# HG changeset patch # User ieguinoa # Date 1606138569 0 # Node ID 87de778e0630de4d032383f1d70b5bc0b45efed4 # Parent 758e5bc32bbb54a1ab29f16574575d6abbe7ad87 Uploaded diff -r 758e5bc32bbb -r 87de778e0630 .shed.yml --- a/.shed.yml Thu Nov 19 10:21:04 2020 +0000 +++ b/.shed.yml Mon Nov 23 13:36:09 2020 +0000 @@ -1,5 +1,5 @@ categories: - - TODO + - Data Export description: | Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). long_description: | @@ -9,4 +9,4 @@ owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload homepage_url: https://github.com/usegalaxy-eu/ena-upload-cli -type: unrestricted \ No newline at end of file +type: unrestricted diff -r 758e5bc32bbb -r 87de778e0630 README.md --- a/README.md Thu Nov 19 10:21:04 2020 +0000 +++ b/README.md Mon Nov 23 13:36:09 2020 +0000 @@ -3,17 +3,25 @@ This tool is shipped in a ready to use Galaxy container found [here](https://github.com/ELIXIR-Belgium/ena-upload-container). -## Set up user credentials on Galaxy +## Setting up credentials on Galaxy -To enable users to set their credentials for this tool, -make sure the file `config/user_preferences_extra_conf.yml` has the following section: +The admin of the server can set up global credentials through a file with the format: +``` +username: webin_id +password: webin_password +``` + +The path to this file must be exported as an environment variable called $GALAXY_ENA_SECRETS + +Alternatively, the admin can enable users to set their own credentials for this tool. +To enable it, make sure the file `config/user_preferences_extra_conf.yml` has the following section: ``` - ena_account: - description: Your ENA Brokering account details + ena_webin_account: + description: Your ENA Webin account details inputs: - name: webin_id - label: webin_id + label: ENA Webin ID type: text required: False - name: password diff -r 758e5bc32bbb -r 87de778e0630 ena_upload.xml --- a/ena_upload.xml Thu Nov 19 10:21:04 2020 +0000 +++ b/ena_upload.xml Mon Nov 23 13:36:09 2020 +0000 @@ -1,6 +1,6 @@ - + - 0.2.3 + 0.2.4 samples_macros.xml @@ -8,45 +8,48 @@ xlrd Preferences -> Manage Information"; - exit 1; - #end if -#end if - -echo "Submissions will be made with user: $webin_id. You can set your credentials via: User -> Preferences -> Manage Information"; - +mkdir ./submission_files; +webin_id=`grep 'username' $credentials`; +if [ "\$webin_id" = "" ]; then + ## No credentials in user defined preferences + ## Fallback to global defined credentials (if exist) + #import os + #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')): + credentials_path=\${ENA_SECRETS}; + webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`; + if [ "\$webin_id" = "" ]; then + echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information"; + exit 1; + fi; + #else: + echo "No global credentials file defined. Set your credentials via: User -> Preferences -> Manage Information"; + exit 1; + #end if +else + credentials_path='$credentials'; +fi; + #set working_dir = os.getcwd() #set $dry_run_option = "False" #set viral_submission = "False" #if $action_options.input_format_conditional.input_format == "build_tables": - python $__tool_directory__/extract_tables.py --action $action_options.action --out_dir \$cwd --studies $studies_json; - #set $studies_table_path = "$cwd/studies.tsv" - #set $samples_table_path = "$cwd/samples.tsv" - #set $experiments_table_path = "$cwd/experiments.tsv" - #set $runs_table_path = "$cwd/runs.tsv" + python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json; + #set $studies_table_path = './submission_files/studies.tsv' + #set $samples_table_path = './submission_files/samples.tsv' + #set $experiments_table_path = './submission_files/experiments.tsv' + #set $runs_table_path = './submission_files/runs.tsv' #end if #if $action_options.input_format_conditional.input_format == "excel_tables": - python $__tool_directory__/process_xlsx.py + python '$__tool_directory__/process_xlsx.py' #if $action_options.input_format_conditional.viral_submission == "true": --vir #end if - --action $action_options.action --form $action_options.input_format_conditional.xlsx_file --out_dir . ; - #set $studies_table_path = "$cwd/studies.tsv" - #set $samples_table_path = "$cwd/samples.tsv" - #set $experiments_table_path = "$cwd/experiments.tsv" - #set $runs_table_path = "$cwd/runs.tsv" + --action '$action_options.action' --form '$action_options.input_format_conditional.xlsx_file' --out_dir ./submission_files ; + #set $studies_table_path = './submission_files/studies.tsv' + #set $samples_table_path = './submission_files/samples.tsv' + #set $experiments_table_path = './submission_files/experiments.tsv' + #set $runs_table_path = './submission_files/runs.tsv' #if $action_options.input_format_conditional.dry_run == "true": #set $dry_run_option = "True" #end if @@ -64,6 +67,7 @@ ## create the list of files to upload and make the symlinks +#import re #set $files_to_upload = list() #if $action_options.input_format_conditional.input_format == "build_tables": #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study: @@ -71,8 +75,9 @@ #for $experiment in $sample.rep_experiment: #for $run in $experiment.rep_runs: #for $file in $run.upload_files: - ln -s $file $file.element_identifier; - $files_to_upload.append(str($file.element_identifier)) + #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) + ln -s '$file' $safename_reads_file && + $files_to_upload.append(str($safename_reads_file)) #end for #end for #end for @@ -80,8 +85,9 @@ #end for #else: #for $file in $action_options.input_format_conditional.data: - ln -s $file $file.element_identifier; - $files_to_upload.append(str($file.element_identifier)) + #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) + ln -s '$file' $safename_reads_file && + $files_to_upload.append(str($safename_reads_file)) #end for #end if @@ -91,29 +97,24 @@ --tool 'ena-upload-cli v@VERSION@ @ Galaxy' --action '$action_options.action' --center '$action_options.center' - --webin_id '$webin_id' - #if $use_secret == "False": - --password $password - #else: - --secret $webin_secret - #end if + --secret \${credentials_path} --data #for $dataset in $files_to_upload: - $dataset + '$dataset' #end for #if $action_options.input_format_conditional.input_format == "user_generated_tables": - --experiment $action_options.input_format_conditional.experiments_users_table - --study $action_options.input_format_conditional.studies_users_table - --run $action_options.input_format_conditional.runs_users_table - --sample $action_options.input_format_conditional.samples_users_table - #if $action_options.input_format_conditional.viral_submission == "true": + --experiment '$action_options.input_format_conditional.experiments_users_table' + --study '$action_options.input_format_conditional.studies_users_table' + --run '$action_options.input_format_conditional.runs_users_table' + --sample '$action_options.input_format_conditional.samples_users_table' + #if "$action_options.input_format_conditional.viral_submission" == "true": --vir #end if #else: - --experiment $experiments_table_path - --study $studies_table_path - --run $runs_table_path - --sample $samples_table_path + --experiment '$experiments_table_path' + --study '$studies_table_path' + --run '$runs_table_path' + --sample '$samples_table_path' #if $action_options.input_format_conditional.input_format == "build_tables": #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true": --vir @@ -127,13 +128,21 @@ #if $action_options.submit_dev == "true": -d #end if - > $output + > '$output' +#else: + exit 0; #end if - - ]]> +]]> - + + #import json +#import re #if $action_options.input_format_conditional.input_format == "build_tables": #set $files_to_upload = list() #set $studies = list() @@ -146,7 +155,8 @@ #for $run in $experiment.rep_runs: #set run_files = list() #for $file in $run.upload_files: - $run_files.append(str($file.element_identifier)) + #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) + $run_files.append(str($safename_reads_file)) #end for $runs.append($run_files) #end for @@ -194,6 +204,91 @@ action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+BABBBFFDABBBGGGGGGGGGGHGHHHHGAGHGGGGGHHHHHHHHGHHHHHGGGGGGFFHHHHHHHHHFHHHHHGGGGCHFHH3FEHHGCGGGDGHHHGFGGHHGGGGHHHHHHG/DGGGHHHHGGGGGCCHGG?CGG1GHHGHHHHBGHHHFHHGHHHHGGADAD00ECEGHEFHHFFAEFFFFFGGFBFBFFFGFFG.;B/99;BCFGGGGEFFFFFFEDA./:ADEB?FBFFFF;FFEBFBFFB./9. +@M01368:8:000000000-A3GHV:1:1107:18714:24788/1 +GTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGA ++ +BBBCCFFFDEDEGGGGGGGGGGHHHHHHGGHHGGHGGHHHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHCFGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHGHHHHHHHHHHHGHHHHGGEGEGCCEGGHHHHHHG:CAFFGGGGGGBFEFGGGGHGAFFGGFGGGGGGGEFFFFFFFFFEF/EDDFFFFFFFFFBFFFFFBBFFBBF/ +@M01368:8:000000000-A3GHV:1:1107:21355:8333/1 +ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATG ++ +ABCBBFFFFFAFGGGGGGGGGGHHHHHHHHFHHHHHGGGGGHHHHHHFHHHGHHHHHHHGGGGGHHHHFFGHGHGGGGGGGHGGEGGGHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHGHHHFHHHHHHHHGHFFHHHHGGHGEGHHGHGFHHFHGHCEFHEGHGHHHGHHHGGGGGGCFFFFBFGGFGGGGFBG?FDGGGEGFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF.AA/9 +@M01368:8:000000000-A3GHV:1:1107:22864:15712/1 +AATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATG ++ +BBBBBFBBFFFFGGGGCEGGGGHGHHDGFHHHHHHHHHHHHHCHHGHFGBGDFGE?GHHGHFBHHFHHHHHHHHHGHFGFGHGHHGGC@DCFGHHGGGGGGGHHHHHHGGGGGFGGGGFFGGGGFADGFEFFFFFFFFFFF9;FFFF/BFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFEAECDFFFFFFFFFBFFFFFFFFFFFFFFEFBFBFFF/FFFDF-;-9;E@>-9DFFF/FFBF;-.:;.9A// +@M01368:8:000000000-A3GHV:1:1107:24817:14233/1 +CTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACAT ++ +3AABABFFBFFFGCFGGGGGGGHHHFGCFGGGFFGHHCGHHHGHGHGHBFFHHHEDGGFGFGHHFFFHGGEGHFHHGHFHGFFHHHFGHHHFHACECEHHHBGFHGFHHHFHHF4GFHFHFHEHGGE/EG:A-CFGGFGADGGGGFGGGGDAAAADFA.