.0	36.0	36.0
28	35.372	36.0	36.0	36.0	36.0	36.0
29	35.37875	36.0	36.0	36.0	36.0	36.0
30	35.171	36.0	36.0	36.0	36.0	36.0
31	35.43625	36.0	36.0	36.0	36.0	36.0
32	35.38875	36.0	36.0	36.0	36.0	36.0
33	35.25925	36.0	36.0	36.0	36.0	36.0
34	35.2875	36.0	36.0	36.0	36.0	36.0
35	35.36575	36.0	36.0	36.0	36.0	36.0
36	35.33425	36.0	36.0	36.0	36.0	36.0
37	35.1465	36.0	36.0	36.0	36.0	36.0
38	35.26925	36.0	36.0	36.0	36.0	36.0
39	35.10725	36.0	36.0	36.0	36.0	36.0
40	35.16	36.0	36.0	36.0	36.0	36.0
41	35.1365	36.0	36.0	36.0	36.0	36.0
42	35.227	36.0	36.0	36.0	36.0	36.0
43	35.23275	36.0	36.0	36.0	36.0	36.0
44	35.08675	36.0	36.0	36.0	36.0	36.0
45	35.09025	36.0	36.0	36.0	36.0	36.0
46	35.19925	36.0	36.0	36.0	36.0	36.0
47	35.189	36.0	36.0	36.0	36.0	36.0
48	35.068	36.0	36.0	36.0	36.0	36.0
49	35.09575	36.0	36.0	36.0	36.0	36.0
50	35.0664	36.0	36.0	36.0	36.0	36.0
51	35.064736630478485	36.0	36.0	36.0	36.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
20	1.0
21	0.0
22	0.0
23	3.0
24	5.0
25	9.0
26	11.0
27	14.0
28	32.0
29	37.0
30	52.0
31	76.0
32	104.0
33	159.0
34	420.0
35	3077.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	14.725	42.55	14.2	28.525
2	15.375	30.15	35.15	19.325
3	24.45	17.9	38.3	19.35
4	35.525	17.925	24.425	22.125
5	44.025	20.974999999999998	18.0	17.0
6	25.351033954557057	20.11743681388818	39.64768955833546	14.8838396732193
7	29.625	21.625	19.1	29.65
8	26.25	30.0	20.5	23.25
9	24.65	32.9	26.974999999999998	15.475
10	35.3	20.575	26.8	17.325
11	42.05	19.225	20.3	18.425
12	18.925	18.95	41.325	20.8
13	34.225	21.725	27.0	17.05
14	20.125	21.2	40.675	18.0
15	29.65	15.5	35.375	19.475
16	38.550000000000004	18.975	21.85	20.625
17	29.599999999999998	19.725	32.5	18.175
18	32.074999999999996	29.7	21.675	16.55
19	22.875	27.275	33.125	16.725
20	24.15	19.3	31.874999999999996	24.675
21	28.9	18.875	22.25	29.975
22	21.5	34.2	21.4	22.900000000000002
23	31.974999999999998	20.575	26.700000000000003	20.75
24	20.549999999999997	19.25	38.4	21.8
25	21.85	35.0	23.175	19.975
26	33.175	20.925	20.1	25.8
27	24.825	30.85	27.875	16.45
28	43.55	21.7	19.75	15.0
29	32.125	21.85	17.05	28.975
30	22.275	34.125	26.8	16.8
31	37.0	21.2	24.575	17.224999999999998
32	22.575	18.875	44.375	14.174999999999999
33	25.45	17.724999999999998	28.749999999999996	28.075
34	30.55	21.125	23.45	24.875
35	34.150000000000006	19.55	34.699999999999996	11.600000000000001
36	27.05	24.875	36.05	12.025
37	29.48974487243622	28.289144572286144	31.190595297648827	11.030515257628814
38	32.824999999999996	22.775000000000002	31.85	12.55
39	27.025	25.75	33.275	13.950000000000001
40	20.25	27.875	29.5	22.375
41	19.675	20.424999999999997	38.4	21.5
42	19.225	12.65	39.0	29.125
43	27.775	8.95	31.324999999999996	31.95
44	34.5	9.0	29.175	27.325
45	38.574999999999996	9.225	23.849999999999998	28.349999999999998
46	42.325	8.3	24.45	24.925
47	51.55	10.375	17.0	21.075
48	47.4	12.9	13.65	26.05
49	36.725	16.6	16.85	29.825000000000003
50	36.32	19.52	16.32	27.839999999999996
51	36.18817852834741	0.0	17.53116204262163	46.28065942903096
>>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	0.0
14	0.0
15	0.5
16	1.0
17	0.5
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	1.5
26	3.0
27	3.0
28	2.0
29	1.5
30	2.5
31	2.0
32	1.0
33	1.0
34	3.5
35	8.5
36	18.5
37	27.0
38	38.5
39	50.0
40	55.0
41	65.5
42	99.5
43	137.5
44	260.0
45	393.5
46	442.5
47	484.0
48	498.0
49	513.0
50	472.0
51	401.5
52	434.0
53	616.0
54	721.5
55	579.0
56	417.0
57	336.0
58	275.0
59	222.0
60	157.0
61	101.5
62	64.0
63	34.0
64	19.5
65	12.0
66	9.0
67	4.5
68	2.0
69	0.5
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	1.0
98	2.0
99	1.5
100	1.0
>>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	2.075
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	0.05
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
51	0.0
>>END_MODULE
>>Sequence Length Distribution	warn
#Length	Count
49	250.0
50	1263.0
51	2487.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	65.625
#Duplication Level	Percentage of deduplicated	Percentage of total
