| Previous changeset 11:7594365c546b (2021-11-27) Next changeset 13:675488238c96 (2022-03-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" |
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modified:
macros.xml quast.xml test-data/test1_circos.png test-data/test1_report.html test-data/test2.log test-data/test2_circos.png test-data/test2_report.html test-data/test2_report.pdf test-data/test3.log test-data/test3_report.html test-data/test3_report.pdf |
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added:
test-data/pacbio_01.fasta.gz test-data/pacbio_02.fasta.gz test-data/pacbio_reads_01.fasta test-data/pacbio_reads_02.fasta test-data/test7.tab |
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| diff -r 7594365c546b -r 875d0f36d66f macros.xml --- a/macros.xml Sat Nov 27 09:45:20 2021 +0000 +++ b/macros.xml Sun Feb 06 21:02:38 2022 +0000 |
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| @@ -11,7 +11,7 @@ </xrefs> </xml> <token name="@TOOL_VERSION@">5.0.2</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <xml name="gene_thresholds"> <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/> </xml> @@ -23,4 +23,4 @@ <citation type="doi">10.1093/bioinformatics/btt086</citation> </citations> </xml> -</macros> \ No newline at end of file +</macros> |
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| diff -r 7594365c546b -r 875d0f36d66f quast.xml --- a/quast.xml Sat Nov 27 09:45:20 2021 +0000 +++ b/quast.xml Sun Feb 06 21:02:38 2022 +0000 |
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| @@ -190,29 +190,29 @@ <when value="disabled"/> <when value="single"> - <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" /> + <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> </when> <when value="paired"> - <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #1" /> - <param name="input_2" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #2" /> + <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" /> + <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" /> </when> <when value="paired_interlaced"> - <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" /> + <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> </when> <when value="mate_paired"> - <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #1" /> - <param name="input_2" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #2" /> + <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" /> + <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" /> </when> <when value="pacbio"> - <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" /> + <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> </when> <when value="nanopore"> - <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" /> + <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> </when> </conditional> @@ -413,7 +413,7 @@ </section> <param name="output_files" value="html"/> <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/> - <output name="circos_output" file="test1_circos.png" ftype="png"/> + <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/> </test> <!-- Test 02: all outputs --> <test expect_num_outputs="8"> @@ -590,6 +590,26 @@ <param name="output_files" value="tabular"/> <output name="quast_tabular" file="test6.tab" ftype="tabular"/> </test> + <!-- Test 7: FASTA.gz read files --> + <test expect_num_outputs="1"> + <conditional name="in"> + <param name="custom" value="true"/> + <repeat name="inputs"> + <param name="input" value="contigs1.fna"/> + <param name="labels" value="contig1"/> + </repeat> + <repeat name="inputs"> + <param name="input" value="contigs2.fna"/> + <param name="labels" value="contig2"/> + </repeat> + </conditional> + <conditional name="reads"> + <param name="reads_option" value="single"/> + <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> + </conditional> + <param name="output_files" value="tabular"/> + <output name="quast_tabular" file="test7.tab" ftype="tabular"/> + </test> </tests> <help> <![CDATA[ |
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| diff -r 7594365c546b -r 875d0f36d66f test-data/test1_report.html --- a/test-data/test1_report.html Sat Nov 27 09:45:20 2021 +0000 +++ b/test-data/test1_report.html Sun Feb 06 21:02:38 2022 +0000 |
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| b'@@ -4639,7 +4639,7 @@\n \n <div class=\'json-code\'>\n <div id=\'total-report-json\'>\n- {"date":"07 November 2021, Sunday, 18:58:22","assembliesNames":["contig1","contig2"],"referenceName":"dataset_bbcdda7d_c0d1_4db4_9a19_23f66480b75e","order":[0,1],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["71.579","100.000"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.000","1.000"],"isMain":true},{"metricName":"# genomic features","quality":"More is better","values":["7 + 7 part","13 + 1 part"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[2030,6650],"isMain":true},{"metricName":"Total aligned length","quality":"More is better","values":[4760,6650],"isMain":true},{"metricName":"NG50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"NG75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA50","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"NGA50","quality":"More