-AFFECFDAAFFFFEFFFFBFF;D;BFFFB/;BFFFFFFFFFFFFFFBFFBF/;//;BFFFF?FFFFFFEDAFFFFFBF//:BFBACF--9/ +@M01368:8:000000000-A3GHV:1:1107:24830:14440/1 +AACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACC ++ +ABBBA@FFFFBBGGGGGGGGGGHGHHGHHGHHHGGHHHHHGHGHHGDHHHHHHAGGGGFHHGHHHHHHGHHHHHHHHHHHEGAFGFHFHHHHGEGHHHHHHHHHHHHHHHHHGGHHHGEFEGGHHGHHHHHGGHGFHH/?GHHHHGFGHGFHCGGBBDAFFFEFFFFFFFFFFFFFF=CDDADDFFFFEF=BFFFEFFFBFFFFEEBF./:FFFFFFFFFFFFFFFFFFFEFFFFFFFFFFF/BFBEFFC- +@M01368:8:000000000-A3GHV:1:1107:26478:23602/1 +GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATCTGTCTCTTATACACCTCTC ++ +1AAAAF1B13BBBEGGGFGGGGGGHHDB1BGFHHHFGFGGG0F00BGBGFGGF1GBGB1BGCGAEE/FGFHGHFHHHHHBFF1B0FGGF//F//FGFGFFF/1@B1DFHHHGGEFEDHFDFAFF0B//1FDD1GFFHHDF?1BD>GF/GCAC0C@?@-;99BBB->@--;-B//99B--9-BF=A--A-:A----9AA9AFBFBBB?E@BBFFFFFFFBFFFFFBFFFBBFFF//B/////-;9 +@M01368:8:000000000-A3GHV:1:1108:11059:23181/1 +GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGAT ++ +CCCCCFFFFFFFGGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHGHHGGGGHIIIHHHHHHHGHHHHGHHHGGHGGHHHHHHHHHHHHHHGGGGGHHGHHHHHHHHHHHHHHHGGGGGHHHHHFGHHHGGGGGGHHHGGGGGHGGGGHHHHHHGGGGGGHGGHEFGGGGGHGGG-ECHHHGGGGGGGGGFGFFGGGGFGGGCF?EFGG0;BFFFFB?9AAFFFFFFBF;BBFFBFFFFE?F/ +@M01368:8:000000000-A3GHV:1:1108:12233:13498/1 +TAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCCTGTCTCTTATACAC ++ +BCCBAFFBCCCCGGGGGGGGGGHHHHGGGGGHHHHHHGHGHBGFHHHHHGGGGGHHGGBFGHHGGGGGGGHHHGGGGHHGGGFHHHHHHGGGGGGHGHHGGGGGGGGGGGGGGHHHHFHHHGHGHHHHHHGHGHHGGFGGGDFFGGHHHGHGH/FHHHFHGHGHHGHHHGHHBAAAA3BDFFFFDGBFFEEGGGGHHGHFHHCFHGHGHHHGF3BFGFHGFEFHFHGH3EGFC1EEGBFGBHFGGFFHHHGHFHGHHGHGGHCEHEBCFF3ED3@GH4FDEG12FFHFFHG/G3FGA/@EFEFCG33FFGBBGHFHH/?BFBGFGFAGC2C/@-;@-;BFFEFADF?DFFFFFF?;AFFA;AD;..FEFFA--;9;D.9BFFBE?;.;///://///99//BB/9;F./B//BBFB9////99/ +@M01368:8:000000000-A3GHV:1:1109:25237:11722/1 +CCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGTATGCCGT ++ +AABBBFFFFFBBF5BGGFGABGHGGAEFGFHHHHFHCHFHHBFGGGEHBGGHFFFFGFAEF5FHH?EGGF5AEG3?EBFHD?C/EFHFFEGEE?CFGGGHHFHB3EEFG?EEGHCFGGGGGGGECA?FFFDFBFGCG4EGFG??GACFGGHFHCFHCHBECDEFCEGHHHHHFFGGF3AFFHHFGEGCGHHGEHGFGHHEGG?EFHHH?EGGHHGGGGHHHHHHEGGGGGHFHHGFDDGGACFCC@?/FDDGHHHGHEFFHHH0FDHHFFEDCD.CFHHGDFGGGGGEFGC?EGHHHB0CGHHGCGHHHHBEHGHH.::ACA;FECFGGGGGFFFEFGGGGGGGFFBBBFGBFFFEFFFFBFFFFFFBBFBFFB9..AF?FFFFFFF9 +@M01368:8:000000000-A3GHV:1:1110:14751:26540/1 +TAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACTGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGTTGTGCACGCGATAGCATTGCGCGACGCTGGCGCCGGCGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTG ++ +AAA?1CFFFFADGEEGFGB1112DGDGHGFGHHCG/ECEBGGHDFGHHFHGHEB1BCGFFE2EGHHGHFFFHHBFFHEFCGGHHFHHHHH111BFFHGHEHBEHGGECEFHGFHFGGDBBGHHBHHHH0GH22FGHGFFFH1BFCG0F@FGG11@GDHFG1D/1FGFHH/FCG.