1	93.18095238095238	61.150000000000006
2	3.5047619047619047	4.6
3	1.0285714285714285	2.025
4	0.5714285714285714	1.5
5	0.2285714285714286	0.75
6	0.19047619047619047	0.75
7	0.0761904761904762	0.35000000000000003
8	0.0761904761904762	0.4
9	0.1523809523809524	0.8999999999999999
>10	0.7619047619047619	10.0
>50	0.1142857142857143	5.125
>100	0.1142857142857143	12.45
>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
GATTGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGCCA	195	4.875	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTTGGAATTCTCGGGTG	167	4.175	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTGGAATTCTCGGGTGC	136	3.4000000000000004	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTTTGGAATTCTCGGGT	80	2.0	No Hit
ATACTGCGATCTGTTGAGACTATCCTTTGATTGAGTGGAATTCTCGGGTGC	68	1.7000000000000002	No Hit
AAGAGAAGGTGTCTTGCTGGCGGTAGTGGAATTCTCGGGTGCCAAGGAACT	57	1.425	RNA PCR Primer, Index 1 (100% over 25bp)
CCTCCAGTTGGTACGTCTGGTTCAGGGTTGTTTTGGAATTCTCGGGTGCC	46	1.15	No Hit
AGTGATTGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGC	34	0.8500000000000001	No Hit
TTGCGGACGCTTTCTGGTGTGTGCTTGGACCTTGGAATTCTCGGGTGCCA	34	0.8500000000000001	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTGGAATTCTCGGGTGCC	30	0.75	No Hit
AACTGTGGTCGTGACTTCTAATTTGCTGGTTTTGGAATTCTCGGGTGCCA	29	0.7250000000000001	No Hit
CGGGGTGCAATTATTAGAACAGACCAAACTGGAATTCTCGGGTGCCAAGG	26	0.65	Illumina Small RNA Adapter 2 (100% over 21bp)
GATTGTGCTTGCTTGCGGACGCTTTCTGGTGTGGAATTCTCGGGTGCCA	21	0.525	No Hit
TTGCGGACGCTTTCTGGTGTGTGCTTGGACCTCTGGAATTCTCGGGTGCC	21	0.525	No Hit
ATTGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGCCA	18	0.44999999999999996	No Hit
AACTGTGGTCGTGACTTCTAATTTGCTGGTTTGGAATTCTCGGGTGCCA	18	0.44999999999999996	No Hit
GGCCAGTTGGTTGATGCTTGTCCGGCGCAGTTCTGGAATTCTCGGGTGCC	15	0.375	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTTTTGGAATTCTCGGG	14	0.35000000000000003	No Hit
GATTGTGCTTGCTTGCGGACGCTTTCTGGTTGGAATTCTCGGGTGCCAAGG	14	0.35000000000000003	Illumina Small RNA Adapter 2 (100% over 21bp)
GTGCTTGGACCTCGGTTCTAGTATCCTGATCGCTCTGGAATTCTCGGGTGC	13	0.325	No Hit
AACTGTGGTCGTGACTTCTAATTTGCTGGTTTGTGGAATTCTCGGGTGCC	12	0.3	No Hit
TGCGGACGCTTTCTGGTGTGTGCTTGGACCTTGGAATTCTCGGGTGCCA	12	0.3	No Hit
ACGGCCTGGGAATCCTGGATGTTGTAAGCTTGGAATTCTCGGGTGCCAAGG	11	0.27499999999999997	Illumina Small RNA Adapter 2 (100% over 21bp)
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCTGGAATTCTCGGGTGCC	11	0.27499999999999997	No Hit
TTGTGATCGTTGCCGGGTGTCGTTTCCTTGGAATTCTCGGGTGCCAAGGA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 22bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC	10	0.25	RNA PCR Primer, Index 6 (100% over 51bp)
TGCGGACGCTTTCTGGTGTGTGCTTGGACCTCTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
GTGCTTGGACCTCGGTTCTAGTATCCTGATCGCTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
GGCCAGTTGGTTGATGCTTGTCCGGCGCAGTGGAATTCTCGGGTGCCAAGG	9	0.22499999999999998	Illumina Small RNA Adapter 2 (100% over 21bp)
GTGCTTGGACCTCGGTTCTAGTATCCTGATCGCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
ACTGCGATCTGTTGAGACTATCCTTTGATTGAGTGGAATTCTCGGGTGCC	8	0.2	No Hit
TCTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTTGGAATTCTCGGGT	8	0.2	No Hit
AGTGATTGTGCTTGCTTGCGGACGCTTTCTGGTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
AACTGTGGTCGTGACTTCTAATTTGCTGGTGGAATTCTCGGGTGCCAAGG	7	0.17500000000000002	Illumina Small RNA Adapter 2 (100% over 21bp)
TCTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTGGAATTCTCGGGTG	6	0.15	No Hit
GATTGNGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
AATTTTCGATTGATGCGGCGCTGAGAAGTGGAATTCTCGGGTGCCAAGGA	6	0.15	RNA PCR Primer, Index 1 (100% over 22bp)
ACCCATAAGGCCGGGGTTCGATTCCCCGCAACGGAACTGGAATTCTCGGGT	6	0.15	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCTGGAATTCTCGGGTGCCAAGG	6	0.15	Illumina Small RNA Adapter 2 (100% over 21bp)
CTTGGNCAAGGTGTTGTATTCAGTAGAGCAGTCCTTTGGAATTCTCGGGTG	5	0.125	No Hit