is better","values":[1610,6650],"isMain":true},{"metricName":"NGA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"LG50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"LG75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA50","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA75","quality":"Less is better","values":[null,1],"isMain":false},{"metricName":"LGA50","quality":"Less is better","values":[2,1],"isMain":true},{"metricName":"LGA75","quality":"Less is better","values":[null,1],"isMain":false}]],["Reads mapping",[]],["Misassemblies",[{"metricName":"# misassemblies","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # relocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # translocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # inversions","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# misassembled contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Misassembled contigs length","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":"# local misassemblies","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap ext. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap loc. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# unaligned mis. contigs","quality":"Less is better","values":[0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Fully unaligned length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[1,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[1950,0],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# indels","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":f'..b',{"metricName":"Fully unaligned length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[1,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[1950,0],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# indels","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[{"metricName":"K-mer-based compl. (%)","quality":"More is better","values":["68.09","100.00"],"isMain":true},{"metricName":"K-mer-based cor. length (%)","quality":"More is better","values":["100.00","100.00"],"isMain":false},{"metricName":"K-mer-based mis. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"K-mer-based undef. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"# k-mer-based misjoins","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # k-mer-based translocations","quality":"Equal","values":[0,0],"isMain":false},{"metricName":" # k-mer-based 100kbp relocations","quality":"Equal","values":[0,0],"isMain":false}]],["Predicted genes",[{"metricName":"# predicted rRNA genes","quality":"More is better","values":["0 + 0 part","0 + 0 part"],"isMain":true}]],["Similarity statistics",[{"metricName":"# similar correct contigs","quality":"Equal","values":[0,0],"isMain":false},{"metricName":"# similar misassembled blocks","quality":"Equal","values":[0,0],"isMain":false}]],["Reference statistics",[{"metricName":"Reference length","quality":"Equal","values":[6650,6650],"isMain":false},{"metricName":"Reference fragments","quality":"Equal","values":[1,1],"isMain":false},{"metricName":"Reference GC (%)","quality":"Equal","values":["52.00","52.00"],"isMain":false},{"metricName":"Reference genomic features","quality":"Equal","values":[14,14],"isMain":false},{"metricName":"Reference operons","quality":"Equal","values":[0,0],"isMain":false}]]],"subreferences":[],"subreports":[],"minContig":500}\n </div>\n <div id=\'qualities-json\'>\n {{ qualities }}\n' |
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| diff -r 7594365c546b -r 875d0f36d66f test-data/test2.log --- a/test-data/test2.log Sat Nov 27 09:45:20 2021 +0000 +++ b/test-data/test2.log Sun Feb 06 21:02:38 2022 +0000 |
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| b"@@ -1,33 +1,34 @@\n-/usr/local/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmpfgnwy_vl/files/7/5/6/dataset_7567d03a-76ca-49a4-aaa2-334a7b5a8f74.dat --features /tmp/tmpfgnwy_vl/files/4/0/6/dataset_406c3bca-dfac-498b-954d-476186610bc9.dat --operons /tmp/tmpfgnwy_vl/files/e/5/8/dataset_e5851e9e-28d2-42f8-9a7a-0d05d0770635.dat --circos --k-mer-stats --k-mer-size 101 --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /tmp/tmpfgnwy_vl/files/2/3/b/dataset_23b499d4-cf8d-47a3-8ba1-906758c987bb.dat /tmp/tmpfgnwy_vl/files/b/3/5/dataset_b3571672-0e6e-4ff5-8e31-b7135a2d1bd6.dat --threads 1\n+/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmpmqu3v_ze/files/f/2/0/dataset_f20bc8a3-6ab5-43f7-a0a3-42dcc6408039.dat --features /tmp/tmpmqu3v_ze/files/2/a/f/dataset_2afd5bcc-2ff5-46bc-83cd-0690bcbd9c67.dat --operons /tmp/tmpmqu3v_ze/files/f/f/a/dataset_ffa07559-8af9-4a08-8719-807dc3575dc8.dat --circos --k-mer-stats --k-mer-size 101 --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --ambiguity-score 0.99 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /tmp/tmpmqu3v_ze/files/a/e/3/dataset_ae3fd171-9eb4-40d1-a8c8-d896fef3f293.dat /tmp/tmpmqu3v_ze/files/f/c/b/dataset_fcbec1fc-e7c4-42db-b9e4-7c32ac9882dd.dat --threads 1\n \n Version: 5.0.2\n \n System information:\n- OS: Linux-5.11.0-37-generic-x86_64-with-debian-10.9 (linux_64)\n+ OS: Linux-5.13.0-28-generic-x86_64-with-debian-bullseye-sid (linux_64)\n Python version: 3.7.12\n CPUs number: 8\n \n-Started: 2021-11-07 18:59:01\n+Started: 2022-02-06 19:54:35\n \n-Logging to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/quast.log\n+Logging to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/quast.log\n+NOTICE: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified\n \n-CWD: /tmp/tmpfgnwy_vl/job_working_directory/000/12/working\n+CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/12/working\n Main parameters: \n MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \\\n- ambiguity: one, threshold for extensive misassembly size: 1000\n+ ambiguity: all, threshold for extensive misassembly size: 1000\n \n Reference:\n- /tmp/tmpfgnwy_vl/files/7/5/6/dataset_7567d03a-76ca-49a4-aaa2-334a7b5a8f74.dat ==> dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74\n+ /tmp/tmpmqu3v_ze/files/f/2/0/dataset_f20bc8a3-6ab5-43f7-a0a3-42dcc6408039.dat ==> dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039\n \n Contigs:\n Pre-processing...\n- 1 /tmp/tmpfgnwy_vl/files/2/3/b/dataset_23b499d4-cf8d-47a3-8ba1-906758c987bb.dat ==> contig1\n- 2 /tmp/tmpfgnwy_vl/files/b/3/5/dataset_b3571672-0e6e-4ff5-8e31-b7135a2d1bd6.dat ==> contig2\n+ 1 /tmp/tmpmqu3v_ze/files/a/e/3/dataset_ae3fd171-9eb4-40d1-a8c8-d896fef3f293.dat ==> contig1\n+ 2 /tmp/tmpmqu3v_ze/files/f/c/b/dataset_fcbec1fc-e7c4-42db-b9e4-7c32ac9882dd.dat ==> contig2\n \n-2021-11-07 18:59:01\n+2022-02-06 19:54:39\n Running Basic statistics processor...\n Reference genome:\n- dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat, length = 6650, num fragments = 1, GC % = 52.00\n+ dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat, length = 6650, num fragments = 1, GC % = 52.00\n Contig files: \n 1 contig1\n 2 contig2\n@@ -35,164 +36,164 @@\n 1 contig1, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00\n 2 contig2, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00\n Drawing Nx plot...\n- saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf\n+ saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf\n Drawing NGx plot...\n- "..b'_vl/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf\n+ saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf\n Drawing genomic features FRCurve plot...\n- saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf\n+ saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf\n Drawing # complete genomic features histogram...\n- saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf\n+ saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf\n Drawing Genome fraction, % histogram...\n- saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf\n+ saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf\n Done.\n \n NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.\n \n-2021-11-07 18:59:05\n+2022-02-06 19:54:42\n Creating large visual summaries...\n This may take a while: press Ctrl-C to skip this step..\n 1 of 3: Creating Icarus viewers...\n 2 of 3: Creating Circos plot...\n-/usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \\\n-2> outputdir/circos/circos.err\n+/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/circos \\\n+-conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err\n 3 of 3: Creating PDF with all tables and plots...\n Done\n \n-2021-11-07 18:59:15\n+2022-02-06 19:54:46\n RESULTS:\n- Text versions of total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex\n- Text versions of transposed total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex\n- HTML version (interactive tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.html\n- PDF version (tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.pdf\n- Circos plot is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)\n- Icarus (contig browser) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/icarus.html\n- Log is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/quast.log\n+ Text versions of total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex\n+ Text versions of transposed total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex\n+ HTML version (interactive tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.html\n+ PDF version (tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.pdf\n+ Circos plot is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)\n+ Icarus (contig browser) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/icarus.html\n+ Log is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/quast.log\n \n-Finished: 2021-11-07 18:59:15\n-Elapsed time: 0:00:13.941680\n+Finished: 2022-02-06 19:54:46\n+Elapsed time: 0:00:11.313989\n NOTICEs: 3; WARNINGs: 3; non-fatal ERRORs: 0\n \n Thank you for using QUAST!\n' |
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| diff -r 7594365c546b -r 875d0f36d66f test-data/test2_report.html --- a/test-data/test2_report.html Sat Nov 27 09:45:20 2021 +0000 +++ b/test-data/test2_report.html Sun Feb 06 21:02:38 2022 +0000 |
