ARTIC pipeline example

This is a brief run through of the ARTIC pipeline. It covers:

  • installing the pipeline
  • what files you need
  • what commands to use
  • what output is produced

Using this notebook

We are using a jupyter notebook for this example so that we can host it on Binder. If you want to run the commands for yourself on the command line, you will need to remove the leading ! which is before all the code in this notebook (which is telling jupyter to execute a system command).

To run this notebook, you can click on each cell and press Run. Be sure to wait for the cell to complete before moving on to the next one. It might take a minute or so for each cell to complete.

Installing the pipeline

If you are using this notebook via Binder, or the GitHub repository, the pipeline is already installed. For reference though, you can install the pipeline from conda:

conda create -n artic-env
conda activate artic-env
conda install -c bioconda -c conda-forge artic

We are using version 1.2.1, check you are on the same:

In [2]:
!artic -v
artic 1.2.1

Data

To begin, we need some data. This repository already has some data for you to use, which was generated from a SARS-COV-2 positive control sample at the University of Birmingham. If you want to obtain the data for yourself, you can run the following:

wget http://artic.s3.climb.ac.uk/BHAM-Run88-PTC.fastq

This test data is only the FASTQ reads from the positive control sample. We have already basecalled, demuxed and filtered them from the original FAST5 data for this sample.

Because we only have FASTQ data, this example will use the medaka workflow of the ARTIC pipeline. This is because the nanopolish version requires FAST5 data as well as FASTQ.

To run the medaka workflow ARTIC pipeline on this data, we need to know:

  • what version of the ARTIC primer scheme was used
    • version 3
  • what medaka model to use
    • use {pore}_{device}_{caller variant}_{caller version}
    • r941_min_high_g351

As well as the FASTQ reads, we will also need:

  • primer scheme (BED format)
  • reference sequence (FASTA format)

Primer scheme and reference sequence

Although the ARTIC pipeline will download these for us, we can also get them for ourselves in order to familiarise ourselves with them:

In [3]:
!artic-tools get_scheme --schemeVersion 3 scov2
[21:41:48] [artic-tools::get_scheme] starting primer scheme downloader
[21:41:48] [artic-tools::get_scheme] 	requested scheme:	scov2
[21:41:48] [artic-tools::get_scheme] 	requested version:	3
[21:41:48] [artic-tools::get_scheme] fetching manifest file
[21:41:48] [artic-tools::get_scheme] 	ARTIC manifest URL:	https://raw.githubusercontent.com/artic-network/primer-schemes/master/schemes_manifest.json
[21:41:50] [artic-tools::get_scheme] 	ARTIC repository DOI:	10.5281/zenodo.4004423
[21:41:50] [artic-tools::get_scheme] finding primer scheme
[21:41:50] [artic-tools::get_scheme] 	found requested scheme:	sars-cov-2 (using alias scov2)
[21:41:50] [artic-tools::get_scheme] downloading primer scheme
[21:41:51] [artic-tools::get_scheme] 	saving primers to:	scov2.v3.primer.bed
[21:41:51] [artic-tools::get_scheme] 	saving reference to:	scov2.v3.reference.fasta
[21:41:51] [artic-tools::get_scheme] comparing checksums
[21:41:51] [artic-tools::get_scheme] 	sha256 for primers:	6e98d7d5d1c6edac8ef0bac70d698e0828ae42bafe8f3bda0a6257d00ce414b5
[21:41:51] [artic-tools::get_scheme] 	sha256 for reference:	b09a4a3d6824dc4a9f3a17d480f3335f73cb1507897f6dad0de871e8f00d8637

This will have downloaded the primer scheme (scov2.v3.primer.bed) and the reference sequence (scov2.v3.reference.fasta). You can get some information on the primer scheme using artic-tools:

In [4]:
!artic-tools validate_scheme scov2.v3.primer.bed
[21:41:56] [artic-tools::validate_scheme] starting primer scheme validator
[21:41:56] [artic-tools::validate_scheme] reading scheme
[21:41:56] [artic-tools::validate_scheme] collecting scheme stats
[21:41:56] [artic-tools::validate_scheme] 	primer scheme file:	scov2.v3.primer.bed
[21:41:56] [artic-tools::validate_scheme] 	reference sequence:	MN908947.3
[21:41:56] [artic-tools::validate_scheme] 	number of pools:	2
[21:41:56] [artic-tools::validate_scheme] 	number of primers:	218 (includes 22 alts)
[21:41:56] [artic-tools::validate_scheme] 	minimum primer size:	22
[21:41:56] [artic-tools::validate_scheme] 	maximum primer size:	57
[21:41:56] [artic-tools::validate_scheme] 	number of amplicons:	98
[21:41:56] [artic-tools::validate_scheme] 	mean amplicon size:	343
[21:41:56] [artic-tools::validate_scheme] 	maximum amplicon size:	375
[21:41:56] [artic-tools::validate_scheme] 	scheme ref. span:	30-29866
[21:41:56] [artic-tools::validate_scheme] 	scheme overlaps:	12.850247%

The primer scheme file is in a BED format, where the columns equate to the following:

column name type description
1 chrom string primer reference sequence
2 chromStart int starting position of the primer in the reference sequence
3 chomEnd int ending position of the primer in the reference sequence
4 name string primer name
5 primerPool int primer pool*
6 strand string (+/-) primer direction

* column 5 in the BED spec is an int for score, whereas here we are using it to denote primerPool.

If you want to look at the primer scheme file, we can do that here with some Python:

In [5]:
with open("scov2.v3.primer.bed", 'r') as f:
    print(f.read())
MN908947.3	30	54	nCoV-2019_1_LEFT	1	+
MN908947.3	385	410	nCoV-2019_1_RIGHT	1	-
MN908947.3	320	342	nCoV-2019_2_LEFT	2	+
MN908947.3	704	726	nCoV-2019_2_RIGHT	2	-
MN908947.3	642	664	nCoV-2019_3_LEFT	1	+
MN908947.3	1004	1028	nCoV-2019_3_RIGHT	1	-
MN908947.3	943	965	nCoV-2019_4_LEFT	2	+
MN908947.3	1312	1337	nCoV-2019_4_RIGHT	2	-
MN908947.3	1242	1264	nCoV-2019_5_LEFT	1	+
MN908947.3	1623	1651	nCoV-2019_5_RIGHT	1	-
MN908947.3	1573	1595	nCoV-2019_6_LEFT	2	+
MN908947.3	1942	1964	nCoV-2019_6_RIGHT	2	-
MN908947.3	1875	1897	nCoV-2019_7_LEFT	1	+
MN908947.3	1868	1890	nCoV-2019_7_LEFT_alt0	1	+
MN908947.3	2247	2269	nCoV-2019_7_RIGHT	1	-
MN908947.3	2242	2264	nCoV-2019_7_RIGHT_alt5	1	-
MN908947.3	2181	2205	nCoV-2019_8_LEFT	2	+
MN908947.3	2568	2592	nCoV-2019_8_RIGHT	2	-
MN908947.3	2505	2529	nCoV-2019_9_LEFT	1	+
MN908947.3	2504	2528	nCoV-2019_9_LEFT_alt4	1	+
MN908947.3	2882	2904	nCoV-2019_9_RIGHT	1	-
MN908947.3	2880	2902	nCoV-2019_9_RIGHT_alt2	1	-
MN908947.3	2826	2850	nCoV-2019_10_LEFT	2	+
MN908947.3	3183	3210	nCoV-2019_10_RIGHT	2	-
MN908947.3	3144	3166	nCoV-2019_11_LEFT	1	+
MN908947.3	3507	3531	nCoV-2019_11_RIGHT	1	-
MN908947.3	3460	3482	nCoV-2019_12_LEFT	2	+
MN908947.3	3826	3853	nCoV-2019_12_RIGHT	2	-
MN908947.3	3771	3795	nCoV-2019_13_LEFT	1	+
MN908947.3	4142	4164	nCoV-2019_13_RIGHT	1	-
MN908947.3	4054	4077	nCoV-2019_14_LEFT	2	+
MN908947.3	4044	4068	nCoV-2019_14_LEFT_alt4	2	+
MN908947.3	4428	4450	nCoV-2019_14_RIGHT	2	-
MN908947.3	4402	4424	nCoV-2019_14_RIGHT_alt2	2	-
MN908947.3	4294	4321	nCoV-2019_15_LEFT	1	+
MN908947.3	4296	4322	nCoV-2019_15_LEFT_alt1	1	+
MN908947.3	4674	4696	nCoV-2019_15_RIGHT	1	-
MN908947.3	4666	4689	nCoV-2019_15_RIGHT_alt3	1	-
MN908947.3	4636	4658	nCoV-2019_16_LEFT	2	+
MN908947.3	4995	5017	nCoV-2019_16_RIGHT	2	-
MN908947.3	4939	4966	nCoV-2019_17_LEFT	1	+
MN908947.3	5296	5321	nCoV-2019_17_RIGHT	1	-
MN908947.3	5230	5259	nCoV-2019_18_LEFT	2	+
MN908947.3	5257	5287	nCoV-2019_18_LEFT_alt2	2	+
MN908947.3	5620	5644	nCoV-2019_18_RIGHT	2	-
MN908947.3	5620	5643	nCoV-2019_18_RIGHT_alt1	2	-
MN908947.3	5563	5586	nCoV-2019_19_LEFT	1	+
MN908947.3	5932	5957	nCoV-2019_19_RIGHT	1	-
MN908947.3	5867	5894	nCoV-2019_20_LEFT	2	+
MN908947.3	6247	6272	nCoV-2019_20_RIGHT	2	-
MN908947.3	6167	6196	nCoV-2019_21_LEFT	1	+
MN908947.3	6168	6197	nCoV-2019_21_LEFT_alt2	1	+
MN908947.3	6528	6550	nCoV-2019_21_RIGHT	1	-
MN908947.3	6526	6548	nCoV-2019_21_RIGHT_alt0	1	-
MN908947.3	6466	6495	nCoV-2019_22_LEFT	2	+
MN908947.3	6846	6873	nCoV-2019_22_RIGHT	2	-
MN908947.3	6718	6745	nCoV-2019_23_LEFT	1	+
MN908947.3	7092	7117	nCoV-2019_23_RIGHT	1	-
MN908947.3	7035	7058	nCoV-2019_24_LEFT	2	+
MN908947.3	7389	7415	nCoV-2019_24_RIGHT	2	-
MN908947.3	7305	7332	nCoV-2019_25_LEFT	1	+
MN908947.3	7671	7694	nCoV-2019_25_RIGHT	1	-
MN908947.3	7626	7651	nCoV-2019_26_LEFT	2	+
MN908947.3	7997	8019	nCoV-2019_26_RIGHT	2	-
MN908947.3	7943	7968	nCoV-2019_27_LEFT	1	+
MN908947.3	8319	8341	nCoV-2019_27_RIGHT	1	-
MN908947.3	8249	8275	nCoV-2019_28_LEFT	2	+
MN908947.3	8635	8661	nCoV-2019_28_RIGHT	2	-
MN908947.3	8595	8619	nCoV-2019_29_LEFT	1	+
MN908947.3	8954	8983	nCoV-2019_29_RIGHT	1	-
MN908947.3	8888	8913	nCoV-2019_30_LEFT	2	+
MN908947.3	9245	9271	nCoV-2019_30_RIGHT	2	-
MN908947.3	9204	9226	nCoV-2019_31_LEFT	1	+
MN908947.3	9557	9585	nCoV-2019_31_RIGHT	1	-
MN908947.3	9477	9502	nCoV-2019_32_LEFT	2	+
MN908947.3	9834	9858	nCoV-2019_32_RIGHT	2	-
MN908947.3	9784	9806	nCoV-2019_33_LEFT	1	+
MN908947.3	10146	10171	nCoV-2019_33_RIGHT	1	-
MN908947.3	10076	10099	nCoV-2019_34_LEFT	2	+
MN908947.3	10437	10459	nCoV-2019_34_RIGHT	2	-
MN908947.3	10362	10384	nCoV-2019_35_LEFT	1	+
MN908947.3	10737	10763	nCoV-2019_35_RIGHT	1	-
MN908947.3	10666	10688	nCoV-2019_36_LEFT	2	+
MN908947.3	11048	11074	nCoV-2019_36_RIGHT	2	-
MN908947.3	10999	11022	nCoV-2019_37_LEFT	1	+
MN908947.3	11372	11394	nCoV-2019_37_RIGHT	1	-
MN908947.3	11306	11331	nCoV-2019_38_LEFT	2	+
MN908947.3	11668	11693	nCoV-2019_38_RIGHT	2	-
MN908947.3	11555	11584	nCoV-2019_39_LEFT	1	+
MN908947.3	11927	11949	nCoV-2019_39_RIGHT	1	-
MN908947.3	11863	11889	nCoV-2019_40_LEFT	2	+
MN908947.3	12234	12256	nCoV-2019_40_RIGHT	2	-
MN908947.3	12110	12133	nCoV-2019_41_LEFT	1	+
MN908947.3	12465	12490	nCoV-2019_41_RIGHT	1	-
MN908947.3	12417	12439	nCoV-2019_42_LEFT	2	+
MN908947.3	12779	12802	nCoV-2019_42_RIGHT	2	-
MN908947.3	12710	12732	nCoV-2019_43_LEFT	1	+
MN908947.3	13074	13096	nCoV-2019_43_RIGHT	1	-
MN908947.3	13005	13027	nCoV-2019_44_LEFT	2	+
MN908947.3	13007	13029	nCoV-2019_44_LEFT_alt3	2	+
MN908947.3	13378	13400	nCoV-2019_44_RIGHT	2	-
MN908947.3	13363	13385	nCoV-2019_44_RIGHT_alt0	2	-
MN908947.3	13319	13344	nCoV-2019_45_LEFT	1	+
MN908947.3	13307	13336	nCoV-2019_45_LEFT_alt2	1	+
MN908947.3	13669	13699	nCoV-2019_45_RIGHT	1	-
MN908947.3	13660	13689	nCoV-2019_45_RIGHT_alt7	1	-
MN908947.3	13599	13621	nCoV-2019_46_LEFT	2	+
MN908947.3	13602	13625	nCoV-2019_46_LEFT_alt1	2	+
MN908947.3	13962	13984	nCoV-2019_46_RIGHT	2	-
MN908947.3	13961	13984	nCoV-2019_46_RIGHT_alt2	2	-
MN908947.3	13918	13946	nCoV-2019_47_LEFT	1	+
MN908947.3	14271	14299	nCoV-2019_47_RIGHT	1	-
MN908947.3	14207	14232	nCoV-2019_48_LEFT	2	+
MN908947.3	14579	14601	nCoV-2019_48_RIGHT	2	-
MN908947.3	14545	14570	nCoV-2019_49_LEFT	1	+
MN908947.3	14898	14926	nCoV-2019_49_RIGHT	1	-
MN908947.3	14865	14895	nCoV-2019_50_LEFT	2	+
MN908947.3	15224	15246	nCoV-2019_50_RIGHT	2	-
MN908947.3	15171	15193	nCoV-2019_51_LEFT	1	+
MN908947.3	15538	15560	nCoV-2019_51_RIGHT	1	-
MN908947.3	15481	15503	nCoV-2019_52_LEFT	2	+
MN908947.3	15861	15886	nCoV-2019_52_RIGHT	2	-
MN908947.3	15827	15851	nCoV-2019_53_LEFT	1	+
MN908947.3	16186	16209	nCoV-2019_53_RIGHT	1	-
MN908947.3	16118	16144	nCoV-2019_54_LEFT	2	+
MN908947.3	16485	16510	nCoV-2019_54_RIGHT	2	-
MN908947.3	16416	16444	nCoV-2019_55_LEFT	1	+
MN908947.3	16804	16833	nCoV-2019_55_RIGHT	1	-
MN908947.3	16748	16770	nCoV-2019_56_LEFT	2	+
MN908947.3	17130	17152	nCoV-2019_56_RIGHT	2	-
MN908947.3	17065	17087	nCoV-2019_57_LEFT	1	+
MN908947.3	17430	17452	nCoV-2019_57_RIGHT	1	-
MN908947.3	17381	17406	nCoV-2019_58_LEFT	2	+
MN908947.3	17738	17761	nCoV-2019_58_RIGHT	2	-
MN908947.3	17674	17697	nCoV-2019_59_LEFT	1	+
MN908947.3	18036	18062	nCoV-2019_59_RIGHT	1	-
MN908947.3	17966	17993	nCoV-2019_60_LEFT	2	+
MN908947.3	18324	18348	nCoV-2019_60_RIGHT	2	-
MN908947.3	18253	18275	nCoV-2019_61_LEFT	1	+
MN908947.3	18650	18672	nCoV-2019_61_RIGHT	1	-
MN908947.3	18596	18618	nCoV-2019_62_LEFT	2	+
MN908947.3	18957	18979	nCoV-2019_62_RIGHT	2	-
MN908947.3	18896	18918	nCoV-2019_63_LEFT	1	+
MN908947.3	19275	19297	nCoV-2019_63_RIGHT	1	-
MN908947.3	19204	19232	nCoV-2019_64_LEFT	2	+
MN908947.3	19591	19616	nCoV-2019_64_RIGHT	2	-
MN908947.3	19548	19570	nCoV-2019_65_LEFT	1	+
MN908947.3	19911	19939	nCoV-2019_65_RIGHT	1	-
MN908947.3	19844	19866	nCoV-2019_66_LEFT	2	+
MN908947.3	20231	20255	nCoV-2019_66_RIGHT	2	-
MN908947.3	20172	20200	nCoV-2019_67_LEFT	1	+
MN908947.3	20542	20572	nCoV-2019_67_RIGHT	1	-
MN908947.3	20472	20496	nCoV-2019_68_LEFT	2	+
MN908947.3	20867	20890	nCoV-2019_68_RIGHT	2	-
MN908947.3	20786	20813	nCoV-2019_69_LEFT	1	+
MN908947.3	21146	21169	nCoV-2019_69_RIGHT	1	-
MN908947.3	21075	21104	nCoV-2019_70_LEFT	2	+
MN908947.3	21427	21455	nCoV-2019_70_RIGHT	2	-
MN908947.3	21357	21386	nCoV-2019_71_LEFT	1	+
MN908947.3	21716	21743	nCoV-2019_71_RIGHT	1	-
MN908947.3	21658	21682	nCoV-2019_72_LEFT	2	+
MN908947.3	22013	22038	nCoV-2019_72_RIGHT	2	-
MN908947.3	21961	21990	nCoV-2019_73_LEFT	1	+
MN908947.3	22324	22346	nCoV-2019_73_RIGHT	1	-
MN908947.3	22262	22290	nCoV-2019_74_LEFT	2	+
MN908947.3	22626	22650	nCoV-2019_74_RIGHT	2	-
MN908947.3	22516	22542	nCoV-2019_75_LEFT	1	+
MN908947.3	22877	22903	nCoV-2019_75_RIGHT	1	-
MN908947.3	22797	22819	nCoV-2019_76_LEFT	2	+
MN908947.3	22798	22821	nCoV-2019_76_LEFT_alt3	2	+
MN908947.3	23192	23214	nCoV-2019_76_RIGHT	2	-
MN908947.3	23189	23212	nCoV-2019_76_RIGHT_alt0	2	-
MN908947.3	23122	23144	nCoV-2019_77_LEFT	1	+
MN908947.3	23500	23522	nCoV-2019_77_RIGHT	1	-
MN908947.3	23443	23466	nCoV-2019_78_LEFT	2	+
MN908947.3	23822	23847	nCoV-2019_78_RIGHT	2	-
MN908947.3	23789	23812	nCoV-2019_79_LEFT	1	+
MN908947.3	24145	24169	nCoV-2019_79_RIGHT	1	-
MN908947.3	24078	24100	nCoV-2019_80_LEFT	2	+
MN908947.3	24443	24467	nCoV-2019_80_RIGHT	2	-
MN908947.3	24391	24416	nCoV-2019_81_LEFT	1	+
MN908947.3	24765	24789	nCoV-2019_81_RIGHT	1	-
MN908947.3	24696	24721	nCoV-2019_82_LEFT	2	+
MN908947.3	25052	25076	nCoV-2019_82_RIGHT	2	-
MN908947.3	24978	25003	nCoV-2019_83_LEFT	1	+
MN908947.3	25347	25369	nCoV-2019_83_RIGHT	1	-
MN908947.3	25279	25301	nCoV-2019_84_LEFT	2	+
MN908947.3	25646	25673	nCoV-2019_84_RIGHT	2	-
MN908947.3	25601	25623	nCoV-2019_85_LEFT	1	+
MN908947.3	25969	25994	nCoV-2019_85_RIGHT	1	-
MN908947.3	25902	25924	nCoV-2019_86_LEFT	2	+
MN908947.3	26290	26315	nCoV-2019_86_RIGHT	2	-
MN908947.3	26197	26219	nCoV-2019_87_LEFT	1	+
MN908947.3	26566	26590	nCoV-2019_87_RIGHT	1	-
MN908947.3	26520	26542	nCoV-2019_88_LEFT	2	+
MN908947.3	26890	26913	nCoV-2019_88_RIGHT	2	-
MN908947.3	26835	26857	nCoV-2019_89_LEFT	1	+
MN908947.3	26838	26860	nCoV-2019_89_LEFT_alt2	1	+
MN908947.3	27202	27227	nCoV-2019_89_RIGHT	1	-
MN908947.3	27190	27215	nCoV-2019_89_RIGHT_alt4	1	-
MN908947.3	27141	27164	nCoV-2019_90_LEFT	2	+
MN908947.3	27511	27533	nCoV-2019_90_RIGHT	2	-
MN908947.3	27446	27471	nCoV-2019_91_LEFT	1	+
MN908947.3	27825	27854	nCoV-2019_91_RIGHT	1	-
MN908947.3	27784	27808	nCoV-2019_92_LEFT	2	+
MN908947.3	28145	28172	nCoV-2019_92_RIGHT	2	-
MN908947.3	28081	28104	nCoV-2019_93_LEFT	1	+
MN908947.3	28442	28464	nCoV-2019_93_RIGHT	1	-
MN908947.3	28394	28416	nCoV-2019_94_LEFT	2	+
MN908947.3	28756	28779	nCoV-2019_94_RIGHT	2	-
MN908947.3	28677	28699	nCoV-2019_95_LEFT	1	+
MN908947.3	29041	29063	nCoV-2019_95_RIGHT	1	-
MN908947.3	28985	29007	nCoV-2019_96_LEFT	2	+
MN908947.3	29356	29378	nCoV-2019_96_RIGHT	2	-
MN908947.3	29288	29316	nCoV-2019_97_LEFT	1	+
MN908947.3	29665	29693	nCoV-2019_97_RIGHT	1	-
MN908947.3	29486	29510	nCoV-2019_98_LEFT	2	+
MN908947.3	29836	29866	nCoV-2019_98_RIGHT	2	-

Running the pipeline

Now we have the primer scheme, reference sequence and our FASTQ data. We can run the pipeline!

In [6]:
!artic minion \
    --normalise 100 \
    --threads 2 \
    --medaka \
    --medaka-model r941_min_high_g351 \
    --strict \
    --read-file ../data/BHAM-Run88-PTC.fastq.gz \
    scov2/V3 \
    my_example
could not find primer scheme and reference sequence, attempting to download
Running:  artic-tools get_scheme scov2 --schemeVersion 3
[21:42:18] [artic-tools::get_scheme] starting primer scheme downloader
[21:42:18] [artic-tools::get_scheme] 	requested scheme:	scov2
[21:42:18] [artic-tools::get_scheme] 	requested version:	3
[21:42:18] [artic-tools::get_scheme] fetching manifest file
[21:42:18] [artic-tools::get_scheme] 	ARTIC manifest URL:	https://raw.githubusercontent.com/artic-network/primer-schemes/master/schemes_manifest.json
[21:42:19] [artic-tools::get_scheme] 	ARTIC repository DOI:	10.5281/zenodo.4004423
[21:42:19] [artic-tools::get_scheme] finding primer scheme
[21:42:19] [artic-tools::get_scheme] 	found requested scheme:	sars-cov-2 (using alias scov2)
[21:42:19] [artic-tools::get_scheme] downloading primer scheme
[21:42:19] [artic-tools::get_scheme] 	saving primers to:	scov2.v3.primer.bed
[21:42:19] [artic-tools::get_scheme] 	saving reference to:	scov2.v3.reference.fasta
[21:42:19] [artic-tools::get_scheme] comparing checksums
[21:42:19] [artic-tools::get_scheme] 	sha256 for primers:	6e98d7d5d1c6edac8ef0bac70d698e0828ae42bafe8f3bda0a6257d00ce414b5
[21:42:19] [artic-tools::get_scheme] 	sha256 for reference:	b09a4a3d6824dc4a9f3a17d480f3335f73cb1507897f6dad0de871e8f00d8637
Running:  artic-tools validate_scheme ./primer-schemes/scov2/V3/scov2.scheme.bed
[21:42:19] [artic-tools::validate_scheme] starting primer scheme validator
[21:42:19] [artic-tools::validate_scheme] reading scheme
[21:42:19] [artic-tools::validate_scheme] collecting scheme stats
[21:42:19] [artic-tools::validate_scheme] 	primer scheme file:	./primer-schemes/scov2/V3/scov2.scheme.bed
[21:42:19] [artic-tools::validate_scheme] 	reference sequence:	MN908947.3
[21:42:19] [artic-tools::validate_scheme] 	number of pools:	2
[21:42:19] [artic-tools::validate_scheme] 	number of primers:	218 (includes 22 alts)
[21:42:19] [artic-tools::validate_scheme] 	minimum primer size:	22
[21:42:19] [artic-tools::validate_scheme] 	maximum primer size:	57
[21:42:19] [artic-tools::validate_scheme] 	number of amplicons:	98
[21:42:19] [artic-tools::validate_scheme] 	mean amplicon size:	343
[21:42:19] [artic-tools::validate_scheme] 	maximum amplicon size:	375
[21:42:19] [artic-tools::validate_scheme] 	scheme ref. span:	30-29866
[21:42:19] [artic-tools::validate_scheme] 	scheme overlaps:	12.850247%
Running: minimap2 -a -x map-ont -t 2 ./primer-schemes/scov2/V3/scov2.reference.fasta ../data/BHAM-Run88-PTC.fastq.gz | samtools view -bS -F 4 - | samtools sort -o my_example.sorted.bam -
[M::mm_idx_gen::0.002*2.10] collected minimizers
[M::mm_idx_gen::0.003*2.02] sorted minimizers
[M::main::0.004*2.01] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.004*1.94] mid_occ = 3
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.004*1.88] distinct minimizers: 5587 (99.93% are singletons); average occurrences: 1.004; average spacing: 5.332
[M::worker_pipeline::11.622*1.58] mapped 124656 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -a -x map-ont -t 2 ./primer-schemes/scov2/V3/scov2.reference.fasta ../data/BHAM-Run88-PTC.fastq.gz
[M::main] Real time: 11.624 sec; CPU: 18.317 sec; Peak RSS: 0.165 GB
Running: samtools index my_example.sorted.bam
Running: align_trim --normalise 100 ./primer-schemes/scov2/V3/scov2.scheme.bed --start --remove-incorrect-pairs --report my_example.alignreport.txt < my_example.sorted.bam 2> my_example.alignreport.er | samtools sort -T my_example - -o my_example.trimmed.rg.sorted.bam
Running: align_trim --normalise 100 ./primer-schemes/scov2/V3/scov2.scheme.bed --remove-incorrect-pairs --report my_example.alignreport.txt < my_example.sorted.bam 2> my_example.alignreport.er | samtools sort -T my_example - -o my_example.primertrimmed.rg.sorted.bam
Running: samtools index my_example.trimmed.rg.sorted.bam
Running: samtools index my_example.primertrimmed.rg.sorted.bam
Running: medaka consensus --model r941_min_high_g351 --threads 2 --chunk_len 800 --chunk_ovlp 400 --RG 1 my_example.trimmed.rg.sorted.bam my_example.1.hdf
[21:43:15 - medaka] Reads will be filtered to only those with RG tag: 1
[21:43:15 - Predict] Processing region(s): MN908947.3:0-29903
[21:43:15 - Predict] Setting tensorflow threads to 2.
[21:43:15 - Predict] Processing 1 long region(s) with batching.
[21:43:15 - Predict] Using model: /Users/willrowe/opt/miniconda3/envs/artic-pipeline-example/lib/python3.6/site-packages/medaka/data/r941_min_high_g351_model.hdf5.
[21:43:15 - ModelLoad] Building model with cudnn optimization: False
[21:43:16 - DLoader] Initializing data loader
[21:43:16 - Sampler] Initializing sampler for consensus of region MN908947.3:0-29903.
[21:43:16 - PWorker] Running inference for 0.0M draft bases.
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 30-409.
[21:43:16 - Feature] Processed MN908947.3:30.0-409.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 642-1027.
[21:43:16 - Feature] Processed MN908947.3:642.0-1027.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 1242-1650.
[21:43:16 - Feature] Processed MN908947.3:1242.0-1650.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 1868-2268.
[21:43:16 - Feature] Processed MN908947.3:1868.0-2268.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 2504-2903.
[21:43:16 - Feature] Processed MN908947.3:2504.0-2903.0 (median depth 177.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 3144-3530.
[21:43:16 - Feature] Processed MN908947.3:3144.0-3530.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 3771-4163.
[21:43:16 - Feature] Processed MN908947.3:3771.0-4163.0 (median depth 192.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 4294-4689.
[21:43:16 - Feature] Processed MN908947.3:4294.0-4689.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 4939-5320.
[21:43:16 - Feature] Processed MN908947.3:4939.0-5320.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 5563-5956.
[21:43:16 - Feature] Processed MN908947.3:5563.0-5956.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 6167-6549.
[21:43:16 - Feature] Processed MN908947.3:6167.0-6549.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 6718-7116.
[21:43:16 - Feature] Processed MN908947.3:6718.0-7116.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 7305-7693.
[21:43:16 - Feature] Processed MN908947.3:7305.0-7693.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 7943-8340.
[21:43:16 - Feature] Processed MN908947.3:7943.0-8340.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 8595-8982.
[21:43:16 - Feature] Processed MN908947.3:8595.0-8982.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 9204-9584.
[21:43:16 - Feature] Processed MN908947.3:9204.0-9584.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 9784-10170.
[21:43:16 - Feature] Processed MN908947.3:9784.0-10170.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 10362-10762.
[21:43:16 - Feature] Processed MN908947.3:10362.0-10762.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 10999-11393.
[21:43:16 - Feature] Processed MN908947.3:10999.0-11393.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 11555-11948.
[21:43:16 - Feature] Processed MN908947.3:11555.0-11948.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 12110-12489.
[21:43:16 - Feature] Processed MN908947.3:12110.0-12489.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 12710-13095.
[21:43:16 - Feature] Processed MN908947.3:12710.0-13095.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 13307-13698.
[21:43:16 - Feature] Processed MN908947.3:13307.0-13698.0 (median depth 197.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 13918-14298.
[21:43:16 - Feature] Processed MN908947.3:13918.0-14298.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 14545-14925.
[21:43:16 - Feature] Processed MN908947.3:14545.0-14925.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 15171-15559.
[21:43:16 - Feature] Processed MN908947.3:15171.0-15559.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 15827-16208.
[21:43:16 - Feature] Processed MN908947.3:15827.0-16208.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 16416-16832.
[21:43:16 - Feature] Processed MN908947.3:16416.0-16832.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 17065-17451.
[21:43:16 - Feature] Processed MN908947.3:17065.0-17451.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 17674-18061.
[21:43:16 - Feature] Processed MN908947.3:17674.0-18061.0 (median depth 162.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 18253-18671.
[21:43:16 - Feature] Processed MN908947.3:18253.0-18671.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 18896-19296.
[21:43:16 - Feature] Processed MN908947.3:18896.0-19296.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 19548-19938.
[21:43:16 - Feature] Processed MN908947.3:19548.0-19938.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 20172-20571.
[21:43:16 - Feature] Processed MN908947.3:20172.0-20571.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 20786-21168.
[21:43:16 - Feature] Processed MN908947.3:20786.0-21168.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 21357-21742.
[21:43:16 - Feature] Processed MN908947.3:21357.0-21742.0 (median depth 119.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 21961-22345.
[21:43:16 - Feature] Processed MN908947.3:21961.0-22345.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 22516-22902.
[21:43:16 - Feature] Processed MN908947.3:22516.0-22902.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 23122-23521.
[21:43:16 - Feature] Processed MN908947.3:23122.0-23521.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 23789-24168.
[21:43:16 - Feature] Processed MN908947.3:23789.0-24168.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 24391-24788.
[21:43:16 - Feature] Processed MN908947.3:24391.0-24788.2 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 24978-25368.
[21:43:16 - Feature] Processed MN908947.3:24978.0-25368.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 25601-25993.
[21:43:16 - Feature] Processed MN908947.3:25601.0-25993.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 26197-26589.
[21:43:16 - Feature] Processed MN908947.3:26197.0-26589.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 26835-27226.
[21:43:16 - Feature] Processed MN908947.3:26835.0-27226.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 27446-27853.
[21:43:16 - Feature] Processed MN908947.3:27446.0-27853.0 (median depth 91.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 28081-28463.
[21:43:16 - Feature] Processed MN908947.3:28081.0-28463.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 28677-29062.
[21:43:16 - Feature] Processed MN908947.3:28677.0-29062.0 (median depth 200.0)
[21:43:16 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 29288-29692.
[21:43:16 - Feature] Processed MN908947.3:29288.0-29692.0 (median depth 200.0)
[21:43:16 - Sampler] Took 0.15s to make features.
[21:43:16 - Sampler] Region MN908947.3:2504.0-2903.0 (794 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:3771.0-4163.0 (771 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:4939.0-5320.0 (770 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:6167.0-6549.0 (771 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:8595.0-8982.0 (778 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:10999.0-11393.0 (757 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:12110.0-12489.0 (748 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:12710.0-13095.0 (793 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:13918.0-14298.0 (777 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:17674.0-18061.0 (750 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:20786.0-21168.0 (797 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:21357.0-21742.0 (714 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:22516.0-22902.0 (787 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:23789.0-24168.0 (773 positions) is smaller than inference chunk length 800, quarantining.
[21:43:16 - Sampler] Region MN908947.3:27446.0-27853.0 (656 positions) is smaller than inference chunk length 800, quarantining.
[21:43:17 - PWorker] All done, 15 remainder regions.
[21:43:17 - Predict] Processing 15 short region(s).
[21:43:17 - ModelLoad] Building model with cudnn optimization: False
[21:43:18 - DLoader] Initializing data loader
[21:43:18 - PWorker] Running inference for 0.0M draft bases.
[21:43:18 - Sampler] Initializing sampler for consensus of region MN908947.3:2504-2904.
[21:43:18 - Feature] Processed MN908947.3:2504.0-2903.0 (median depth 177.0)
[21:43:18 - Sampler] Took 0.01s to make features.
[21:43:19 - PWorker] All done, 0 remainder regions.
[21:43:19 - DLoader] Initializing data loader
[21:43:19 - Sampler] Initializing sampler for consensus of region MN908947.3:3771-4164.
[21:43:19 - PWorker] Running inference for 0.0M draft bases.
[21:43:19 - Feature] Processed MN908947.3:3771.0-4163.0 (median depth 192.0)
[21:43:19 - Sampler] Took 0.02s to make features.
[21:43:20 - PWorker] All done, 0 remainder regions.
[21:43:20 - DLoader] Initializing data loader
[21:43:20 - Sampler] Initializing sampler for consensus of region MN908947.3:4939-5321.
[21:43:20 - PWorker] Running inference for 0.0M draft bases.
[21:43:20 - Feature] Processed MN908947.3:4939.0-5320.0 (median depth 200.0)
[21:43:20 - Sampler] Took 0.02s to make features.
[21:43:20 - PWorker] All done, 0 remainder regions.
[21:43:20 - DLoader] Initializing data loader
[21:43:20 - Sampler] Initializing sampler for consensus of region MN908947.3:6167-6550.
[21:43:20 - PWorker] Running inference for 0.0M draft bases.
[21:43:21 - Feature] Processed MN908947.3:6167.0-6549.0 (median depth 200.0)
[21:43:21 - Sampler] Took 0.01s to make features.
[21:43:21 - PWorker] All done, 0 remainder regions.
[21:43:21 - DLoader] Initializing data loader
[21:43:21 - Sampler] Initializing sampler for consensus of region MN908947.3:8595-8983.
[21:43:21 - PWorker] Running inference for 0.0M draft bases.
[21:43:21 - Feature] Processed MN908947.3:8595.0-8982.0 (median depth 200.0)
[21:43:21 - Sampler] Took 0.02s to make features.
[21:43:21 - PWorker] All done, 0 remainder regions.
[21:43:21 - DLoader] Initializing data loader
[21:43:21 - Sampler] Initializing sampler for consensus of region MN908947.3:10999-11394.
[21:43:21 - PWorker] Running inference for 0.0M draft bases.
[21:43:21 - Feature] Processed MN908947.3:10999.0-11393.0 (median depth 200.0)
[21:43:21 - Sampler] Took 0.02s to make features.
[21:43:21 - PWorker] All done, 0 remainder regions.
[21:43:21 - DLoader] Initializing data loader
[21:43:21 - PWorker] Running inference for 0.0M draft bases.
[21:43:21 - Sampler] Initializing sampler for consensus of region MN908947.3:12110-12490.
[21:43:21 - Feature] Processed MN908947.3:12110.0-12489.0 (median depth 200.0)
[21:43:21 - Sampler] Took 0.02s to make features.
[21:43:22 - PWorker] All done, 0 remainder regions.
[21:43:22 - DLoader] Initializing data loader
[21:43:22 - PWorker] Running inference for 0.0M draft bases.
[21:43:22 - Sampler] Initializing sampler for consensus of region MN908947.3:12710-13096.
[21:43:22 - Feature] Processed MN908947.3:12710.0-13095.0 (median depth 200.0)
[21:43:22 - Sampler] Took 0.02s to make features.
[21:43:22 - PWorker] All done, 0 remainder regions.
[21:43:22 - DLoader] Initializing data loader
[21:43:22 - PWorker] Running inference for 0.0M draft bases.
[21:43:22 - Sampler] Initializing sampler for consensus of region MN908947.3:13918-14299.
[21:43:22 - Feature] Processed MN908947.3:13918.0-14298.0 (median depth 200.0)
[21:43:22 - Sampler] Took 0.03s to make features.
[21:43:23 - PWorker] All done, 0 remainder regions.
[21:43:23 - DLoader] Initializing data loader
[21:43:23 - Sampler] Initializing sampler for consensus of region MN908947.3:17674-18062.
[21:43:23 - PWorker] Running inference for 0.0M draft bases.
[21:43:23 - Feature] Processed MN908947.3:17674.0-18061.0 (median depth 162.0)
[21:43:23 - Sampler] Took 0.01s to make features.
[21:43:23 - PWorker] All done, 0 remainder regions.
[21:43:23 - DLoader] Initializing data loader
[21:43:23 - Sampler] Initializing sampler for consensus of region MN908947.3:20786-21169.
[21:43:23 - PWorker] Running inference for 0.0M draft bases.
[21:43:23 - Feature] Processed MN908947.3:20786.0-21168.0 (median depth 200.0)
[21:43:23 - Sampler] Took 0.03s to make features.
[21:43:24 - PWorker] All done, 0 remainder regions.
[21:43:24 - DLoader] Initializing data loader
[21:43:24 - PWorker] Running inference for 0.0M draft bases.
[21:43:24 - Sampler] Initializing sampler for consensus of region MN908947.3:21357-21743.
[21:43:24 - Feature] Processed MN908947.3:21357.0-21742.0 (median depth 119.0)
[21:43:24 - Sampler] Took 0.03s to make features.
[21:43:25 - PWorker] All done, 0 remainder regions.
[21:43:25 - DLoader] Initializing data loader
[21:43:25 - Sampler] Initializing sampler for consensus of region MN908947.3:22516-22903.
[21:43:25 - PWorker] Running inference for 0.0M draft bases.
[21:43:25 - Feature] Processed MN908947.3:22516.0-22902.0 (median depth 200.0)
[21:43:25 - Sampler] Took 0.03s to make features.
[21:43:25 - PWorker] All done, 0 remainder regions.
[21:43:25 - DLoader] Initializing data loader
[21:43:25 - PWorker] Running inference for 0.0M draft bases.
[21:43:25 - Sampler] Initializing sampler for consensus of region MN908947.3:23789-24169.
[21:43:26 - Feature] Processed MN908947.3:23789.0-24168.0 (median depth 200.0)
[21:43:26 - Sampler] Took 0.03s to make features.
[21:43:26 - PWorker] All done, 0 remainder regions.
[21:43:26 - DLoader] Initializing data loader
[21:43:26 - Sampler] Initializing sampler for consensus of region MN908947.3:27446-27854.
[21:43:26 - PWorker] Running inference for 0.0M draft bases.
[21:43:26 - Feature] Processed MN908947.3:27446.0-27853.0 (median depth 91.0)
[21:43:26 - Sampler] Took 0.04s to make features.
[21:43:27 - PWorker] All done, 0 remainder regions.
[21:43:27 - Predict] Finished processing all regions.
Running: medaka variant ./primer-schemes/scov2/V3/scov2.reference.fasta my_example.1.hdf my_example.1.vcf
[21:43:32 - DataIndex] Loaded 1/1 (100.00%) sample files.
[21:43:32 - Variants] Processing MN908947.3:0-.
[21:43:32 - TrimOverlap] MN908947.3:56.1-409.0 and MN908947.3:642.0-984.3 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:683.2-1027.0 and MN908947.3:1242.0-1613.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:1274.0-1650.0 and MN908947.3:1868.0-2236.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:1894.0-2268.0 and MN908947.3:2504.0-2903.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:2504.0-2903.0 and MN908947.3:3144.0-3514.3 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:3155.0-3530.0 and MN908947.3:3771.0-4163.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:3771.0-4163.0 and MN908947.3:4294.0-4678.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:4303.5-4689.0 and MN908947.3:4939.0-5320.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:4939.0-5320.0 and MN908947.3:5563.0-5920.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:5599.1-5956.0 and MN908947.3:6167.0-6549.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:6167.0-6549.0 and MN908947.3:6718.0-7076.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:6757.1-7116.0 and MN908947.3:7305.0-7669.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:32 - TrimOverlap] MN908947.3:7328.0-7693.0 and MN908947.3:7943.0-8311.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:7965.2-8340.0 and MN908947.3:8595.0-8982.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:8595.0-8982.0 and MN908947.3:9204.0-9558.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:9229.1-9584.0 and MN908947.3:9784.0-10152.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:9801.0-10170.0 and MN908947.3:10362.0-10750.3 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:10374.0-10762.0 and MN908947.3:10999.0-11393.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:10999.0-11393.0 and MN908947.3:11555.0-11925.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:11576.0-11948.0 and MN908947.3:12110.0-12489.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:12110.0-12489.0 and MN908947.3:12710.0-13095.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:12710.0-13095.0 and MN908947.3:13307.0-13670.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:13336.2-13698.0 and MN908947.3:13918.0-14298.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:13918.0-14298.0 and MN908947.3:14545.0-14918.3 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:14551.1-14925.0 and MN908947.3:15171.0-15553.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:15175.1-15559.0 and MN908947.3:15827.0-16202.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:15833.3-16208.0 and MN908947.3:16416.0-16802.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:16452.0-16832.0 and MN908947.3:17065.0-17401.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:17115.1-17451.0 and MN908947.3:17674.0-18061.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:17674.0-18061.0 and MN908947.3:18253.0-18604.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:18316.1-18671.0 and MN908947.3:18896.0-19255.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:18934.1-19296.0 and MN908947.3:19548.0-19920.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:19559.0-19938.0 and MN908947.3:20172.0-20554.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:20189.0-20571.0 and MN908947.3:20786.0-21168.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:20786.0-21168.0 and MN908947.3:21357.0-21742.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:21357.0-21742.0 and MN908947.3:21961.0-22340.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:21968.0-22345.0 and MN908947.3:22516.0-22902.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:22516.0-22902.0 and MN908947.3:23122.0-23497.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:23154.1-23521.0 and MN908947.3:23789.0-24168.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:23789.0-24168.0 and MN908947.3:24391.0-24755.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:24419.1-24788.2 and MN908947.3:24978.0-25356.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:24986.3-25368.0 and MN908947.3:25601.0-25948.9 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:25632.1-25993.0 and MN908947.3:26197.0-26516.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:26274.3-26589.0 and MN908947.3:26835.0-27188.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:26863.1-27226.0 and MN908947.3:27446.0-27853.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:27446.0-27853.0 and MN908947.3:28081.0-28445.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:28102.0-28463.0 and MN908947.3:28677.0-29035.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:33 - TrimOverlap] MN908947.3:28705.2-29062.0 and MN908947.3:29288.0-29642.1 cannot be concatenated as there is no overlap and they do not abut.
Running: medaka consensus --model r941_min_high_g351 --threads 2 --chunk_len 800 --chunk_ovlp 400 --RG 2 my_example.trimmed.rg.sorted.bam my_example.2.hdf
[21:43:37 - medaka] Reads will be filtered to only those with RG tag: 2
[21:43:37 - Predict] Processing region(s): MN908947.3:0-29903
[21:43:37 - Predict] Setting tensorflow threads to 2.
[21:43:37 - Predict] Processing 1 long region(s) with batching.
[21:43:37 - Predict] Using model: /Users/willrowe/opt/miniconda3/envs/artic-pipeline-example/lib/python3.6/site-packages/medaka/data/r941_min_high_g351_model.hdf5.
[21:43:37 - ModelLoad] Building model with cudnn optimization: False
[21:43:39 - DLoader] Initializing data loader
[21:43:39 - Sampler] Initializing sampler for consensus of region MN908947.3:0-29903.
[21:43:39 - PWorker] Running inference for 0.0M draft bases.
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 320-725.
[21:43:39 - Feature] Processed MN908947.3:320.0-725.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 943-1336.
[21:43:39 - Feature] Processed MN908947.3:943.0-1336.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 1573-1963.
[21:43:39 - Feature] Processed MN908947.3:1573.0-1963.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 2181-2591.
[21:43:39 - Feature] Processed MN908947.3:2181.0-2591.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 2826-3209.
[21:43:39 - Feature] Processed MN908947.3:2826.0-3209.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 3460-3852.
[21:43:39 - Feature] Processed MN908947.3:3460.0-3852.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 4044-4449.
[21:43:39 - Feature] Processed MN908947.3:4044.0-4449.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 4636-5016.
[21:43:39 - Feature] Processed MN908947.3:4636.0-5016.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 5230-5643.
[21:43:39 - Feature] Processed MN908947.3:5230.0-5643.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 5867-6271.
[21:43:39 - Feature] Processed MN908947.3:5867.0-6271.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 6466-6872.
[21:43:39 - Feature] Processed MN908947.3:6466.0-6872.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 7035-7414.
[21:43:39 - Feature] Processed MN908947.3:7035.0-7414.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 7626-8018.
[21:43:39 - Feature] Processed MN908947.3:7626.0-8018.0 (median depth 117.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 8249-8660.
[21:43:39 - Feature] Processed MN908947.3:8249.0-8660.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 8888-9270.
[21:43:39 - Feature] Processed MN908947.3:8888.0-9270.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 9477-9857.
[21:43:39 - Feature] Processed MN908947.3:9477.0-9857.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 10076-10458.
[21:43:39 - Feature] Processed MN908947.3:10076.0-10458.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 10666-11073.
[21:43:39 - Feature] Processed MN908947.3:10666.0-11073.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 11306-11692.
[21:43:39 - Feature] Processed MN908947.3:11306.0-11692.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 11863-12255.
[21:43:39 - Feature] Processed MN908947.3:11863.0-12255.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 12417-12801.
[21:43:39 - Feature] Processed MN908947.3:12417.0-12801.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 13005-13399.
[21:43:39 - Feature] Processed MN908947.3:13005.0-13399.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 13599-13983.
[21:43:39 - Feature] Processed MN908947.3:13599.0-13983.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 14207-14600.
[21:43:39 - Feature] Processed MN908947.3:14207.0-14600.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 14865-15245.
[21:43:39 - Feature] Processed MN908947.3:14865.0-15245.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 15481-15885.
[21:43:39 - Feature] Processed MN908947.3:15481.0-15885.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 16118-16509.
[21:43:39 - Feature] Processed MN908947.3:16118.0-16509.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 16748-17151.
[21:43:39 - Feature] Processed MN908947.3:16748.0-17151.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 17381-17760.
[21:43:39 - Feature] Processed MN908947.3:17381.0-17760.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 17966-18347.
[21:43:39 - Feature] Processed MN908947.3:17966.0-18347.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 18596-18978.
[21:43:39 - Feature] Processed MN908947.3:18596.0-18978.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 19204-19615.
[21:43:39 - Feature] Processed MN908947.3:19204.0-19615.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 19844-20254.
[21:43:39 - Feature] Processed MN908947.3:19844.0-20254.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 20472-20889.
[21:43:39 - Feature] Processed MN908947.3:20472.0-20889.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 21075-21454.
[21:43:39 - Feature] Processed MN908947.3:21075.0-21454.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 21658-22037.
[21:43:39 - Feature] Processed MN908947.3:21658.0-22037.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 22262-22649.
[21:43:39 - Feature] Processed MN908947.3:22262.0-22649.0 (median depth 34.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 22797-23213.
[21:43:39 - Feature] Processed MN908947.3:22797.0-23213.0 (median depth 121.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 23443-23846.
[21:43:39 - Feature] Processed MN908947.3:23443.0-23846.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 24078-24466.
[21:43:39 - Feature] Processed MN908947.3:24078.0-24466.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 24696-25075.
[21:43:39 - Feature] Processed MN908947.3:24696.0-25075.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 25279-25672.
[21:43:39 - Feature] Processed MN908947.3:25279.0-25672.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 25902-26314.
[21:43:39 - Feature] Processed MN908947.3:25902.0-26314.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 26520-26912.
[21:43:39 - Feature] Processed MN908947.3:26520.0-26912.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 27141-27532.
[21:43:39 - Feature] Processed MN908947.3:27141.0-27532.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 27784-28171.
[21:43:39 - Feature] Processed MN908947.3:27784.0-28171.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 28394-28778.
[21:43:39 - Feature] Processed MN908947.3:28394.0-28778.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 28985-29377.
[21:43:39 - Feature] Processed MN908947.3:28985.0-29377.0 (median depth 200.0)
[21:43:39 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 29486-29865.
[21:43:39 - Feature] Processed MN908947.3:29486.0-29865.0 (median depth 200.0)
[21:43:39 - Sampler] Took 0.14s to make features.
[21:43:39 - Sampler] Region MN908947.3:4044.0-4449.0 (794 positions) is smaller than inference chunk length 800, quarantining.
[21:43:39 - Sampler] Region MN908947.3:4636.0-5016.0 (784 positions) is smaller than inference chunk length 800, quarantining.
[21:43:39 - Sampler] Region MN908947.3:7035.0-7414.0 (759 positions) is smaller than inference chunk length 800, quarantining.
[21:43:39 - Sampler] Region MN908947.3:7626.0-8018.0 (687 positions) is smaller than inference chunk length 800, quarantining.
[21:43:39 - Sampler] Region MN908947.3:12417.0-12801.0 (778 positions) is smaller than inference chunk length 800, quarantining.
[21:43:39 - Sampler] Region MN908947.3:14865.0-15245.0 (779 positions) is smaller than inference chunk length 800, quarantining.
[21:43:39 - Sampler] Region MN908947.3:17381.0-17760.0 (793 positions) is smaller than inference chunk length 800, quarantining.
[21:43:39 - Sampler] Region MN908947.3:21075.0-21454.0 (799 positions) is smaller than inference chunk length 800, quarantining.
[21:43:39 - Sampler] Region MN908947.3:22262.0-22649.0 (488 positions) is smaller than inference chunk length 800, quarantining.
[21:43:39 - Sampler] Region MN908947.3:22797.0-23213.0 (687 positions) is smaller than inference chunk length 800, quarantining.
[21:43:42 - PWorker] All done, 10 remainder regions.
[21:43:42 - Predict] Processing 10 short region(s).
[21:43:42 - ModelLoad] Building model with cudnn optimization: False
[21:43:44 - DLoader] Initializing data loader
[21:43:44 - Sampler] Initializing sampler for consensus of region MN908947.3:4044-4450.
[21:43:44 - PWorker] Running inference for 0.0M draft bases.
[21:43:44 - Feature] Processed MN908947.3:4044.0-4449.0 (median depth 200.0)
[21:43:44 - Sampler] Took 0.01s to make features.
[21:43:44 - PWorker] All done, 0 remainder regions.
[21:43:44 - DLoader] Initializing data loader
[21:43:44 - PWorker] Running inference for 0.0M draft bases.
[21:43:44 - Sampler] Initializing sampler for consensus of region MN908947.3:4636-5017.
[21:43:44 - Feature] Processed MN908947.3:4636.0-5016.0 (median depth 200.0)
[21:43:44 - Sampler] Took 0.02s to make features.
[21:43:45 - PWorker] All done, 0 remainder regions.
[21:43:45 - DLoader] Initializing data loader
[21:43:45 - PWorker] Running inference for 0.0M draft bases.
[21:43:45 - Sampler] Initializing sampler for consensus of region MN908947.3:7035-7415.
[21:43:45 - Feature] Processed MN908947.3:7035.0-7414.0 (median depth 200.0)
[21:43:45 - Sampler] Took 0.02s to make features.
[21:43:45 - PWorker] All done, 0 remainder regions.
[21:43:45 - DLoader] Initializing data loader
[21:43:45 - PWorker] Running inference for 0.0M draft bases.
[21:43:45 - Sampler] Initializing sampler for consensus of region MN908947.3:7626-8019.
[21:43:45 - Feature] Processed MN908947.3:7626.0-8018.0 (median depth 117.0)
[21:43:45 - Sampler] Took 0.02s to make features.
[21:43:45 - PWorker] All done, 0 remainder regions.
[21:43:45 - DLoader] Initializing data loader
[21:43:45 - Sampler] Initializing sampler for consensus of region MN908947.3:12417-12802.
[21:43:45 - PWorker] Running inference for 0.0M draft bases.
[21:43:45 - Feature] Processed MN908947.3:12417.0-12801.0 (median depth 200.0)
[21:43:45 - Sampler] Took 0.02s to make features.
[21:43:46 - PWorker] All done, 0 remainder regions.
[21:43:46 - DLoader] Initializing data loader
[21:43:46 - Sampler] Initializing sampler for consensus of region MN908947.3:14865-15246.
[21:43:46 - PWorker] Running inference for 0.0M draft bases.
[21:43:46 - Feature] Processed MN908947.3:14865.0-15245.0 (median depth 200.0)
[21:43:46 - Sampler] Took 0.03s to make features.
[21:43:46 - PWorker] All done, 0 remainder regions.
[21:43:46 - DLoader] Initializing data loader
[21:43:46 - Sampler] Initializing sampler for consensus of region MN908947.3:17381-17761.
[21:43:46 - PWorker] Running inference for 0.0M draft bases.
[21:43:46 - Feature] Processed MN908947.3:17381.0-17760.0 (median depth 200.0)
[21:43:46 - Sampler] Took 0.01s to make features.
[21:43:46 - PWorker] All done, 0 remainder regions.
[21:43:46 - DLoader] Initializing data loader
[21:43:46 - Sampler] Initializing sampler for consensus of region MN908947.3:21075-21455.
[21:43:46 - PWorker] Running inference for 0.0M draft bases.
[21:43:46 - Feature] Processed MN908947.3:21075.0-21454.0 (median depth 200.0)
[21:43:46 - Sampler] Took 0.01s to make features.
[21:43:46 - PWorker] All done, 0 remainder regions.
[21:43:46 - DLoader] Initializing data loader
[21:43:46 - PWorker] Running inference for 0.0M draft bases.
[21:43:46 - Sampler] Initializing sampler for consensus of region MN908947.3:22262-22650.
[21:43:47 - Feature] Processed MN908947.3:22262.0-22649.0 (median depth 34.0)
[21:43:47 - Sampler] Took 0.01s to make features.
[21:43:47 - PWorker] All done, 0 remainder regions.
[21:43:47 - DLoader] Initializing data loader
[21:43:47 - PWorker] Running inference for 0.0M draft bases.
[21:43:47 - Sampler] Initializing sampler for consensus of region MN908947.3:22797-23214.
[21:43:47 - Feature] Processed MN908947.3:22797.0-23213.0 (median depth 121.0)
[21:43:47 - Sampler] Took 0.02s to make features.
[21:43:48 - PWorker] All done, 0 remainder regions.
[21:43:48 - Predict] Finished processing all regions.
Running: medaka variant ./primer-schemes/scov2/V3/scov2.reference.fasta my_example.2.hdf my_example.2.vcf
[21:43:53 - DataIndex] Loaded 1/1 (100.00%) sample files.
[21:43:53 - Variants] Processing MN908947.3:0-.
[21:43:53 - TrimOverlap] MN908947.3:366.2-725.0 and MN908947.3:943.0-1291.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:989.1-1336.0 and MN908947.3:1573.0-1958.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:1578.0-1963.0 and MN908947.3:2181.0-2546.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:2219.1-2591.0 and MN908947.3:2826.0-3193.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:2838.0-3209.0 and MN908947.3:3460.0-3810.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:3498.2-3852.0 and MN908947.3:4044.0-4449.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:4044.0-4449.0 and MN908947.3:4636.0-5016.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:4636.0-5016.0 and MN908947.3:5230.0-5630.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:5250.0-5643.0 and MN908947.3:5867.0-6256.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:5877.4-6271.0 and MN908947.3:6466.0-6858.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:6479.1-6872.0 and MN908947.3:7035.0-7414.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:7035.0-7414.0 and MN908947.3:7626.0-8018.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:7626.0-8018.0 and MN908947.3:8249.0-8622.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:8291.0-8660.0 and MN908947.3:8888.0-9263.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:8893.3-9270.0 and MN908947.3:9477.0-9794.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:9540.1-9857.0 and MN908947.3:10076.0-10449.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:10083.0-10458.0 and MN908947.3:10666.0-11056.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:10679.1-11073.0 and MN908947.3:11306.0-11672.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:11325.2-11692.0 and MN908947.3:11863.0-12246.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:11872.3-12255.0 and MN908947.3:12417.0-12801.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:12417.0-12801.0 and MN908947.3:13005.0-13368.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:13027.1-13399.0 and MN908947.3:13599.0-13975.3 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:13604.2-13983.0 and MN908947.3:14207.0-14580.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:14230.0-14600.0 and MN908947.3:14865.0-15245.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:14865.0-15245.0 and MN908947.3:15481.0-15862.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:15501.1-15885.0 and MN908947.3:16118.0-16483.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:16145.3-16509.0 and MN908947.3:16748.0-17112.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:16790.0-17151.0 and MN908947.3:17381.0-17760.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:17381.0-17760.0 and MN908947.3:17966.0-18321.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:17985.0-18347.0 and MN908947.3:18596.0-18972.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:18599.2-18978.0 and MN908947.3:19204.0-19540.3 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:19272.1-19615.0 and MN908947.3:19844.0-20219.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:19868.5-20254.0 and MN908947.3:20472.0-20865.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:20497.1-20889.0 and MN908947.3:21075.0-21454.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:21075.0-21454.0 and MN908947.3:21658.0-22024.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:21669.1-22037.0 and MN908947.3:22262.0-22649.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:22262.0-22649.0 and MN908947.3:22797.0-23213.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:22797.0-23213.0 and MN908947.3:23443.0-23765.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:23510.2-23846.0 and MN908947.3:24078.0-24445.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:53 - TrimOverlap] MN908947.3:24092.1-24466.0 and MN908947.3:24696.0-25044.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:54 - TrimOverlap] MN908947.3:24720.1-25075.0 and MN908947.3:25279.0-25642.0 cannot be concatenated as there is no overlap and they do not abut.
[21:43:54 - TrimOverlap] MN908947.3:25302.0-25672.0 and MN908947.3:25902.0-26253.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:54 - TrimOverlap] MN908947.3:25954.2-26314.0 and MN908947.3:26520.0-26895.3 cannot be concatenated as there is no overlap and they do not abut.
[21:43:54 - TrimOverlap] MN908947.3:26539.2-26912.0 and MN908947.3:27141.0-27522.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:54 - TrimOverlap] MN908947.3:27152.1-27532.0 and MN908947.3:27784.0-28160.1 cannot be concatenated as there is no overlap and they do not abut.
[21:43:54 - TrimOverlap] MN908947.3:27795.1-28171.0 and MN908947.3:28394.0-28756.9 cannot be concatenated as there is no overlap and they do not abut.
[21:43:54 - TrimOverlap] MN908947.3:28418.2-28778.0 and MN908947.3:28985.0-29352.2 cannot be concatenated as there is no overlap and they do not abut.
[21:43:54 - TrimOverlap] MN908947.3:29015.1-29377.0 and MN908947.3:29486.0-29859.1 cannot be concatenated as there is no overlap and they do not abut.
Running: artic_vcf_merge my_example ./primer-schemes/scov2/V3/scov2.scheme.bed 2> my_example.primersitereport.txt 1:my_example.1.vcf 2:my_example.2.vcf
Running: bgzip -f my_example.merged.vcf
Running: tabix -p vcf my_example.merged.vcf.gz
Running: artic-tools check_vcf --dropPrimerVars --dropOverlapFails --vcfOut my_example.merged.filtered.vcf my_example.merged.vcf.gz ./primer-schemes/scov2/V3/scov2.scheme.bed 2> my_example.vcfreport.txt
Running: mv my_example.merged.filtered.vcf my_example.merged.vcf
Running: bgzip -f my_example.merged.vcf
Running: tabix -f -p vcf my_example.merged.vcf.gz
Running: longshot -P 0 -F -A --no_haps --bam my_example.primertrimmed.rg.sorted.bam --ref ./primer-schemes/scov2/V3/scov2.reference.fasta --out my_example.merged.vcf --potential_variants my_example.merged.vcf.gz

2021-01-14 21:43:56 Automatically determining max read coverage.
2021-01-14 21:43:56 Estimating mean read coverage...
2021-01-14 21:43:56 Total reference positions: 29903
2021-01-14 21:43:56 Total bases in bam: 6503829
2021-01-14 21:43:56 Mean read coverage: 217.50
2021-01-14 21:43:56 Min read coverage set to 6.
2021-01-14 21:43:56 Max read coverage set to 291.
2021-01-14 21:43:56 Estimating alignment parameters...
2021-01-14 21:43:56 Done estimating alignment parameters.

                    Transition Probabilities:
                    match -> match:          0.983
                    match -> insertion:      0.007
                    match -> deletion:       0.010
                    deletion -> match:       0.647
                    deletion -> deletion:    0.353
                    insertion -> match:      0.673
                    insertion -> insertion:  0.327

                    Emission Probabilities:
                    match (equal):           0.987
                    match (not equal):       0.004
                    insertion:               1.000
                    deletion:                1.000

                    GENOTYPE PRIORS:
                    REF G1/G2 PROB
                    C D/I 0.0000000000015624993116907664
                    G A/A 0.00016666692910805806
                    G D/I 0.0000000000015624993116907664
                    T T/T 0.9984401606149776
                    A C/D 0.0000000004166671407128834
                    A A/T 0.0003333338549006453
                    C A/A 0.00016666692910805806
                    G T/T 0.00016666692910805806
                    C C/T 0.0003333338549006453
                    T A/T 0.0003333338549006453
                    G G/I 0.000001250002950856874
                    T D/I 0.0000000000015624993116907664
                    C D/D 0.000006249988919003825
                    T G/D 0.0000000004166671407128834
                    C A/T 0.00000011111137065235802
                    C G/D 0.0000000004166671407128834
                    G T/I 0.0000000004166671407128834
                    C C/C 0.9984401606149776
                    A G/G 0.00016666692910805806
                    A A/I 0.000001250002950856874
                    A A/C 0.0003333338549006453
                    T T/I 0.000001250002950856874
                    G G/D 0.000001250002950856874
                    T C/G 0.00000011111137065235802
                    G C/G 0.0003333338549006453
                    G A/I 0.0000000004166671407128834
                    G C/I 0.0000000004166671407128834
                    C T/D 0.0000000004166671407128834
                    G A/C 0.00000011111137065235802
                    A I/I 0.000006249988919003825
                    A G/T 0.00000011111137065235802
                    C G/I 0.0000000004166671407128834
                    T A/C 0.00000011111137065235802
                    T A/I 0.0000000004166671407128834
                    C A/G 0.00000011111137065235802
                    T T/D 0.000001250002950856874
                    A C/T 0.00000011111137065235802
                    A A/D 0.000001250002950856874
                    A T/T 0.00016666692910805806
                    A D/I 0.0000000000015624993116907664
                    G A/T 0.00000011111137065235802
                    G G/G 0.9984401606149776
                    G C/T 0.00000011111137065235802
                    G I/I 0.000006249988919003825
                    T A/D 0.0000000004166671407128834
                    T C/D 0.0000000004166671407128834
                    T I/I 0.000006249988919003825
                    A C/G 0.00000011111137065235802
                    C C/G 0.0003333338549006453
                    C A/D 0.0000000004166671407128834
                    C G/T 0.00000011111137065235802
                    T D/D 0.000006249988919003825
                    A A/G 0.0003333338549006453
                    T C/I 0.0000000004166671407128834
                    A D/D 0.000006249988919003825
                    T A/A 0.00016666692910805806
                    T G/I 0.0000000004166671407128834
                    G G/T 0.0003333338549006453
                    C G/G 0.00016666692910805806
                    G T/D 0.0000000004166671407128834
                    C C/D 0.000001250002950856874
                    A G/D 0.0000000004166671407128834
                    C A/C 0.0003333338549006453
                    C A/I 0.0000000004166671407128834
                    T G/T 0.0003333338549006453
                    A T/D 0.0000000004166671407128834
                    G C/D 0.0000000004166671407128834
                    G A/D 0.0000000004166671407128834
                    C T/I 0.0000000004166671407128834
                    C C/I 0.000001250002950856874
                    T C/T 0.0003333338549006453
                    A C/I 0.0000000004166671407128834
                    A C/C 0.00016666692910805806
                    C I/I 0.000006249988919003825
                    G D/D 0.000006249988919003825
                    A A/A 0.9984401606149776
                    A G/I 0.0000000004166671407128834
                    C T/T 0.00016666692910805806
                    T C/C 0.00016666692910805806
                    G C/C 0.00016666692910805806
                    T A/G 0.00000011111137065235802
                    T G/G 0.00016666692910805806
                    A T/I 0.0000000004166671407128834
                    G A/G 0.0003333338549006453
2021-01-14 21:43:56 Reading potential variants from input VCF...
2021-01-14 21:43:56 13 potential variants identified.
2021-01-14 21:43:56 Generating haplotype fragments from reads...
2021-01-14 21:43:56    10% of variants processed...
2021-01-14 21:43:56    20% of variants processed...
2021-01-14 21:43:56    30% of variants processed...
2021-01-14 21:43:56    40% of variants processed...
2021-01-14 21:43:56    50% of variants processed...
2021-01-14 21:43:57    60% of variants processed...
2021-01-14 21:43:57    70% of variants processed...
2021-01-14 21:43:57    80% of variants processed...
2021-01-14 21:43:57    100% of variants processed.
2021-01-14 21:43:57 Calling initial genotypes using pair-HMM realignment...
Running: artic_vcf_filter --medaka my_example.merged.vcf my_example.pass.vcf my_example.fail.vcf
Running: bgzip -f my_example.pass.vcf
Running: tabix -p vcf my_example.pass.vcf.gz
Running: artic_make_depth_mask --store-rg-depths ./primer-schemes/scov2/V3/scov2.reference.fasta my_example.primertrimmed.rg.sorted.bam my_example.coverage_mask.txt
Running: artic_mask ./primer-schemes/scov2/V3/scov2.reference.fasta my_example.coverage_mask.txt my_example.fail.vcf my_example.preconsensus.fasta
Running: bcftools consensus -f my_example.preconsensus.fasta my_example.pass.vcf.gz -m my_example.coverage_mask.txt -o my_example.consensus.fasta
Note: the --sample option not given, applying all records regardless of the genotype
Applied 9 variants
Running: artic_fasta_header my_example.consensus.fasta "my_example/ARTIC/medaka"
Running: cat my_example.consensus.fasta ./primer-schemes/scov2/V3/scov2.reference.fasta > my_example.muscle.in.fasta
Running: muscle -in my_example.muscle.in.fasta -out my_example.muscle.out.fasta

MUSCLE v3.8.1551 by Robert C. Edgar

http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

my_example.muscle.in 2 seqs, lengths min 29903, max 29903, avg 29903
00:00:00      2 MB(0%)  Iter   1  100.00%  K-mer dist pass 1
00:00:00      2 MB(0%)  Iter   1  100.00%  K-mer dist pass 2
00:00:15    970 MB(6%)  Iter   1  100.00%  Align node       
00:00:15    970 MB(6%)  Iter   1  100.00%  Root alignment
Running: artic_get_stats --scheme ./primer-schemes/scov2/V3/scov2.scheme.bed --align-report my_example.alignreport.txt --vcf-report my_example.vcfreport.txt my_example

That's it! Let's have a quick run through of the parameters we used so that we can understand what was happening.

parameter explanation
normalise This caps amplicon coverage to 200 reads, used mainly to speed up the pipeline run.
threads This sets the number of CPU threads to use during the pipeline. We set this to 2 here as that is the limit on Binder, but if you are playing along at home you can increase this to make things run a bit more quickly.
medaka This tells the ARTIC pipeline to use the medaka workflow
medaka-model This specifies which model to use for the medaka program calls.
strict This runs an additional filtering of reported variants, checking them in overlap regions of the primer scheme to see if they are artifacts reported in only one primer pool.
read-file This tells the pipeline where to find the reads.
scov/V3 This specifies the name of the primer scheme and the version to use. If it isn't found locally, the pipeline will try finding it in the ARTIC primer scheme repository.
my_exmple The name to give this pipeline run, all output will have this prepended to the filenames.

Pipeline output

Files

Now it is time to check what the pipeline has produced for us. The files we are most interested in are:

filename description
my_example.trimmed.rg.sorted.bam the post-processed alignment of reads to the reference genome.
my_example.primertrimmed.rg.sorted.bam the post-processed alignment with additional softmasking to exclude primer sequences.
my_example.vcfreport.txt a report evaluating reported variants against the primer scheme.
my_example.pass.vcf.gz detected variants that passed filters.
my_example.consensus.fasta the consensus sequence for the input sample.
my_example..muscle.out.fasta an alignment of the consensus sequence against the reference sequence.

QC report

Before we look at these files, we can use MultiQC to check our amplicon coverage (pre-normalisation to 100) and if we have any variants reported that may be a result of contamination. Use the ARTIC MultiQC plugin:

In [7]:
!multiqc .
[INFO   ]         multiqc : This is MultiQC v1.9
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /Users/willrowe/Desktop/artic-pipeline-example/notebooks
Searching 37 files..  [####################################]  100%          
[INFO   ]  custom_content : custom_data_lineplot: Found 1 samples (linegraph)
[INFO   ]  custom_content : custom_data_json_table: Found 1 samples (table)
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete

This will have produced a report HTML file called multiqc_report.html. You can click on that link or use the following code to view it in this notebook:

In [8]:
from IPython.display import IFrame
IFrame(src='./multiqc_report.html', width=600, height=400)
Out[8]:

Use the report to see if any amplicons are marked as low coverage due to insufficient reads being assigned. Also use the report to see if there are any overlap variant fails. This is when a variant is idenified within an amplicon overlap region of the scheme but is found in only one amplicon.

VCF files

As mentioned above, the file containing the filtered variants is my_example.pass.vcf.gz. Let's take a look:

In [9]:
# import pyVCF and open the variant file
import vcf
vcf_reader = vcf.Reader(filename="my_example.pass.vcf.gz")

# print the variants
print("chromosome\tpos\tref\talt")
for record in vcf_reader:
    print("{}\t{}\t{}\t{}" .format(record.CHROM, record.POS, record.REF, record.ALT))
chromosome	pos	ref	alt
MN908947.3	2618	A	[G]
MN908947.3	8782	C	[T]
MN908947.3	18488	T	[C]
MN908947.3	21846	C	[T]
MN908947.3	23605	T	[G]
MN908947.3	26354	T	[A]
MN908947.3	28144	T	[C]
MN908947.3	29366	C	[T]
MN908947.3	29596	A	[G]

FASTA files

We also have the consensus sequence and the alignment files to look out. Here is an example of how we can look at them with Python:

In [10]:
from Bio import AlignIO
alignment = AlignIO.read("my_example.muscle.out.fasta", "fasta")
print("alignment length= {}\n" .format(alignment.get_alignment_length()))
for record in alignment:
    print("{}\n{}".format(record.id, record.seq))
alignment length= 29903

my_example/ARTIC/medaka
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTGTTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTTAAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAATGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGTGAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTAAACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAACTCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCAGATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTGATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTATTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGCAGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAATATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTATGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTTTCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAGAACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACAACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCACCTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTAAGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACAACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGTAAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTGATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAATGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAAATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTAACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAATTTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGTTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAGTTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAACCATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAACCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGTGATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAACCTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTGTCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGAATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGAAAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTGCTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTACAACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTATTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAGCAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAATTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTACTCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAGGCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCTTAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAATGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCTATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTCTTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATCTTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTTGTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAGGTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGTGATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAAGACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCATCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGACAACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAATGTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACTAGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTTAATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTGAACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGTTGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTTACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTGGTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGATATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAGAATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAGCACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTTTGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAAATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTAACAAACATGCTGATTTTGACACATGGTTTAGTCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCCATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGCACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACACCATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTTTAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTATGAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACCTTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATCAGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCAGGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTGGTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTACTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTCCTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTTACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTTCACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGGTTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTGCGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTACGCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGCTACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTCTTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCCATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAGTTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTTACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTTTCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTAACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTGCTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGATGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACAATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTCAATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCCACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTCTTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTGGTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAAGAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTAGCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACTTGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCACAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAAATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTTGTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTCCAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCAACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGTTGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTAAAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATGACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGGACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAGCTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGTATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTCAGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCCTACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTCTCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAGGAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAGTGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTTAGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATAGATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACCAGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGCATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTATGCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTATGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATACAATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCCGGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTATAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATACATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGATAACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTGTTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTTATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTATGTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATTGTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAATACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGTGATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTGAGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCTTTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACTAAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATCTCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGGGACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACATTAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGAAATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTATAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGCTCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTAATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACTCATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAAGAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTGTTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTATGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCACACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAAAGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAACCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGTGACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTGTATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAGAGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCACACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTCCATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTATAACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCTTATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGAACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGGACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTAAACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGACTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAACCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTATTTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCCCAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAGAAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTAAACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATTAGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTACTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTACAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTTATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTGACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAAAATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCTATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTCGCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTATACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTACGGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGATTGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAAATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCTAGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATGGGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTGGATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTGGAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTAAGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAGGTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAACAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCATTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCGCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGAATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCTTGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGTGTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTGGCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAATAATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTTCTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTACTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATGGGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCATCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTCACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATTCCCATCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATGTATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAATTTTAGTAGTGCTATCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
MN908947.3
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTTAAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAATGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGTGAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTAAACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAACTCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCAGATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTGATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTATTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGCAGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAATATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTATGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTTTCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAGAACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACAACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCACCTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTAAGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACAACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGTAAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTGATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAATGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAAATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTAACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAATTTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGTTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAGTTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAACCATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAACCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGTGATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAACCTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTGTCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGAATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGAAAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTGCTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTACAACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTATTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAGCAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAATTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTACTCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAGGCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCTTAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAATGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCTATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTCTTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATCTTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTTGTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAGGTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGTGATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAAGACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCATCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGACAACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAATGTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACTAGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTTAATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTGAACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGTTGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTTACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTGGTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGATATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAGAATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAGCACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTTTGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAAATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTAACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCCATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGCACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACACCATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTTTAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTATGAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACCTTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATCAGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCAGGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTGGTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTACTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTCCTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTTACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTTCACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGGTTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTGCGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTACGCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGCTACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTCTTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCCATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAGTTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTTACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTTTCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTAACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTGCTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGATGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACAATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTCAATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCCACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTCTTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTGGTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAAGAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTAGCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACTTGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCACAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAAATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTTGTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTCCAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCAACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGTTGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTAAAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATGACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGGACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAGCTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGTATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTCAGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCCTACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTCTCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAGGAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAGTGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTTAGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATAGATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACCAGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGCATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTATGCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTATGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATACAATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCCGGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTATAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATACATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGATAACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTGTTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTTATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTATGTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATTGTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAATACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGTGATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTGAGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCTTTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACTAAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATCTCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGGGACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACATTAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGAAATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTATAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGCTCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTAATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACTCATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAAGAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTGTTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTATGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAAAGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAACCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGTGACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTGTATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAGAGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCACACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTCCATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTATAACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCTTATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGAACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGGACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTAAACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGACTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAACCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTATTTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCCCAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAGAAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTAAACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATTAGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTACTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTACAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTTATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTGACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAAAATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCTATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTCGCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTATACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTACGGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGATTGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAAATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCTAGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATGGGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTGGATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTGGAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTAAGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAGGTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAACAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGAATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCTTGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGTGTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTGGCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAATAATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTTCTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTACTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATGGGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAATTTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Questions

Now we have reached the end of the example, here are some questions for you to try. You might need to add a few more cells below so that you can use the files and Python that we used earlier to help answer them:

  • how many amplicons were classed as low coverage and what was the reported coverage for these?
  • how many variants were identified that were subsequently marked as FAIL?
  • how many variants were incorporated into the consensus genome?
  • how many Ns are in the consensus genome and why might they be there?
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