AGTGATTGTGCTTGCTTGCGGACGCTTTCTGGTTGGAATTCTCGGGTGCC	5	0.125	No Hit
ATTGGTTTGAACCGGGTAAAAGTCGTAACTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
TGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
CTTGGNCAAGGTGTTGTATTCAGTAGAGCAGTCCTTGGAATTCTCGGGTGC	5	0.125	No Hit
TGTGATCGTTGCCGGGTGTCGTTTCCTTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
>>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	0.25	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.275	0.0	0.0	0.0
4	0.0	0.275	0.0	0.0	0.0
5	0.0	0.55	0.0	0.0	0.0
6	0.0	1.25	0.0	0.0	0.0
7	0.0	2.375	0.0	0.0	0.0
8	0.0	3.95	0.0	0.0	0.0
9	0.0	4.55	0.0	0.0	0.0
10	0.0	5.075	0.0	0.0	0.0
11	0.0	5.175	0.0	0.0	0.0
12	0.0	5.475	0.0	0.0	0.0
13	0.0	5.65	0.0	0.0	0.0
14	0.0	5.9	0.0	0.0	0.0
15	0.0	6.275	0.0	0.0	0.0
16	0.0	6.625	0.0	0.0	0.0
17	0.0	6.85	0.0	0.0	0.0
18	0.0	7.25	0.0	0.0	0.0
19	0.0	7.525	0.0	0.0	0.0
20	0.0	7.75	0.0	0.0	0.0
21	0.0	8.05	0.0	0.0	0.0
22	0.0	8.35	0.0	0.0	0.0
23	0.0	8.7	0.0	0.0	0.0
24	0.0	8.975	0.0	0.0	0.0
25	0.0	9.375	0.0	0.0	0.0
26	0.0	9.95	0.0	0.0	0.0
27	0.0	12.25	0.0	0.0	0.0
28	0.0	14.175	0.0	0.0	0.0
29	0.0	16.575	0.0	0.0	0.0
30	0.0	20.0	0.0	0.0	0.0
31	0.0	24.475	0.0	0.0	0.0
32	0.0	30.125	0.0	0.0	0.0
33	0.0	42.925	0.0	0.0	0.0
34	0.0	53.475	0.0	0.0	0.0
35	0.0	61.875	0.0	0.0	0.0
36	0.0	75.2	0.0	0.0	0.0
37	0.0	86.425	0.0	0.0	0.0
38	0.0	92.825	0.0	0.0	0.0
39	0.0	95.775	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AGCAGTC	60	0.0	44.5125	27
AGAGCAG	60	0.0	44.5125	25
CAGTCCT	55	0.0	44.512497	29
GTCCTTT	40	4.796675E-9	44.512497	31
GCAGTCC	55	0.0	44.512497	28
TAGAGCA	55	0.0	44.512497	24
AGTCCTT	55	0.0	44.512497	30
TGGTCAA	65	0.0	41.608566	3
GGTCAAG	65	0.0	41.608566	4
CTTGGTC	65	0.0	41.608566	1
TTGGTCA	65	0.0	41.608566	2
TGTTGTA	65	0.0	41.08846	12
GTGTTGT	65	0.0	41.08846	11
TTGTATT	65	0.0	41.08846	14
GTATTCA	65	0.0	41.08846	16
GAGCAGT	65	0.0	41.08846	26
TATTCAG	65	0.0	41.08846	17
TGTATTC	65	0.0	41.08846	15
GTTGTAT	65	0.0	41.08846	13
GTAGAGC	60	1.8189894E-12	40.803127	23
>>END_MODULE
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
Written 462793 spots for SRR9060556.sra
Rejected 462793 READS because READLEN < 1
Read 462793 spots for SRR9060556.sra
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SRR ids: ['SRR9060556.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6cqj0qhv
SRR9060556.sra spots: 29618802
blocks: [[1, 462793], [462794, 925586], [925587, 1388379], [1388380, 1851172], [1851173, 2313965], [2313966, 2776758], [2776759, 3239551], [3239552, 3702344], [3702345, 4165137], [4165138, 4627930], [4627931, 5090723], [5090724, 5553516], [5553517, 6016309], [6016310, 6479102], [6479103, 6941895], [6941896, 7404688], [7404689, 7867481], [7867482, 8330274], [8330275, 8793067], [8793068, 9255860], [9255861, 9718653], [9718654, 10181446], [10181447, 10644239], [10644240, 11107032], [11107033, 11569825], [11569826, 12032618], [12032619, 12495411], [12495412, 12958204], [12958205, 13420997], [13420998, 13883790], [13883791, 14346583], [14346584, 14809376], [14809377, 15272169], [15272170, 15734962], [15734963, 16197755], [16197756, 16660548], [16660549, 17123341], [17123342, 17586134], [17586135, 18048927], [18048928, 18511720], [18511721, 18974513], [18974514, 19437306], [19437307, 19900099], [19900100, 20362892], [20362893, 20825685], [20825686, 21288478], [21288479, 21751271], [21751272, 22214064], [22214065, 22676857], [22676858, 23139650], [23139651, 23602443], [23602444, 24065236], [24065237, 24528029], [24528030, 24990822], [24990823, 25453615], [25453616, 25916408], [25916409, 26379201], [26379202, 26841994], [26841995, 27304787], [27304788, 27767580], [27767581, 28230373], [28230374, 28693166], [28693167, 29155959], [29155960, 29618802]]
SRR9060556 file size 4175896
SRR9060556 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 64 -o SRR9060556 SRR9060556_1.fastq
Input file:	SRR9060556_1.fastq
trimmed:	SRR9060556-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):	32
Thu Feb 13 06:27:33 2020 >> started