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| b'@@ -4639,7 +4639,7 @@\n \n <div class=\'json-code\'>\n <div id=\'total-report-json\'>\n- {"date":"07 November 2021, Sunday, 18:59:15","assembliesNames":["contig1","contig2"],"referenceName":"dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74","order":[0,1],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["71.579","100.000"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.000","1.000"],"isMain":true},{"metricName":"# genomic features","quality":"More is better","values":["7 + 7 part","13 + 1 part"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[2030,6650],"isMain":true},{"metricName":"Total aligned length","quality":"More is better","values":[4760,6650],"isMain":true},{"metricName":"NG50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"NG75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA50","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"NGA50","quality":"More is better","values":[1610,6650],"isMain":true},{"metricName":"NGA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"LG50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"LG75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA50","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA75","quality":"Less is better","values":[null,1],"isMain":false},{"metricName":"LGA50","quality":"Less is better","values":[2,1],"isMain":true},{"metricName":"LGA75","quality":"Less is better","values":[null,1],"isMain":false}]],["Reads mapping",[]],["Misassemblies",[{"metricName":"# misassemblies","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # relocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # translocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # inversions","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# misassembled contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Misassembled contigs length","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":"# local misassemblies","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap ext. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap loc. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# unaligned mis. contigs","quality":"Less is better","values":[0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Fully unaligned length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[1,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[1950,0],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# indels","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":f'..b'}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Fully unaligned length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[1,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[1950,0],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# indels","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[{"metricName":"K-mer-based compl. (%)","quality":"More is better","values":["68.09","100.00"],"isMain":true},{"metricName":"K-mer-based cor. length (%)","quality":"More is better","values":["100.00","100.00"],"isMain":false},{"metricName":"K-mer-based mis. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"K-mer-based undef. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"# k-mer-based misjoins","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # k-mer-based translocations","quality":"Equal","values":[0,0],"isMain":false},{"metricName":" # k-mer-based 100kbp relocations","quality":"Equal","values":[0,0],"isMain":false}]],["Predicted genes",[]],["Similarity statistics",[{"metricName":"# similar correct contigs","quality":"Equal","values":[0,0],"isMain":false},{"metricName":"# similar misassembled blocks","quality":"Equal","values":[0,0],"isMain":false}]],["Reference statistics",[{"metricName":"Reference length","quality":"Equal","values":[6650,6650],"isMain":false},{"metricName":"Reference fragments","quality":"Equal","values":[1,1],"isMain":false},{"metricName":"Reference GC (%)","quality":"Equal","values":["52.00","52.00"],"isMain":false},{"metricName":"Reference genomic features","quality":"Equal","values":[14,14],"isMain":false},{"metricName":"Reference operons","quality":"Equal","values":[0,0],"isMain":false}]]],"subreferences":[],"subreports":[],"minContig":500}\n </div>\n <div id=\'qualities-json\'>\n {{ qualities }}\n' |
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| diff -r 7594365c546b -r 875d0f36d66f test-data/test3.log --- a/test-data/test3.log Sat Nov 27 09:45:20 2021 +0000 +++ b/test-data/test3.log Sun Feb 06 21:02:38 2022 +0000 |
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| @@ -1,27 +1,28 @@ -/usr/local/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs /tmp/tmpfgnwy_vl/files/7/8/2/dataset_78284ced-4f1f-4eb6-a4e0-97cb937c125a.dat /tmp/tmpfgnwy_vl/files/6/b/d/dataset_6bd1949d-014f-47ff-8b78-b609c6a19455.dat --threads 1 +/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --ambiguity-score 0.99 --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs /tmp/tmpmqu3v_ze/files/c/a/f/dataset_cafcd90b-16e7-46aa-8617-cdefd1766b23.dat /tmp/tmpmqu3v_ze/files/6/4/e/dataset_64ec6db4-a92f-4ec5-b641-96e96830b6b5.dat --threads 1 Version: 5.0.2 System information: - OS: Linux-5.11.0-37-generic-x86_64-with-debian-10.9 (linux_64) + OS: Linux-5.13.0-28-generic-x86_64-with-debian-bullseye-sid (linux_64) Python version: 3.7.12 CPUs number: 8 -Started: 2021-11-07 18:59:34 +Started: 2022-02-06 19:55:07 -Logging to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/quast.log +Logging to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/quast.log +NOTICE: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified -CWD: /tmp/tmpfgnwy_vl/job_working_directory/000/15/working +CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/15/working Main parameters: MODE: default, threads: 1, eukaryotic: true, minimum contig length: 500, minimum alignment length: 65, \ - ambiguity: one, threshold for extensive misassembly size: 1000 + ambiguity: all, threshold for extensive misassembly size: 1000 Contigs: Pre-processing... - 1 /tmp/tmpfgnwy_vl/files/7/8/2/dataset_78284ced-4f1f-4eb6-a4e0-97cb937c125a.dat ==> contigs1_fna - 2 /tmp/tmpfgnwy_vl/files/6/b/d/dataset_6bd1949d-014f-47ff-8b78-b609c6a19455.dat ==> contigs2_fna + 1 /tmp/tmpmqu3v_ze/files/c/a/f/dataset_cafcd90b-16e7-46aa-8617-cdefd1766b23.dat ==> contigs1_fna + 2 /tmp/tmpmqu3v_ze/files/6/4/e/dataset_64ec6db4-a92f-4ec5-b641-96e96830b6b5.dat ==> contigs2_fna -2021-11-07 18:59:34 +2022-02-06 19:55:10 Running Basic statistics processor... Contig files: 1 contigs1_fna @@ -30,37 +31,37 @@ 1 contigs1_fna, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 2 contigs2_fna, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 Drawing Nx plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf + saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf Drawing cumulative plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf + saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf + saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf Drawing contigs1_fna GC content plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf + saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf Drawing contigs2_fna GC content plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf + saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. -2021-11-07 18:59:35 +2022-02-06 19:55:11 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 2: Creating Icarus viewers... 2 of 2: Creating PDF with all tables and plots... Done -2021-11-07 18:59:36 +2022-02-06 19:55:12 RESULTS: - Text versions of total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex - Text versions of transposed total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex - HTML version (interactive tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/report.html - PDF version (tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/report.pdf - Icarus (contig browser) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/icarus.html - Log is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/quast.log + Text versions of total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex + Text versions of transposed total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex + HTML version (interactive tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.pdf + Icarus (contig browser) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/icarus.html + Log is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/quast.log -Finished: 2021-11-07 18:59:36 -Elapsed time: 0:00:02.245904 -NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 +Finished: 2022-02-06 19:55:12 +Elapsed time: 0:00:04.673393 +NOTICEs: 2; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST! |
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| @@ -4639,7 +4639,7 @@ <div class='json-code'> <div id='total-report-json'> - {"date":"07 November 2021, Sunday, 18:59:36","assembliesNames":["contigs1_fna","contigs2_fna"],"referenceName":"","order":[0,1],"report":[["Genome statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N's","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 500 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 500 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500} + {"date":"06 February 2022, Sunday, 19:55:12","assembliesNames":["contigs1_fna","contigs2_fna"],"referenceName":"","order":[0,1],"report":[["Genome statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N's","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 500 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 500 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500} </div> <div id='qualities-json'> {{ qualities }} |
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| diff -r 7594365c546b -r 875d0f36d66f test-data/test7.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test7.tab Sun Feb 06 21:02:38 2022 +0000 |
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| @@ -0,0 +1,21 @@ +Assembly contig1 contig2 +# contigs (>= 0 bp) 3 1 +# contigs (>= 1000 bp) 3 1 +Total length (>= 0 bp) 6710 6650 +Total length (>= 1000 bp) 6710 6650 +# contigs 3 1 +Largest contig 3980 6650 +Total length 6710 6650 +GC (%) 51.28 52.00 +N50 3980 6650 +N75 1610 6650 +L50 1 1 +L75 2 1 +# total reads 167 167 +# left 0 0 +# right 0 0 +Mapped (%) 2.4 2.4 +Properly paired (%) 0.0 0.0 +Avg. coverage depth 0 0 +Coverage >= 1x (%) 27.08 47.32 +# N's per 100 kbp 0.00 0.00 |