>0><-<@CCFFG.CC-@C?C9FFF0C---;------;9----9-9@-AAFF9B9---9-/;B9BF/9BB//B/;/// +@M01368:8:000000000-A3GHV:1:1110:15519:10008/1 +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACC ++ +BBBBBFFFFFFFGGGGGGCBGGE?GGGHHHHHGHHBEGGHHGGGGGHHHHHHHHHHHGGHHHHGFGGGGHGHGCFGHHHGGGCGGHGHGGGGGHFGGGHHHHHHGCEFGGHHHHGGGGGGGHGG/CEGHHHHGFHHHGFHHGFFHGHGHFGGEGFDDGGBCGHHGFHH/CHHHHGHGHF0CFGGGGGGGFFFFFBFFFFFFGFFGGF?DGEDEEFEFFFF?FFFFFFFFFFFFFFFBFFF.BFFFBFBBA; +@M01368:8:000000000-A3GHV:1:1110:16559:7507/1 +CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAACTGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATC ++ +ABBBAFFFFFFFFGGGGGGGFGGGGAGHHGCHHGHHHHHHHHHHHGHHGHHHHHHHHHHHHHHHHFGGGHHHHHHHHBDHHHHHGGHFEEGHGGHHHHHHHGHHHEHFGGGGGGHHHF33FGHHG3GDDGH//EEGHHFFBF?GHHFCC@DGFCGGB?DGHAFGGHHGFH0E??<@DGHGGCFGGF?DGGGFFGGGGGGGG.C/0BBF?FBBEGG0FFF.AA9;B9/E////99;;:.//:FFFFBBF//9 +@M01368:8:000000000-A3GHV:1:1110:16700:6843/1 +AAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCTGTCTCTTATACACATCTCCGAGCC ++ +BBBBBFFFFFFFGGGGGGGGGGHHHHGHHHHHHHHHHHHGGGGGHHHHHGGHGHGGGGGGHHHGFFGHHGGGGHHHHHHCGG@FGHFHFEGGGGGGHGGGGDGHHHHHHHHHHHHHHGHHGHGHHGGGGGCGHEHGHHHFHHHFF.DGHHHHHHGHHHHHHGFGHGCGHGHHHHHHHHGHHHCD?:A::FCDGEGFGFFBFGBFGGGF00CBFFFF/BFBFFFFAE.FBBFBFFFFB/BFFBFFF/ADCAD +@M01368:8:000000000-A3GHV:1:1110:18014:7856/1 +ATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAAAAAAAAAATAG ++ +AABBBFFFFFFFCGGGCGGGGGGHHHHHGFHHHHHHGHHHGGGGGFHHGHFGGHHHGGFGGGHHGGGGGHHGGGGHGGHHHGGGGGGHHGHGDGGGGGGGGB/A99FE//BBFFF.9/FF?DA=@9./9 +@M01368:8:000000000-A3GHV:1:1110:23303:11846/1 +ACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGTGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTC ++ +3ABB?FAB?DAAGGGFBGGBB5AFFFGFHHGGGEGHHHFHHF3EGFHHHHEFHHGGHHHGH3EFHHHHHBDGHHE?ECHGHGHHHHHHFHHHGHHHHHHHGGHGGFHHHFHHGFFHHFEGFHHHHHHEHHFDAGHHHH/BDDFGGH1FDBGHHHHHHHCGHHHFH?0CGCF>CC=@--AFBFFB?=BFDFFF//FDB;-9A-AD-.A.A=?-9-:B/AEB/BFF.A;DDFFFBBFFFF/BBFFFFBFF9B; +@M01368:8:000000000-A3GHV:1:1111:13195:14562/1 +ATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTCCGAGCCCACGAGA ++ +ABAAAFFFFFFFGGGGGGGGGGGHHGG4FDFGFGGCGGGHGHG?EGHEGFFDHFHHHHGGFE@EHHGEEEGFCCEFFGFG/EHHHHHBFBGGHFHFHEHGHEFGGGED/EFDEFFEHHBGHHCFFFDFGGHHGFFFHHHHGFG>0<0DGGFHBGHFBDFGHGFFGGAGHHGCGBHFFHHHFFFBFGGGGF/:FFFCB9F9FF0FEFE?FF0BED-D.//BF9//BBFF/BFFFEFFFFED-DCFF?.:BFA +@M01368:8:000000000-A3GHV:1:1111:14287:20817/1 +GCCAACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTCATCGCACCTACGTTCACTATTACAGGCGAACATACTTATTAAAGTGTGTTAATTAAT ++ +>>A3>AAAACFFFGFGFGGGGGHGHHHHHHHGGGGGHGHFFCGHHGBGHFHHHHAGHHHHEHHAGFFEHEAE?GHHHHEGFFFDGHGHBFFHFHHHGHGHGHBECG@@@EHGGEGCGGGGFFGGGG?BGGGGGG.-C.FEDCFFFEFFFAF/99BEFA.:9BFB/9FFFEFFFFFFEFFF/FBBFFFFFFFFFFFB//;.@@//;DFFFF//BBFFFBF;A;DF=>B//;9B//B/;/;9//9//;B/:B9 +@M01368:8:000000000-A3GHV:1:1111:23624:14516/1 +GTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGGGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAG ++ +3>3AAFFFFFAFGGGGGGGGBGHHHHHHGGHGGHEHGHADFHHHHEGGGHBGHFFHHEHHGHFHGG5FBEEGEGHHHGHHHEFDGHHFFGFGGHHGHHHGHBHGHFHFHHGGGGFCFBGFGE?GFBECEGDGHEHGDGCGHGC/DF@GHGFFCGGGGFFFFDD?@C@GFEC?