Thu Feb 13 06:27:58 2020 >> done (24.252s)
29618802 reads processed; of these:
       0 ( 0.00%) short reads filtered out after trimming by size control
       0 ( 0.00%) empty reads filtered out after trimming by size control
29618802 (100.00%) reads available; of these:
     226 ( 0.00%) trimmed reads available after processing
29618576 (100.00%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 37	       1	  0.00%
 38	       0	  0.00%
 39	       0	  0.00%
 40	       1	  0.00%
 41	       7	  0.00%
 42	       1	  0.00%
 43	       1	  0.00%
 44	       5	  0.00%
 45	      56	  0.00%
 46	      95	  0.00%
 47	     223	  0.00%
 48	    2760	  0.01%
 49	 1977938	  6.68%
 50	 9040681	 30.52%
 51	18597033	 62.79%
29618802 reads passed initial QC


criterion=sequence-density
sequence-density=95.77
sequence-density-rank=1
fanout-score=27.74
fanout-score-rank=1
prefix-density=97.82
prefix-fanout=27.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC


criterion=fanout-score
sequence-density=95.77
sequence-density-rank=1
fanout-score=27.74
fanout-score-rank=1
prefix-density=97.82
prefix-fanout=27.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC
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 64 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC -o SRR9060556 -
Input file:	STDIN
trimmed:	SRR9060556-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC
-- 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):	32
Thu Feb 13 06:29:26 2020 >> started

Thu Feb 13 06:30:44 2020 >> done (78.169s)
29001744 reads processed; of these:
 2259921 ( 7.79%) short reads filtered out after trimming by size control
   59899 ( 0.21%) empty reads filtered out after trimming by size control
26681924 (92.00%) reads available; of these:
26319114 (98.64%) trimmed reads available after processing
  362810 ( 1.36%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   98606	  0.37%
 19	   93969	  0.35%
 20	   94598	  0.35%
 21	  107072	  0.40%
 22	  107948	  0.40%
 23	   70154	  0.26%
 24	  132380	  0.50%
 25	  200726	  0.75%
 26	  749345	  2.81%
 27	  500588	  1.88%
 28	  632321	  2.37%
 29	 1073595	  4.02%
 30	 1312339	  4.92%
 31	 1804091	  6.76%
 32	 3720395	 13.94%
 33	 2821608	 10.57%
 34	 2371599	  8.89%
 35	 4084679	 15.31%
 36	 3058226	 11.46%
 37	 1712347	  6.42%
 38	  935302	  3.51%
 39	  356896	  1.34%
 40	  130294	  0.49%
 41	   66061	  0.25%
 42	   23350	  0.09%
 43	   24269	  0.09%
 44	   11235	  0.04%
 45	   11933	  0.04%
 46	    4109	  0.02%
 47	    4294	  0.02%
 48	    6601	  0.02%
 49	   26469	  0.10%
 50	  115562	  0.43%
 51	  218963	  0.82%


criterion=sequence-density
sequence-density=0.25
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=ACACAGAAGGTCGGTGGTTCGAGCCCGCCCGAGATCACC


criterion=fanout-score
sequence-density=0.09
sequence-density-rank=10
fanout-score=27.23
fanout-score-rank=1
prefix-density=0.27
prefix-fanout=9.5
sequence=GGAATTCTCGGG
                                 Started job on |	Feb 13 06:31:48
                             Started mapping on |	Feb 13 06:31:49
                                    Finished on |	Feb 13 06:33:03
       Mapping speed, Million of reads per hour |	1328.06

                          Number of input reads |	27298982
                      Average input read length |	33
                                    UNIQUE READS:
                   Uniquely mapped reads number |	18419847
                        Uniquely mapped reads % |	67.47%
                          Average mapped length |	32.63
                       Number of splices: Total |	1256803
            Number of splices: Annotated (sjdb) |	1238870
                       Number of splices: GT/AG |	1244164
                       Number of splices: GC/AG |	5752
                       Number of splices: AT/AC |	145
               Number of splices: Non-canonical |	6742
                      Mismatch rate per base, % |	0.10%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	7740822
             % of reads mapped to multiple loci |	28.36%
        Number of reads mapped to too many loci |	623646
             % of reads mapped to too many loci |	2.28%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	1.88%
                     % of reads unmapped: other |	0.00%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1138313	1138313	1138313
N_multimapping	7740822	7740822	7740822
N_noFeature	88862	96092	18320887
N_ambiguous	112844	21812	319
UnstrandedReadsAssigned:18218141 PositiveStrandReadsAssigned:18301943 NegativeStrandReadsAssigned:98641
Dataset is classified positive stranded
MeadianReadLen=33 20thPercentileLength=31 echo kmer=27
SRR9060556 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=27

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[index] k-mer length: 27
[index] number of targets: 33,746
[index] number of k-mers: 28,936,155
[index] number of equivalence classes: 55,453
[quant] running in single-end mode
[quant] will process file 1: SRR9060556-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 27,298,982 reads, 12,976,340 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,347 rounds

  33747 SRR9060556.ke.tsv
  46739 SRR9060556.se.tsv
  80486 total
==> SRR9060556.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Y110A7A.10	1787	1688	474	19.549
F27C8.1	1940	1841	81	3.06303
F07C3.7	1728	1629	45	1.92314
F52H2.2a	1739	1640	88	3.73558
F52H2.2b	1840	1741	0	0
T13A10.10a	1734	1635	60.1103	2.55947
T13A10.10b	1598	1499	33.8897	1.57393
C55C2.5a	1840	1741	14.8804	0.595024
C55C2.5b	1606	1507	48.1185	2.2229

==> SRR9060556.se.tsv <==
WBGene00197333	0
WBGene00198386	0
WBGene00015153	1
WBGene00002061	6668
WBGene00255704	1
WBGene00235314	0
WBGene00001177	347
WBGene00169236	0
WBGene00219784	0
WBGene00015152	6
SRR9060556 completed mapping pipeline successfully