-ADHFFHBGHFBHFG0CC//.;B0/CA.;AA.;@.AB/9BB/A/.AFFFE/BFFF///9B/FBDE9/;99/B/BFFEF/ +@M01368:8:000000000-A3GHV:1:1111:7437:24508/1 +ACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTGTCTCTTATACACATCTCCGAGCCCACGAG ++ +CBCCDCFFFFFFGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHGGGFFEHGGHHHHHHHHHHHGHHGGGGGHHHHHHFHHHHGHHHHGHGGGGGHHHHHGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGCGHHHHGHHGHHHHHHHEDHHGHGGGGGD;BEGGGFFGGGGC:CFGGGGGGGGGFGGGFFFGFFFFF;FFF;BFFFFFFFFFFFB:FFFFD=CAEEEF>- +@M01368:8:000000000-A3GHV:1:1111:8665:25542/1 +TCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTGTCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCG ++ +AA3AAFFFFFFFGGGFGFFGGGGHGH4AGGGFHHCGEE2FGHHHHHHHHHHGFHGF53FHEGGFAF5CFHHGGFGHFHHGGHHHCHHHHHHHFHHGH?EEEG1FFFEHHFHFGGHHGG?F4FBGHGHCHEF0//-9--;0CFGG?@BGDGFFFFEFBBBDA?FFBFFFF=B;-9.AA9EFFFF/;9BD.//;9/9/B:/:BFBFFBFFF/B:BFF//;/B/FFFBFF.A-BFFFBA/F//BFFFBF/;/A- +@M01368:8:000000000-A3GHV:1:1111:9655:13916/1 +GGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGCGGTGTCCACGCAATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA ++ +1>>1AAFFFFFBGGFE1EEEEGGHGHHH2FGHHHFGFGHGCFGGGEFHGGEGGHHHHGHEFBFEGHHHGHHBEHHHHGHGFHHHGGGGHHEGGGGHHHGFHGHHHH1FHHG?G/AGF1GBFGEFFHF2FDD0FG--99@=---AAABA-BF/B?A@F-9BBFF//BB/9/ +@M01368:8:000000000-A3GHV:1:1112:10272:7828/1 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTT ++ +AAABABBBBBBFGGGGGGGGGGHGHHGHGHHHHHHHHHGHHHGGHDGHHHGGGGHHHHHHHHHHHHHHHFHGHHHHGGHGGHHHFHHHHHCGHFFHHHHHHHHHHHHHGHGEFGAEEEEHHGHHGHGHHHHHHHGHHHHHHGHGHFFBC/BA?BGGGFFFFFFFFFFFFFFFC-@DDFFFFFFFEFAFFFFFFBFBFFFFFFFFFFFFFFFFBFF->@FFFFFFFFFFBFBFAD--.99;A?////:.9A. +@M01368:8:000000000-A3GHV:1:1112:9832:16531/1 +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGCTGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCTTGAAGTAGGAACC ++ +AABABFFFFFFFF4GGGGEBGEFGHGGHGHGHHHGGHFBGFGGGGGHHEFHGEHFHFHEHHHHHGCGGGHFHHCFGHE@1EEEFFGB?EEEEHBGGGCHHGHHBEE@>EAHHFAEBDGGGCEFF?CEGFFHHHHHFHHHFHGHCGCAHHF<..C.D=0CD.GFHHHG.CAGHC:CHB0GGGFFB0:CFA.A-;9.;000CBBFFBFGA.9AA;A;EDDE.ABBFFFF9;BEFFF/BF//9/B//9:B//.. +@M01368:8:000000000-A3GHV:1:1112:9832:6701/1 +CGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGA ++ +AABBBBFFFFFFGGGFGGGGGGHHHGGHGGHHHHHHHHHHHGHHGGGGGHHHHHHHHHHHHHHHHHHGGCGDHHHHFGGHHHGGGGGFGGHGGGGHHGGGGHHHHHHGGGGGGHHGGGGDGGFGHGGFCDCHHHHGHHHHGHHFAGFGGEHFGEG.C1>11F1D1DDFFFFGGG1FH3GHGHGHGHFHEC?EC0B1FBGFB1GHHH21AF2HH2FEGEHAE10AAE/>/FFHE?/E/?E1@EFFH?E@/EGGG//B11B//<@@C0F/<0AAAAFFFBFFFGGGGGGGGGGHHFHGHHHHGHHHHHHHHHHHGGGGHHHHFHHHHFHGHHHHGAFFEFHEGHHHHHHHHGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF +@M01368:8:000000000-A3GHV:1:1113:5741:16959/1 +TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA ++ +ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./B/..9.9:...////// +@M01368:8:000000000-A3GHV:1:1114:14540:5315/1 +CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT ++ +AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE. +@M01368:8:000000000-A3GHV:1:1114:15066:16302/1 +TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA ++ +BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/; +@M01368:8:000000000-A3GHV:1:1114:2404:13066/1 +TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC ++ +CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0 +@M01368:8:000000000-A3GHV:1:1114:9184:6959/1 +GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTTA ++ +AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF/