Mercurial > repos > oinizan > frogs
changeset 6:192cac570229 draft
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.3.1 commit 90093162b8cfb3e75908323761f4ef246222abea"
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--- a/README.md Fri Jun 04 11:09:35 2021 +0000 +++ b/README.md Mon Jun 21 14:09:38 2021 +0000 @@ -6,7 +6,7 @@ Visit our web site : http://frogs.toulouse.inrae.fr/ -[](https://github.com/geraldinepascal/FROGS-wrappers/releases)[<img src="https://www.podcastscience.fm/wp-content/uploads/2017/12/deezer.png" width="5%" style="display: block; margin: auto;"/>](https://www.deezer.com/fr/playlist/5233843102?utm_source=deezer&utm_content=playlist-5233843102&utm_term=18632989_1545296531&utm_medium=web) +[](https://github.com/geraldinepascal/FROGS-wrappers/releases)[<img src="https://www.podcastscience.fm/wp-content/uploads/2017/12/deezer.png" width="5%" style="display: block; margin: auto;"/>](https://www.deezer.com/fr/playlist/5233843102?utm_source=deezer&utm_content=playlist-5233843102&utm_term=18632989_1545296531&utm_medium=web) @@ -50,41 +50,41 @@ We suppose that you installed FROGS in a specific section named `FROGS`. ``` -<section id="FROGS" name="FROGS" version=""> +<section id="FROGS_3.2.3.1" name="FROGS" version=""> - <label id="FROGS_OTU_toolshed_3.2.3" text="OTUs reconstruction" version="" /> + <label id="FROGS_OTU_toolshed_3.2.3.1" text="OTUs reconstruction" version="" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_demultiplex/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clustering/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_postprocess/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_stdBiom/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_tsv/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_tsv_to_biom/3.2.3" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_demultiplex/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clustering/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_postprocess/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_stdBiom/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_tsv/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_tsv_to_biom/3.2.3.1" /> - <label id="FROGSSTAT_Phyloseq_toolshed_3.2.3" text="OTUs structure and composition analysis" version="" /> + <label id="FROGSSTAT_Phyloseq_toolshed_3.2.3.1" text="OTUs structure and composition analysis" version="" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Import_Data/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Composition_Visualisation/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Alpha_Diversity/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Beta_Diversity/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Sample_Clustering/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Structure_Visualisation/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.2.3" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Import_Data/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Composition_Visualisation/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Alpha_Diversity/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Beta_Diversity/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Sample_Clustering/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Structure_Visualisation/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.2.3.1" /> - <label id="FROGSSTAT_DESeq_toolshed_3.2.3" text="Differential abundance analysis" version="" /> + <label id="FROGSSTAT_DESeq_toolshed_3.2.3.1" text="Differential abundance analysis" version="" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Preprocess/3.2.3" /> - <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Visualisation/3.2.3" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Preprocess/3.2.3.1" /> + <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Visualisation/3.2.3.1" /> </section> ```
--- a/RELEASE_NOTE.md Fri Jun 04 11:09:35 2021 +0000 +++ b/RELEASE_NOTE.md Mon Jun 21 14:09:38 2021 +0000 @@ -1,3 +1,13 @@ +# v3.2.3.1 [2021-06] + +This version still refers to FROGS_3.2.3 suit. + +## Modifications: + +* DESeq2 visualisation : correctly use the reference modality (in the tool conf pannel) as the expected modality2 in the deseq2_visualisation.py command line. Results were correct in the previous version but the reference condition was not the one precised by the user. + + + # v3.2.3 [2021-06] ## Modifications:
--- a/affiliation_OTU.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/affiliation_OTU.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="3.2.3"> +<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="3.2.3."> <description>Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/affiliation_filters.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/affiliation_filters.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_affiliation_filters" name="FROGS Affiliation Filters" version="3.2.3"> +<tool id="FROGS_affiliation_filters" name="FROGS Affiliation Filters" version="3.2.3.1"> <description>Filters OTUs on several affiliation criteria.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/affiliation_postprocess.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/affiliation_postprocess.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_affiliation_postprocess" name="FROGS Affiliation postprocess" version="3.2.3"> +<tool id="FROGS_affiliation_postprocess" name="FROGS Affiliation postprocess" version="3.2.3.1"> <description>Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/affiliations_stat.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/affiliations_stat.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="3.2.3"> +<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="3.2.3.1"> <description>Process some metrics on taxonomies.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/biom_to_stdBiom.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/biom_to_stdBiom.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="3.2.3"> +<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="3.2.3.1"> <description>Converts a FROGS BIOM in fully compatible BIOM.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/biom_to_tsv.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/biom_to_tsv.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_biom_to_tsv" name="FROGS BIOM to TSV" version="3.2.3"> +<tool id="FROGS_biom_to_tsv" name="FROGS BIOM to TSV" version="3.2.3.1"> <description>Converts a BIOM file in TSV file.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/clustering.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/clustering.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_clustering" name="FROGS Clustering swarm" version="3.2.3"> +<tool id="FROGS_clustering" name="FROGS Clustering swarm" version="3.2.3.1"> <description>Single-linkage clustering on sequences</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/clusters_stat.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/clusters_stat.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_clusters_stat" name="FROGS Clusters stat" version="3.2.3"> +<tool id="FROGS_clusters_stat" name="FROGS Clusters stat" version="3.2.3.1"> <description>Process some metrics on clusters.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/demultiplex.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/demultiplex.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_demultiplex" name="FROGS Demultiplex reads" version="3.2.3"> +<tool id="FROGS_demultiplex" name="FROGS Demultiplex reads" version="3.2.3.1"> <description>Attribute reads to samples in function of inner barcode.</description> <requirements> <requirement type="binary">perl</requirement>
--- a/deseq2_preprocess.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/deseq2_preprocess.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool name="FROGSSTAT DESeq2 Preprocess" id="FROGSSTAT_DESeq2_Preprocess" version="3.2.3"> +<tool name="FROGSSTAT DESeq2 Preprocess" id="FROGSSTAT_DESeq2_Preprocess" version="3.2.3.1"> <description>import a Phyloseq object and prepare it for DESeq2 differential abundance analysis </description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/deseq2_visualisation.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/deseq2_visualisation.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool name="FROGSTAT Deseq2 Visualisation" id="FROGSSTAT_DESeq2_Visualisation" version="3.2.3"> +<tool name="FROGSTAT Deseq2 Visualisation" id="FROGSSTAT_DESeq2_Visualisation" version="3.2.3.1"> <description>to extract and visualise differentially abundant OTUs</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement> @@ -56,10 +56,10 @@ <option value="quant">quantitative</option> </param> <when value="qual"> - <param type="text" name="mod1" label="Condition 1 considered as reference" help="One condition of the experimental variable (e.g. with)." optional="false" value="" size="20"> + <param type="text" name="mod2" label="Condition 1 considered as reference" help="One condition of the experimental variable (e.g. with)." optional="false" value="" size="20"> <validator type="empty_field" message="This parameter is required." /> </param> - <param type="text" name="mod2" label="Condition 2 to be compared to the reference" help="Another condition of the experimental variable (e.g. without)." optional="false" value="" size="20"> + <param type="text" name="mod1" label="Condition 2 to be compared to the reference" help="Another condition of the experimental variable (e.g. without)." optional="false" value="" size="20"> <validator type="empty_field" message="This parameter is required." /> </param> </when>
--- a/itsx.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/itsx.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_itsx" name="FROGS ITSx" version="3.2.3"> +<tool id="FROGS_itsx" name="FROGS ITSx" version="3.2.3.1"> <description>Extract the highly variable ITS1 and ITS2 subregions from ITS sequences.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/normalisation.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/normalisation.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="3.2.3"> +<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="3.2.3.1"> <description>Normalise OTUs abundance.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/otu_filters.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/otu_filters.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_OTU_filters" name="FROGS OTU Filters" version="3.2.3"> +<tool id="FROGS_OTU_filters" name="FROGS OTU Filters" version="3.2.3.1"> <description>Filters OTUs on several criteria.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/phyloseq_alpha_diversity.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/phyloseq_alpha_diversity.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.2.3"> +<tool name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.2.3.1"> <description>with richness plot</description> <requirements> <requirement type="package" version="3.2.">frogs</requirement>
--- a/phyloseq_beta_diversity.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/phyloseq_beta_diversity.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool name="FROGSSTAT Phyloseq Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="3.2.3"> +<tool name="FROGSSTAT Phyloseq Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="3.2.3.1"> <description>distance matrix</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/phyloseq_clustering.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/phyloseq_clustering.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="3.2.3"> +<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="3.2.3.1"> <description>of samples using different linkage methods</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/phyloseq_composition.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/phyloseq_composition.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="3.2.3"> +<tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="3.2.3.1"> <description>with bar plot and composition plot</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/phyloseq_import_data.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/phyloseq_import_data.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.2.3"> +<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.2.3.1"> <description>from 3 files: biomfile, samplefile, treefile </description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/phyloseq_manova.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/phyloseq_manova.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="3.2.3"> +<tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="3.2.3.1"> <description>perform Multivariate Analysis of Variance (MANOVA)</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/phyloseq_structure.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/phyloseq_structure.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool name="FROGSSTAT Phyloseq Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="3.2.3"> +<tool name="FROGSSTAT Phyloseq Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="3.2.3.1"> <description>with heatmap plot and ordination plot</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/preprocess.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/preprocess.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_preprocess" name="FROGS Pre-process" version="3.2.3"> +<tool id="FROGS_preprocess" name="FROGS Pre-process" version="3.2.3.1"> <description>merging, denoising and dereplication.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/remove_chimera.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/remove_chimera.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="3.2.3"> +<tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="3.2.3.1"> <description>Remove PCR chimera in each sample.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-flash.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,335 @@ +## Application +Software: preprocess.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/preprocess.py illumina --min-amplicon-size 44 --max-amplicon-size 490 --five-prim-primer GGCGVACGGGTGAGTAA --three-prim-primer GTGCCAGCNGCNGCGG --R1-size 267 --R2-size 266 --expected-amplicon-size 420 --merge-software flash --nb-cpus 2 --mismatch-rate 0.15 --keep-unmerged --input-archive data/test_dataset2.tar.gz --output-dereplicated res_3.2.3/01-prepro-flash.fasta --output-count res_3.2.3/01-prepro-flash.tsv --summary res_3.2.3/01-prepro-flash.html --log-file res_3.2.3/01-prepro-flash.log + +## Application +Software: preprocess.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/preprocess.py illumina --min-amplicon-size 44 --max-amplicon-size 490 --five-prim-primer GGCGVACGGGTGAGTAA --three-prim-primer GTGCCAGCNGCNGCGG --R1-size 267 --R2-size 266 --expected-amplicon-size 420 --merge-software flash --nb-cpus 2 --mismatch-rate 0.15 --keep-unmerged --input-archive /test/data/test_dataset.tar.gz --output-dereplicated res_3.2.3/01-prepro-flash.fasta --output-count res_3.2.3/01-prepro-flash.tsv --summary res_3.2.3/01-prepro-flash.html --log-file res_3.2.3/01-prepro-flash.log + +## Application +Software: preprocess.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/preprocess.py illumina --min-amplicon-size 44 --max-amplicon-size 490 --five-prim-primer GGCGVACGGGTGAGTAA --three-prim-primer GTGCCAGCNGCNGCGG --R1-size 267 --R2-size 266 --expected-amplicon-size 420 --merge-software flash --nb-cpus 2 --mismatch-rate 0.15 --keep-unmerged --input-archive data/test_dataset.tar.gz --output-dereplicated res_3.2.3/01-prepro-flash.fasta --output-count res_3.2.3/01-prepro-flash.tsv --summary res_3.2.3/01-prepro-flash.html --log-file res_3.2.3/01-prepro-flash.log + + +##Sample +R1 : res_3.2.3/1622730611.4716644_32639_01_subsample_R1.fastq.gz +R2 : res_3.2.3/1622730611.4716644_32639_01_subsample_R2.fastq.gz +Sample name : 01_subsample +nb seq before process : 50000 +##Commands +######################################################################################################## +# Join overlapping paired reads. (flash version : v1.2.11) +Command: + flash --threads 1 --allow-outies --min-overlap 43 --max-overlap 133 --max-mismatch-density 0.15 --compress res_3.2.3/1622730611.4716644_32639_01_subsample_R1.fastq.gz res_3.2.3/1622730611.4716644_32639_01_subsample_R2.fastq.gz --output-directory res_3.2.3 --output-prefix 1622730611.8620374_32640_01_subsample_flash 2> res_3.2.3/1622730611.8620374_32640_01_subsample_flash.stderr + +Execution: + start: 03 Jun 2021 16:30:12 + end: 03 Jun 2021 16:30:17 + +Results: + nb seq paired-end assembled: 29070 +######################################################################################################## +# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.3/1622730611.8620374_32640_01_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.3/1622730611.8620374_32640_01_subsample_flash.extendedFrags.fastq.gz > res_3.2.3/1622730611.8620374_32640_01_subsample_cutadapt_5prim_log.txt 2> res_3.2.3/1622730611.8620374_32640_01_subsample_cutadapt_5prim_err.txt + +Execution: + start: 03 Jun 2021 16:30:18 + end: 03 Jun 2021 16:30:21 + +Results: + nb seq with 5' primer : 29070 +######################################################################################################## +# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.3/1622730611.8620374_32640_01_subsample_cutadapt.fastq.gz res_3.2.3/1622730611.8620374_32640_01_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.3/1622730611.8620374_32640_01_subsample_cutadapt_3prim_log.txt 2> res_3.2.3/1622730611.8620374_32640_01_subsample_cutadapt_3prim_err.txt + +Execution: + start: 03 Jun 2021 16:30:21 + end: 03 Jun 2021 16:30:24 + +Results: + nb seq with 3' primer : 29070 +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.3/1622730611.8620374_32640_01_subsample_cutadapt.fastq.gz --output-file res_3.2.3/1622730611.8620374_32640_01_subsample_N_and_length_filter.fasta --log-file res_3.2.3/1622730611.8620374_32640_01_subsample_N_and_length_filter_log.txt + +Execution: + start: 03 Jun 2021 16:30:25 + end: 03 Jun 2021 16:30:25 + +Results: + nb seq with expected length : 29070 + nb seq without N : 29070 +######################################################################################################## +# Removes read pairs without the 5' and 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.3/1622730611.8620374_32640_01_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.3/1622730611.8620374_32640_01_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.3/1622730611.8620374_32640_01_subsample_flash.notCombined_1.fastq.gz res_3.2.3/1622730611.8620374_32640_01_subsample_flash.notCombined_2.fastq.gz > res_3.2.3/1622730611.8620374_32640_01_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.3/1622730611.8620374_32640_01_subsample_uncomb_cutadapt_paired_err.txt + +Execution: + start: 03 Jun 2021 16:30:26 + end: 03 Jun 2021 16:30:29 + +Results: + nb seq with 5' primer : 20930 + nb seq with 3' primer : 20930 +######################################################################################################## +# Concatenate paired reads. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730611.8620374_32640_01_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.3/1622730611.8620374_32640_01_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.3/1622730611.8620374_32640_01_subsample_artificial_combined.fastq.gz + +Execution: + start: 03 Jun 2021 16:30:29 + end: 03 Jun 2021 16:30:38 + +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.3/1622730611.8620374_32640_01_subsample_artificial_combined.fastq.gz --output-file res_3.2.3/1622730611.8620374_32640_01_subsample_art_N_filter.fasta --log-file res_3.2.3/1622730611.8620374_32640_01_subsample_art_N_filter_log.txt + +Execution: + start: 03 Jun 2021 16:30:38 + end: 03 Jun 2021 16:30:39 + +Results: + nb seq with expected length : 20930 + nb seq without N : 20930 +######################################################################################################## +# Replace join tag. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730611.8620374_32640_01_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.3/1622730611.8620374_32640_01_subsample_art_XtoN.fasta + +Execution: + start: 03 Jun 2021 16:30:39 + end: 03 Jun 2021 16:30:40 + +######################################################################################################## +# Dereplicates sample sequences. (derepSamples.py version : 1.6.1) +Command: + derepSamples.py --sequences-files res_3.2.3/1622730611.8620374_32640_01_subsample_N_and_length_filter.fasta res_3.2.3/1622730611.8620374_32640_01_subsample_art_XtoN.fasta --dereplicated-file res_3.2.3/1622730611.4716644_32639_01_subsample_filtered.fasta --count-file res_3.2.3/1622730611.8620374_32640_01_subsample_derep_count.tsv + +Execution: + start: 03 Jun 2021 16:30:40 + end: 03 Jun 2021 16:30:42 + + +##Sample +R1 : res_3.2.3/1622730611.4716644_32639_02_subsample_R1.fastq.gz +R2 : res_3.2.3/1622730611.4716644_32639_02_subsample_R2.fastq.gz +Sample name : 02_subsample +nb seq before process : 50000 +##Commands +######################################################################################################## +# Join overlapping paired reads. (flash version : v1.2.11) +Command: + flash --threads 1 --allow-outies --min-overlap 43 --max-overlap 133 --max-mismatch-density 0.15 --compress res_3.2.3/1622730611.4716644_32639_02_subsample_R1.fastq.gz res_3.2.3/1622730611.4716644_32639_02_subsample_R2.fastq.gz --output-directory res_3.2.3 --output-prefix 1622730611.8628595_32641_02_subsample_flash 2> res_3.2.3/1622730611.8628595_32641_02_subsample_flash.stderr + +Execution: + start: 03 Jun 2021 16:30:12 + end: 03 Jun 2021 16:30:17 + +Results: + nb seq paired-end assembled: 29180 +######################################################################################################## +# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.3/1622730611.8628595_32641_02_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.3/1622730611.8628595_32641_02_subsample_flash.extendedFrags.fastq.gz > res_3.2.3/1622730611.8628595_32641_02_subsample_cutadapt_5prim_log.txt 2> res_3.2.3/1622730611.8628595_32641_02_subsample_cutadapt_5prim_err.txt + +Execution: + start: 03 Jun 2021 16:30:18 + end: 03 Jun 2021 16:30:21 + +Results: + nb seq with 5' primer : 29180 +######################################################################################################## +# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.3/1622730611.8628595_32641_02_subsample_cutadapt.fastq.gz res_3.2.3/1622730611.8628595_32641_02_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.3/1622730611.8628595_32641_02_subsample_cutadapt_3prim_log.txt 2> res_3.2.3/1622730611.8628595_32641_02_subsample_cutadapt_3prim_err.txt + +Execution: + start: 03 Jun 2021 16:30:21 + end: 03 Jun 2021 16:30:24 + +Results: + nb seq with 3' primer : 29180 +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.3/1622730611.8628595_32641_02_subsample_cutadapt.fastq.gz --output-file res_3.2.3/1622730611.8628595_32641_02_subsample_N_and_length_filter.fasta --log-file res_3.2.3/1622730611.8628595_32641_02_subsample_N_and_length_filter_log.txt + +Execution: + start: 03 Jun 2021 16:30:25 + end: 03 Jun 2021 16:30:25 + +Results: + nb seq with expected length : 29180 + nb seq without N : 29180 +######################################################################################################## +# Removes read pairs without the 5' and 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.3/1622730611.8628595_32641_02_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.3/1622730611.8628595_32641_02_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.3/1622730611.8628595_32641_02_subsample_flash.notCombined_1.fastq.gz res_3.2.3/1622730611.8628595_32641_02_subsample_flash.notCombined_2.fastq.gz > res_3.2.3/1622730611.8628595_32641_02_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.3/1622730611.8628595_32641_02_subsample_uncomb_cutadapt_paired_err.txt + +Execution: + start: 03 Jun 2021 16:30:26 + end: 03 Jun 2021 16:30:29 + +Results: + nb seq with 5' primer : 20820 + nb seq with 3' primer : 20820 +######################################################################################################## +# Concatenate paired reads. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730611.8628595_32641_02_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.3/1622730611.8628595_32641_02_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.3/1622730611.8628595_32641_02_subsample_artificial_combined.fastq.gz + +Execution: + start: 03 Jun 2021 16:30:29 + end: 03 Jun 2021 16:30:39 + +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.3/1622730611.8628595_32641_02_subsample_artificial_combined.fastq.gz --output-file res_3.2.3/1622730611.8628595_32641_02_subsample_art_N_filter.fasta --log-file res_3.2.3/1622730611.8628595_32641_02_subsample_art_N_filter_log.txt + +Execution: + start: 03 Jun 2021 16:30:39 + end: 03 Jun 2021 16:30:40 + +Results: + nb seq with expected length : 20820 + nb seq without N : 20820 +######################################################################################################## +# Replace join tag. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730611.8628595_32641_02_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.3/1622730611.8628595_32641_02_subsample_art_XtoN.fasta + +Execution: + start: 03 Jun 2021 16:30:40 + end: 03 Jun 2021 16:30:41 + +######################################################################################################## +# Dereplicates sample sequences. (derepSamples.py version : 1.6.1) +Command: + derepSamples.py --sequences-files res_3.2.3/1622730611.8628595_32641_02_subsample_N_and_length_filter.fasta res_3.2.3/1622730611.8628595_32641_02_subsample_art_XtoN.fasta --dereplicated-file res_3.2.3/1622730611.4716644_32639_02_subsample_filtered.fasta --count-file res_3.2.3/1622730611.8628595_32641_02_subsample_derep_count.tsv + +Execution: + start: 03 Jun 2021 16:30:41 + end: 03 Jun 2021 16:30:43 + + +##Sample +R1 : res_3.2.3/1622730611.4716644_32639_03_subsample_R1.fastq.gz +R2 : res_3.2.3/1622730611.4716644_32639_03_subsample_R2.fastq.gz +Sample name : 03_subsample +nb seq before process : 50000 +##Commands +######################################################################################################## +# Join overlapping paired reads. (flash version : v1.2.11) +Command: + flash --threads 1 --allow-outies --min-overlap 43 --max-overlap 133 --max-mismatch-density 0.15 --compress res_3.2.3/1622730611.4716644_32639_03_subsample_R1.fastq.gz res_3.2.3/1622730611.4716644_32639_03_subsample_R2.fastq.gz --output-directory res_3.2.3 --output-prefix 1622730642.8083694_32640_03_subsample_flash 2> res_3.2.3/1622730642.8083694_32640_03_subsample_flash.stderr + +Execution: + start: 03 Jun 2021 16:30:43 + end: 03 Jun 2021 16:30:46 + +Results: + nb seq paired-end assembled: 29149 +######################################################################################################## +# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.3/1622730642.8083694_32640_03_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.3/1622730642.8083694_32640_03_subsample_flash.extendedFrags.fastq.gz > res_3.2.3/1622730642.8083694_32640_03_subsample_cutadapt_5prim_log.txt 2> res_3.2.3/1622730642.8083694_32640_03_subsample_cutadapt_5prim_err.txt + +Execution: + start: 03 Jun 2021 16:30:47 + end: 03 Jun 2021 16:30:49 + +Results: + nb seq with 5' primer : 29149 +######################################################################################################## +# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.3/1622730642.8083694_32640_03_subsample_cutadapt.fastq.gz res_3.2.3/1622730642.8083694_32640_03_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.3/1622730642.8083694_32640_03_subsample_cutadapt_3prim_log.txt 2> res_3.2.3/1622730642.8083694_32640_03_subsample_cutadapt_3prim_err.txt + +Execution: + start: 03 Jun 2021 16:30:49 + end: 03 Jun 2021 16:30:52 + +Results: + nb seq with 3' primer : 29149 +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.3/1622730642.8083694_32640_03_subsample_cutadapt.fastq.gz --output-file res_3.2.3/1622730642.8083694_32640_03_subsample_N_and_length_filter.fasta --log-file res_3.2.3/1622730642.8083694_32640_03_subsample_N_and_length_filter_log.txt + +Execution: + start: 03 Jun 2021 16:30:52 + end: 03 Jun 2021 16:30:53 + +Results: + nb seq with expected length : 29149 + nb seq without N : 29149 +######################################################################################################## +# Removes read pairs without the 5' and 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.3/1622730642.8083694_32640_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.3/1622730642.8083694_32640_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.3/1622730642.8083694_32640_03_subsample_flash.notCombined_1.fastq.gz res_3.2.3/1622730642.8083694_32640_03_subsample_flash.notCombined_2.fastq.gz > res_3.2.3/1622730642.8083694_32640_03_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.3/1622730642.8083694_32640_03_subsample_uncomb_cutadapt_paired_err.txt + +Execution: + start: 03 Jun 2021 16:30:54 + end: 03 Jun 2021 16:30:57 + +Results: + nb seq with 5' primer : 20851 + nb seq with 3' primer : 20851 +######################################################################################################## +# Concatenate paired reads. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730642.8083694_32640_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.3/1622730642.8083694_32640_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.3/1622730642.8083694_32640_03_subsample_artificial_combined.fastq.gz + +Execution: + start: 03 Jun 2021 16:30:57 + end: 03 Jun 2021 16:31:06 + +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.3/1622730642.8083694_32640_03_subsample_artificial_combined.fastq.gz --output-file res_3.2.3/1622730642.8083694_32640_03_subsample_art_N_filter.fasta --log-file res_3.2.3/1622730642.8083694_32640_03_subsample_art_N_filter_log.txt + +Execution: + start: 03 Jun 2021 16:31:06 + end: 03 Jun 2021 16:31:06 + +Results: + nb seq with expected length : 20851 + nb seq without N : 20851 +######################################################################################################## +# Replace join tag. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730642.8083694_32640_03_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.3/1622730642.8083694_32640_03_subsample_art_XtoN.fasta + +Execution: + start: 03 Jun 2021 16:31:06 + end: 03 Jun 2021 16:31:07 + +######################################################################################################## +# Dereplicates sample sequences. (derepSamples.py version : 1.6.1) +Command: + derepSamples.py --sequences-files res_3.2.3/1622730642.8083694_32640_03_subsample_N_and_length_filter.fasta res_3.2.3/1622730642.8083694_32640_03_subsample_art_XtoN.fasta --dereplicated-file res_3.2.3/1622730611.4716644_32639_03_subsample_filtered.fasta --count-file res_3.2.3/1622730642.8083694_32640_03_subsample_derep_count.tsv + +Execution: + start: 03 Jun 2021 16:31:07 + end: 03 Jun 2021 16:31:09 + + + +##Sample +All +##Commands +######################################################################################################## +# Dereplicates together sequences from several samples. (derepSamples.py version : 1.6.1) +Command: + derepSamples.py --nb-cpus 2 --size-separator ';size=' --samples-ref res_3.2.3/1622730611.4716644_32639_derep_inputs.tsv --dereplicated-file res_3.2.3/01-prepro-flash.fasta --count-file res_3.2.3/01-prepro-flash.tsv + +Execution: + start: 03 Jun 2021 16:31:09 + end: 03 Jun 2021 16:31:13 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-vsearch.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,327 @@ +## Application +Software: preprocess.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/preprocess.py illumina --min-amplicon-size 44 --max-amplicon-size 490 --five-prim-primer GGCGVACGGGTGAGTAA --three-prim-primer GTGCCAGCNGCNGCGG --R1-size 267 --R2-size 266 --merge-software vsearch --nb-cpus 2 --mismatch-rate 0.15 --keep-unmerged --input-archive data/test_dataset.tar.gz --output-dereplicated res_3.2.3/01-prepro-vsearch.fasta --output-count res_3.2.3/01-prepro-vsearch.tsv --summary res_3.2.3/01-prepro-vsearch.html --log-file res_3.2.3/01-prepro-vsearch.log + + +##Sample +R1 : res_3.2.3/1622730673.3474987_323_01_subsample_R1.fastq.gz +R2 : res_3.2.3/1622730673.3474987_323_01_subsample_R2.fastq.gz +Sample name : 01_subsample +nb seq before process : 50000 +##Commands +######################################################################################################## +# join overlapping paired reads (vsearch version : v2.17.0_linux_x86_64) +Command: + vsearch --threads 1 --fastq_mergepairs res_3.2.3/1622730673.3474987_323_01_subsample_R1.fastq.gz --reverse res_3.2.3/1622730673.3474987_323_01_subsample_R2.fastq.gz --fastqout res_3.2.3/1622730673.528893_324_01_subsample_vsearch.assembled.fastq --fastqout_notmerged_fwd res_3.2.3/1622730673.528893_324_01_subsample_vsearch.unassembled_R1.fastq --fastqout_notmerged_rev res_3.2.3/1622730673.528893_324_01_subsample_vsearch.unassembled_R2.fastq --fastq_allowmergestagger --fastq_ascii 33 --fastq_maxdiffpct 15.0 --fastq_minovlen 43 2> res_3.2.3/1622730673.528893_324_01_subsample_vsearch.log + +Execution: + start: 03 Jun 2021 16:31:14 + end: 03 Jun 2021 16:31:16 + +Results: + nb seq paired-end assembled: 24402 +######################################################################################################## +# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.3/1622730673.528893_324_01_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.3/1622730673.528893_324_01_subsample_vsearch.assembled.fastq > res_3.2.3/1622730673.528893_324_01_subsample_cutadapt_5prim_log.txt 2> res_3.2.3/1622730673.528893_324_01_subsample_cutadapt_5prim_err.txt + +Execution: + start: 03 Jun 2021 16:31:16 + end: 03 Jun 2021 16:31:18 + +Results: + nb seq with 5' primer : 24402 +######################################################################################################## +# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.3/1622730673.528893_324_01_subsample_cutadapt.fastq.gz res_3.2.3/1622730673.528893_324_01_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.3/1622730673.528893_324_01_subsample_cutadapt_3prim_log.txt 2> res_3.2.3/1622730673.528893_324_01_subsample_cutadapt_3prim_err.txt + +Execution: + start: 03 Jun 2021 16:31:19 + end: 03 Jun 2021 16:31:21 + +Results: + nb seq with 3' primer : 24402 +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.3/1622730673.528893_324_01_subsample_cutadapt.fastq.gz --output-file res_3.2.3/1622730673.528893_324_01_subsample_N_and_length_filter.fasta --log-file res_3.2.3/1622730673.528893_324_01_subsample_N_and_length_filter_log.txt + +Execution: + start: 03 Jun 2021 16:31:21 + end: 03 Jun 2021 16:31:22 + +Results: + nb seq with expected length : 24402 + nb seq without N : 24402 +######################################################################################################## +# Removes read pairs without the 5' and 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.3/1622730673.528893_324_01_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.3/1622730673.528893_324_01_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.3/1622730673.528893_324_01_subsample_vsearch.unassembled_R1.fastq res_3.2.3/1622730673.528893_324_01_subsample_vsearch.unassembled_R2.fastq > res_3.2.3/1622730673.528893_324_01_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.3/1622730673.528893_324_01_subsample_uncomb_cutadapt_paired_err.txt + +Execution: + start: 03 Jun 2021 16:31:23 + end: 03 Jun 2021 16:31:28 + +Results: + nb seq with 5' primer : 25598 + nb seq with 3' primer : 25598 +######################################################################################################## +# Concatenate paired reads. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730673.528893_324_01_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.3/1622730673.528893_324_01_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.3/1622730673.528893_324_01_subsample_artificial_combined.fastq.gz + +Execution: + start: 03 Jun 2021 16:31:28 + end: 03 Jun 2021 16:31:40 + +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.3/1622730673.528893_324_01_subsample_artificial_combined.fastq.gz --output-file res_3.2.3/1622730673.528893_324_01_subsample_art_N_filter.fasta --log-file res_3.2.3/1622730673.528893_324_01_subsample_art_N_filter_log.txt + +Execution: + start: 03 Jun 2021 16:31:40 + end: 03 Jun 2021 16:31:41 + +Results: + nb seq with expected length : 25598 + nb seq without N : 25598 +######################################################################################################## +# Replace join tag. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730673.528893_324_01_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.3/1622730673.528893_324_01_subsample_art_XtoN.fasta + +Execution: + start: 03 Jun 2021 16:31:41 + end: 03 Jun 2021 16:31:43 + +######################################################################################################## +# Dereplicates sample sequences. (derepSamples.py version : 1.6.1) +Command: + derepSamples.py --sequences-files res_3.2.3/1622730673.528893_324_01_subsample_N_and_length_filter.fasta res_3.2.3/1622730673.528893_324_01_subsample_art_XtoN.fasta --dereplicated-file res_3.2.3/1622730673.3474987_323_01_subsample_filtered.fasta --count-file res_3.2.3/1622730673.528893_324_01_subsample_derep_count.tsv + +Execution: + start: 03 Jun 2021 16:31:43 + end: 03 Jun 2021 16:31:45 + + +##Sample +R1 : res_3.2.3/1622730673.3474987_323_02_subsample_R1.fastq.gz +R2 : res_3.2.3/1622730673.3474987_323_02_subsample_R2.fastq.gz +Sample name : 02_subsample +nb seq before process : 50000 +##Commands +######################################################################################################## +# join overlapping paired reads (vsearch version : v2.17.0_linux_x86_64) +Command: + vsearch --threads 1 --fastq_mergepairs res_3.2.3/1622730673.3474987_323_02_subsample_R1.fastq.gz --reverse res_3.2.3/1622730673.3474987_323_02_subsample_R2.fastq.gz --fastqout res_3.2.3/1622730673.530438_325_02_subsample_vsearch.assembled.fastq --fastqout_notmerged_fwd res_3.2.3/1622730673.530438_325_02_subsample_vsearch.unassembled_R1.fastq --fastqout_notmerged_rev res_3.2.3/1622730673.530438_325_02_subsample_vsearch.unassembled_R2.fastq --fastq_allowmergestagger --fastq_ascii 33 --fastq_maxdiffpct 15.0 --fastq_minovlen 43 2> res_3.2.3/1622730673.530438_325_02_subsample_vsearch.log + +Execution: + start: 03 Jun 2021 16:31:14 + end: 03 Jun 2021 16:31:16 + +Results: + nb seq paired-end assembled: 24590 +######################################################################################################## +# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.3/1622730673.530438_325_02_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.3/1622730673.530438_325_02_subsample_vsearch.assembled.fastq > res_3.2.3/1622730673.530438_325_02_subsample_cutadapt_5prim_log.txt 2> res_3.2.3/1622730673.530438_325_02_subsample_cutadapt_5prim_err.txt + +Execution: + start: 03 Jun 2021 16:31:16 + end: 03 Jun 2021 16:31:18 + +Results: + nb seq with 5' primer : 24590 +######################################################################################################## +# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.3/1622730673.530438_325_02_subsample_cutadapt.fastq.gz res_3.2.3/1622730673.530438_325_02_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.3/1622730673.530438_325_02_subsample_cutadapt_3prim_log.txt 2> res_3.2.3/1622730673.530438_325_02_subsample_cutadapt_3prim_err.txt + +Execution: + start: 03 Jun 2021 16:31:19 + end: 03 Jun 2021 16:31:21 + +Results: + nb seq with 3' primer : 24590 +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.3/1622730673.530438_325_02_subsample_cutadapt.fastq.gz --output-file res_3.2.3/1622730673.530438_325_02_subsample_N_and_length_filter.fasta --log-file res_3.2.3/1622730673.530438_325_02_subsample_N_and_length_filter_log.txt + +Execution: + start: 03 Jun 2021 16:31:21 + end: 03 Jun 2021 16:31:22 + +Results: + nb seq with expected length : 24590 + nb seq without N : 24590 +######################################################################################################## +# Removes read pairs without the 5' and 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.3/1622730673.530438_325_02_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.3/1622730673.530438_325_02_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.3/1622730673.530438_325_02_subsample_vsearch.unassembled_R1.fastq res_3.2.3/1622730673.530438_325_02_subsample_vsearch.unassembled_R2.fastq > res_3.2.3/1622730673.530438_325_02_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.3/1622730673.530438_325_02_subsample_uncomb_cutadapt_paired_err.txt + +Execution: + start: 03 Jun 2021 16:31:23 + end: 03 Jun 2021 16:31:28 + +Results: + nb seq with 5' primer : 25410 + nb seq with 3' primer : 25410 +######################################################################################################## +# Concatenate paired reads. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730673.530438_325_02_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.3/1622730673.530438_325_02_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.3/1622730673.530438_325_02_subsample_artificial_combined.fastq.gz + +Execution: + start: 03 Jun 2021 16:31:28 + end: 03 Jun 2021 16:31:39 + +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.3/1622730673.530438_325_02_subsample_artificial_combined.fastq.gz --output-file res_3.2.3/1622730673.530438_325_02_subsample_art_N_filter.fasta --log-file res_3.2.3/1622730673.530438_325_02_subsample_art_N_filter_log.txt + +Execution: + start: 03 Jun 2021 16:31:39 + end: 03 Jun 2021 16:31:40 + +Results: + nb seq with expected length : 25410 + nb seq without N : 25410 +######################################################################################################## +# Replace join tag. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730673.530438_325_02_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.3/1622730673.530438_325_02_subsample_art_XtoN.fasta + +Execution: + start: 03 Jun 2021 16:31:40 + end: 03 Jun 2021 16:31:42 + +######################################################################################################## +# Dereplicates sample sequences. (derepSamples.py version : 1.6.1) +Command: + derepSamples.py --sequences-files res_3.2.3/1622730673.530438_325_02_subsample_N_and_length_filter.fasta res_3.2.3/1622730673.530438_325_02_subsample_art_XtoN.fasta --dereplicated-file res_3.2.3/1622730673.3474987_323_02_subsample_filtered.fasta --count-file res_3.2.3/1622730673.530438_325_02_subsample_derep_count.tsv + +Execution: + start: 03 Jun 2021 16:31:42 + end: 03 Jun 2021 16:31:44 + + +##Sample +R1 : res_3.2.3/1622730673.3474987_323_03_subsample_R1.fastq.gz +R2 : res_3.2.3/1622730673.3474987_323_03_subsample_R2.fastq.gz +Sample name : 03_subsample +nb seq before process : 50000 +##Commands +######################################################################################################## +# join overlapping paired reads (vsearch version : v2.17.0_linux_x86_64) +Command: + vsearch --threads 1 --fastq_mergepairs res_3.2.3/1622730673.3474987_323_03_subsample_R1.fastq.gz --reverse res_3.2.3/1622730673.3474987_323_03_subsample_R2.fastq.gz --fastqout res_3.2.3/1622730705.6637666_324_03_subsample_vsearch.assembled.fastq --fastqout_notmerged_fwd res_3.2.3/1622730705.6637666_324_03_subsample_vsearch.unassembled_R1.fastq --fastqout_notmerged_rev res_3.2.3/1622730705.6637666_324_03_subsample_vsearch.unassembled_R2.fastq --fastq_allowmergestagger --fastq_ascii 33 --fastq_maxdiffpct 15.0 --fastq_minovlen 43 2> res_3.2.3/1622730705.6637666_324_03_subsample_vsearch.log + +Execution: + start: 03 Jun 2021 16:31:46 + end: 03 Jun 2021 16:31:47 + +Results: + nb seq paired-end assembled: 24543 +######################################################################################################## +# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.3/1622730705.6637666_324_03_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.3/1622730705.6637666_324_03_subsample_vsearch.assembled.fastq > res_3.2.3/1622730705.6637666_324_03_subsample_cutadapt_5prim_log.txt 2> res_3.2.3/1622730705.6637666_324_03_subsample_cutadapt_5prim_err.txt + +Execution: + start: 03 Jun 2021 16:31:48 + end: 03 Jun 2021 16:31:49 + +Results: + nb seq with 5' primer : 24543 +######################################################################################################## +# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.3/1622730705.6637666_324_03_subsample_cutadapt.fastq.gz res_3.2.3/1622730705.6637666_324_03_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.3/1622730705.6637666_324_03_subsample_cutadapt_3prim_log.txt 2> res_3.2.3/1622730705.6637666_324_03_subsample_cutadapt_3prim_err.txt + +Execution: + start: 03 Jun 2021 16:31:50 + end: 03 Jun 2021 16:31:52 + +Results: + nb seq with 3' primer : 24543 +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.3/1622730705.6637666_324_03_subsample_cutadapt.fastq.gz --output-file res_3.2.3/1622730705.6637666_324_03_subsample_N_and_length_filter.fasta --log-file res_3.2.3/1622730705.6637666_324_03_subsample_N_and_length_filter_log.txt + +Execution: + start: 03 Jun 2021 16:31:53 + end: 03 Jun 2021 16:31:53 + +Results: + nb seq with expected length : 24543 + nb seq without N : 24543 +######################################################################################################## +# Removes read pairs without the 5' and 3' primer and removes primer sequence. (cutadapt version : 2.10) +Command: + cutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.3/1622730705.6637666_324_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.3/1622730705.6637666_324_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.3/1622730705.6637666_324_03_subsample_vsearch.unassembled_R1.fastq res_3.2.3/1622730705.6637666_324_03_subsample_vsearch.unassembled_R2.fastq > res_3.2.3/1622730705.6637666_324_03_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.3/1622730705.6637666_324_03_subsample_uncomb_cutadapt_paired_err.txt + +Execution: + start: 03 Jun 2021 16:31:54 + end: 03 Jun 2021 16:31:58 + +Results: + nb seq with 5' primer : 25457 + nb seq with 3' primer : 25457 +######################################################################################################## +# Concatenate paired reads. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730705.6637666_324_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.3/1622730705.6637666_324_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.3/1622730705.6637666_324_03_subsample_artificial_combined.fastq.gz + +Execution: + start: 03 Jun 2021 16:31:58 + end: 03 Jun 2021 16:32:08 + +######################################################################################################## +# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0) +Command: + filterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.3/1622730705.6637666_324_03_subsample_artificial_combined.fastq.gz --output-file res_3.2.3/1622730705.6637666_324_03_subsample_art_N_filter.fasta --log-file res_3.2.3/1622730705.6637666_324_03_subsample_art_N_filter_log.txt + +Execution: + start: 03 Jun 2021 16:32:08 + end: 03 Jun 2021 16:32:09 + +Results: + nb seq with expected length : 25457 + nb seq without N : 25457 +######################################################################################################## +# Replace join tag. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622730705.6637666_324_03_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.3/1622730705.6637666_324_03_subsample_art_XtoN.fasta + +Execution: + start: 03 Jun 2021 16:32:09 + end: 03 Jun 2021 16:32:10 + +######################################################################################################## +# Dereplicates sample sequences. (derepSamples.py version : 1.6.1) +Command: + derepSamples.py --sequences-files res_3.2.3/1622730705.6637666_324_03_subsample_N_and_length_filter.fasta res_3.2.3/1622730705.6637666_324_03_subsample_art_XtoN.fasta --dereplicated-file res_3.2.3/1622730673.3474987_323_03_subsample_filtered.fasta --count-file res_3.2.3/1622730705.6637666_324_03_subsample_derep_count.tsv + +Execution: + start: 03 Jun 2021 16:32:10 + end: 03 Jun 2021 16:32:12 + + + +##Sample +All +##Commands +######################################################################################################## +# Dereplicates together sequences from several samples. (derepSamples.py version : 1.6.1) +Command: + derepSamples.py --nb-cpus 2 --size-separator ';size=' --samples-ref res_3.2.3/1622730673.3474987_323_derep_inputs.tsv --dereplicated-file res_3.2.3/01-prepro-vsearch.fasta --count-file res_3.2.3/01-prepro-vsearch.tsv + +Execution: + start: 03 Jun 2021 16:32:12 + end: 03 Jun 2021 16:32:16 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/02-clustering_denoising.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,69 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/clustering.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/clustering.py --distance 3 --denoising --input-fasta res_3.2.3/01-prepro-vsearch.fasta --input-count res_3.2.3/01-prepro-vsearch.tsv --output-biom res_3.2.3/02-clustering_denoising.biom --output-fasta res_3.2.3/02-clustering_denoising.fasta --output-compo res_3.2.3/02-clustering_denoising_compo.tsv --log-file res_3.2.3/02-clustering_denoising.log --nb-cpus 2 + +######################################################################################################## +# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0) +Command: + sortAbundancies.py --size-separator ';size=' --input-file res_3.2.3/01-prepro-vsearch.fasta --output-file res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_sorted.fasta + +Execution: + start: 03 Jun 2021 16:32:42 + end: 03 Jun 2021 16:32:44 + +repalce 100 N tags by 50A-50C in: res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_sorted.fasta out : res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_sorted_NtoA.fasta +######################################################################################################## +# Clustering sequences. (swarm version : 3.0.0) +Command: + swarm --differences 1 --threads 2 --log res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_denoising_log.txt --output-file res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_denoising_composition.txt res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_sorted_NtoA.fasta + +Execution: + start: 03 Jun 2021 16:32:46 + end: 03 Jun 2021 16:32:48 + +######################################################################################################## +# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1) +Command: + extractSwarmsFasta.py --input-fasta res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_sorted_NtoA.fasta --input-swarms res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_denoising_composition.txt --output-fasta res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_denoising_seeds.fasta + +Execution: + start: 03 Jun 2021 16:32:48 + end: 03 Jun 2021 16:32:50 + +######################################################################################################## +# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0) +Command: + sortAbundancies.py --size-separator '_' --input-file res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_denoising_resizedSeeds.fasta --output-file res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_denoising_sortedSeeds.fasta + +Execution: + start: 03 Jun 2021 16:32:51 + end: 03 Jun 2021 16:32:53 + +######################################################################################################## +# Clustering sequences. (swarm version : 3.0.0) +Command: + swarm --differences 3 --threads 2 --log res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_swarm_log.txt --output-file res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_swarmD3_composition.txt res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_denoising_sortedSeeds.fasta + +Execution: + start: 03 Jun 2021 16:32:53 + end: 03 Jun 2021 16:34:32 + +######################################################################################################## +# Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0) +Command: + swarm2biom.py --clusters-file res_3.2.3/02-clustering_denoising_compo.tsv --count-file res_3.2.3/01-prepro-vsearch.tsv --output-file res_3.2.3/02-clustering_denoising.biom + +Execution: + start: 03 Jun 2021 16:34:33 + end: 03 Jun 2021 16:34:36 + +######################################################################################################## +# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1) +Command: + extractSwarmsFasta.py --input-fasta res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_denoising_sortedSeeds.fasta --input-swarms res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_swarmD3_composition.txt --output-fasta res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_final_seeds.fasta + +Execution: + start: 03 Jun 2021 16:34:36 + end: 03 Jun 2021 16:34:37 + +replace 50A-50C tags by N. in: res_3.2.3/1622730762.8371043_481_01-prepro-vsearch_final_seeds.fasta out : res_3.2.3/02-clustering_denoising.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/02-clustering_fastidious.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,42 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/clustering.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/clustering.py --distance 1 --fastidious --input-fasta res_3.2.3/01-prepro-vsearch.fasta --input-count res_3.2.3/01-prepro-vsearch.tsv --output-biom res_3.2.3/02-clustering_fastidious.biom --output-fasta res_3.2.3/02-clustering_fastidious.fasta --output-compo res_3.2.3/02-clustering_fastidious_compo.tsv --log-file res_3.2.3/02-clustering_fastidious.log --nb-cpus 2 + +######################################################################################################## +# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0) +Command: + sortAbundancies.py --size-separator ';size=' --input-file res_3.2.3/01-prepro-vsearch.fasta --output-file res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted.fasta + +Execution: + start: 03 Jun 2021 16:32:16 + end: 03 Jun 2021 16:32:18 + +repalce 100 N tags by 50A-50C in: res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted.fasta out : res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted_NtoA.fasta +######################################################################################################## +# Clustering sequences. (swarm version : 3.0.0) +Command: + swarm --differences 1 --fastidious --threads 2 --log res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_swarm_log.txt --output-file res_3.2.3/02-clustering_fastidious_compo.tsv res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted_NtoA.fasta + +Execution: + start: 03 Jun 2021 16:32:20 + end: 03 Jun 2021 16:32:36 + +######################################################################################################## +# Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0) +Command: + swarm2biom.py --clusters-file res_3.2.3/02-clustering_fastidious_compo.tsv --count-file res_3.2.3/01-prepro-vsearch.tsv --output-file res_3.2.3/02-clustering_fastidious.biom + +Execution: + start: 03 Jun 2021 16:32:36 + end: 03 Jun 2021 16:32:39 + +######################################################################################################## +# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1) +Command: + extractSwarmsFasta.py --input-fasta res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted_NtoA.fasta --input-swarms res_3.2.3/02-clustering_fastidious_compo.tsv --output-fasta res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_final_seeds.fasta + +Execution: + start: 03 Jun 2021 16:32:40 + end: 03 Jun 2021 16:32:41 + +replace 50A-50C tags by N. in: res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_final_seeds.fasta out : res_3.2.3/02-clustering_fastidious.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/03-chimera.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,49 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/remove_chimera.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/remove_chimera.py --input-fasta res_3.2.3/02-clustering_fastidious.fasta --input-biom res_3.2.3/02-clustering_fastidious.biom --non-chimera res_3.2.3/03-chimera.fasta --out-abundance res_3.2.3/03-chimera.biom --summary res_3.2.3/03-chimera.html --log-file res_3.2.3/03-chimera.log --nb-cpus 2 + +######################################################################################################## +# Removes PCR chimera by samples. (parallelChimera.py version : 0.7.2 [vsearch v2.17.0_linux_x86_64]) +Command: + parallelChimera.py --lenient-filter --nb-cpus 2 --sequences res_3.2.3/02-clustering_fastidious.fasta --biom res_3.2.3/02-clustering_fastidious.biom --non-chimera res_3.2.3/03-chimera.fasta --out-abundance res_3.2.3/03-chimera.biom --summary res_3.2.3/1622730879.569383_528_03-chimera.fasta_summary.tsv --log-file res_3.2.3/1622730879.569383_528_03-chimera.fasta_tmp.log + +Execution: + start: 03 Jun 2021 16:34:39 + end: 03 Jun 2021 16:36:07 + + + +##Sample : 01_subsample +## Vsearch command: vsearch --uchime_denovo res_3.2.3/1622730879.7708952_533_01_subsample.fasta.tmp --nonchimeras res_3.2.3/1622730879.7708952_533_01_subsample.fasta --uchimeout res_3.2.3/1622730879.7708952_533_01_subsample.fasta.log +##Results +sample_name: 01_subsample +nb_chimera: 0 +chimera_abun: 0 +max_chimera_abun: 0 +nb_non_chimera: 25127 +non_chimera_abun: 50000 + +##Sample : 02_subsample +## Vsearch command: vsearch --uchime_denovo res_3.2.3/1622730879.7708952_533_02_subsample.fasta.tmp --nonchimeras res_3.2.3/1622730879.7708952_533_02_subsample.fasta --uchimeout res_3.2.3/1622730879.7708952_533_02_subsample.fasta.log +##Results +sample_name: 02_subsample +nb_chimera: 1 +chimera_abun: 1 +max_chimera_abun: 1 +nb_non_chimera: 24947 +non_chimera_abun: 49999 + +##Sample : 03_subsample +## Vsearch command: vsearch --uchime_denovo res_3.2.3/1622730879.7708952_533_03_subsample.fasta.tmp --nonchimeras res_3.2.3/1622730879.7708952_533_03_subsample.fasta --uchimeout res_3.2.3/1622730879.7708952_533_03_subsample.fasta.log +##Results +sample_name: 03_subsample +nb_chimera: 1 +chimera_abun: 1 +max_chimera_abun: 1 +nb_non_chimera: 24960 +non_chimera_abun: 49999 + + +## Removes the chimera observation from BIOM. + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/04-filters.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,26 @@ +## Application +Software: otu_filters.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/otu_filters.py --min-abundance 0.00005 --min-sample-presence 3 --contaminant data/phi.fa --nb-cpus 2 --input-biom res_3.2.3/03-chimera.biom --input-fasta res_3.2.3/03-chimera.fasta --output-fasta res_3.2.3/04-filters.fasta --output-biom res_3.2.3/04-filters.biom --excluded res_3.2.3/04-filters.excluded --summary res_3.2.3/04-filters.html --log-file res_3.2.3/04-filters.log + +######################################################################################################## +# Removes contaminant sequences. (removeConta.py version : 1.0) +Command: + removeConta.py --nb-cpus 2 --word-size 40 --min-identity 0.8 --min-coverage 0.8 --input-fasta res_3.2.3/03-chimera.fasta --contaminant-db data/phi.fa --input-biom res_3.2.3/03-chimera.biom --clean-fasta res_3.2.3/1622730967.3539724_570_cleaned_sequences.fasta --clean-biom res_3.2.3/1622730967.3539724_570_cleaned_abundance.biom --conta-fasta res_3.2.3/1622730967.3539724_570_contaminated_sequences.fasta --log-file res_3.2.3/1622730967.3539724_570_clean.log + +Execution: + start: 03 Jun 2021 16:36:11 + end: 03 Jun 2021 16:36:39 + +Results: + number of processed sequences: 74920 + number of removed contaminated sequences: 0 + +######################################################################################################## +# Updates fasta file based on sequence in biom file. (biomFastaUpdate.py version : 1.0.1) +Command: + biomFastaUpdate.py --input-biom res_3.2.3/04-filters.biom --input-fasta res_3.2.3/03-chimera.fasta --output-file res_3.2.3/04-filters.fasta --log res_3.2.3/1622730967.3539724_570_update_fasta_log.txt + +Execution: + start: 03 Jun 2021 16:36:40 + end: 03 Jun 2021 16:36:41 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/05-itsx.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,35 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/itsx.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/itsx.py --input-fasta res_3.2.3/04-filters.fasta --input-biom res_3.2.3/04-filters.biom --region ITS1 --nb-cpus 2 --out-abundance res_3.2.3/05-itsx.biom --summary res_3.2.3/05-itsx.html --log-file res_3.2.3/05-itsx.log --out-fasta res_3.2.3/05-itsx.fasta --out-removed res_3.2.3/05-itsx-excluded.fasta + +######################################################################################################## +# identifies ITS sequences and extracts the ITS region (parallelITSx.py version : 1.0.0 [ITSx 1.1.2]) +Command: + parallelITSx.py -f res_3.2.3/04-filters.fasta -b res_3.2.3/04-filters.biom --nb-cpus 2 --its ITS1 --organism-groups F -o res_3.2.3/05-itsx.fasta -m res_3.2.3/05-itsx-excluded.fasta -a res_3.2.3/05-itsx.biom --log-file res_3.2.3/1622731003.783737_622_ITSx.log + +Execution: + start: 03 Jun 2021 16:36:43 + end: 03 Jun 2021 16:36:52 + +Results: + +# split res_3.2.3/04-filters.fasta in 1 fasta files +Results + Wrote 55 records to res_3.2.3/1622731004.0408096_627_04-filters.fasta_0 + +## Input file : 1622731004.0408096_627_04-filters.fasta_0 +## in working directory: res_3.2.3/1622731004.0408096_627_1622731004.0408096_627_04-filters.fasta_0 +## ITSx command: ITSx -i /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731004.0408096_627_04-filters.fasta_0 -o 1622731004.0408096_627_04-filters --preserve T -t F --save_regions all +##Results + nb SSU (removed): 1 + nb full (removed): 0 + nb no_detections (removed): 0 + nb LSU (removed): 0 + nb ITS1 (kept): 55 + nb ITS2 (removed): 0 + nb 5_8S (removed): 0 + + +## Removes the observations after ITSx. + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/06-affiliation.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,106 @@ +## Application +Software: affiliation_OTU.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/affiliation_OTU.py --reference data/ITS1.rdp.fasta --input-fasta res_3.2.3/04-filters.fasta --input-biom res_3.2.3/04-filters.biom --output-biom res_3.2.3/06-affiliation.biom --summary res_3.2.3/06-affiliation.html --log-file res_3.2.3/06-affiliation.log --nb-cpus 2 --java-mem 4 --rdp + +Nb seq : 55 + with nb seq artificially combined :1 + +######################################################################################################## +# split res_3.2.3/04-filters.fasta in smaller fasta files +Results + Wrote 55 records to res_3.2.3/1622731012.9402058_1787_04-filters.fasta_0 +######################################################################################################## +# Split on tag. (combine_and_split.py version : 1.0.0) +Command: + combine_and_split.py --reads1 res_3.2.3/1622731012.9402058_1787_04-filters.fasta_FROGS_combined -s NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --split-output1 res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_R1.fasta --split-output2 res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_R2.fasta + +Execution: + start: 03 Jun 2021 16:36:55 + end: 03 Jun 2021 16:36:55 + +######################################################################################################## +# blast taxonomic affiliation (blastn version : 2.10.1+) +Command: + blastn -num_threads 2 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_R1.fasta -out res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_R1.fasta.blast -db data/ITS1.rdp.fasta + +Execution: + start: 03 Jun 2021 16:36:55 + end: 03 Jun 2021 16:36:55 + +######################################################################################################## +# blast taxonomic affiliation (blastn version : 2.10.1+) +Command: + blastn -num_threads 2 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_R2.fasta -out res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_R2.fasta.blast -db data/ITS1.rdp.fasta + +Execution: + start: 03 Jun 2021 16:36:55 + end: 03 Jun 2021 16:36:55 + +######################################################################################################## +# Reduced reference fasta file based on R1 and R2 100 best score blast alignment (reduce_ref_for_needleall.py version : 1.0) +Command: + reduce_ref_for_needleall.py -r data/ITS1.rdp.fasta --query-blast-R1 res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_R1.fasta.blast --query-blast-R2 res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_R2.fasta.blast -f res_3.2.3/1622731012.9402058_1787_reduced_ITS1.rdp.fasta -l res_3.2.3/1622731012.9402058_1787_reduced_ITS1.rdp.fasta.log + +Execution: + start: 03 Jun 2021 16:36:55 + end: 03 Jun 2021 16:36:55 + + # Parsing blast alignment results to reduce reference databse + Reducing reference databases from 102 to 32 sequences + + +######################################################################################################## +# split res_3.2.3/1622731012.9402058_1787_04-filters.fasta_FROGS_combined in smaller fasta files +Results + Generate -1 fasta files of 10 reads + Generate 1 fasta file of 1 reads + +######################################################################################################## +# rdp taxonomic affiliation (classifier.jar version : unknown) +Command: + java -Xmx4g -jar /home/maria/miniconda3/envs/frogs@3.2.3/bin/classifier.jar classify -c 0.0 -t data/ITS1.rdp.fasta.properties -o res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_0.rdp res_3.2.3/1622731012.9402058_1787_04-filters.fasta_0 + +Execution: + start: 03 Jun 2021 16:36:52 + end: 03 Jun 2021 16:36:55 + + +######################################################################################################## +# Perform global alignment (needleall version : EMBOSS:6.6.0.0) +Command: + needleall -asequence res_3.2.3/1622731012.9402058_1787_reduced_ITS1.rdp.fasta -bsequence res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_0 -outfile res_3.2.3/_1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_0.needleall.sam -aformat3 sam -gapopen 10.0 -gapextend 0.5 -errfile res_3.2.3/_1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_0.needleall.log + +Execution: + start: 03 Jun 2021 16:36:56 + end: 03 Jun 2021 16:36:56 + +######################################################################################################## +# convert NeedleAll Sam output in blast like tsv output sorted by bitscore (needleallSam_to_tsv.py version : 1.0.0) +Command: + needleallSam_to_tsv.py -n res_3.2.3/_1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_0.needleall.sam -r res_3.2.3/1622731012.9402058_1787_reduced_ITS1.rdp.fasta -b res_3.2.3/_1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_0.needleall.blast_like + +Execution: + start: 03 Jun 2021 16:36:56 + end: 03 Jun 2021 16:36:56 + + +######################################################################################################## +# blast taxonomic affiliation (blastn version : 2.10.1+) +Command: + blastn -num_threads 2 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res_3.2.3/1622731012.9402058_1787_04-filters.fasta_FROGS_full_length -out res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_full_length.blast -db data/ITS1.rdp.fasta + +Execution: + start: 03 Jun 2021 16:36:56 + end: 03 Jun 2021 16:36:57 + + + +######################################################################################################## +# Add Blast and/or RDP affiliation to biom (addAffiliation2biom.py version : 2.3.0) +Command: + addAffiliation2biom.py -f data/ITS1.rdp.fasta -i res_3.2.3/04-filters.biom -o res_3.2.3/06-affiliation.biom -b res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_full_length.blast res_3.2.3/_1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_FROGS_combined_0.needleall.blast_like -r res_3.2.3/1622731012.9402058_1787_1622731012.9402058_1787_04-filters.fasta_0.rdp + +Execution: + start: 03 Jun 2021 16:36:57 + end: 03 Jun 2021 16:36:57 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/07-affiliation_filter_delMode.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,26 @@ +## Application +Software: affiliation_filters.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/affiliation_filters.py --input-biom res_3.2.3/06-affiliation.biom --input-fasta res_3.2.3/04-filters.fasta --output-biom res_3.2.3/07-affiliation_deleted.biom --output-fasta res_3.2.3/07-affiliation_deleted.fasta --summary res_3.2.3/07-affiliation_deleted.html --impacted res_3.2.3/07-impacted_OTU_deleted.tsv --impacted-multihit res_3.2.3/07-impacted_OTU_deleted_multihit.tsv --log-file res_3.2.3/07-affiliation_filter_delMode.log --min-rdp-bootstrap Species:0.8 --min-blast-length 150 --min-blast-identity 1.0 --min-blast-coverage 1.0 --max-blast-evalue 1e-150 --ignore-blast-taxa "g__Sarcodon" "s__Trichoderma" --delete --taxonomic-ranks Domain Phylum Class Order Family Genus Species + +Identify OTU with : + - Blast evalue > 1e-150 : 30 + - Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma : 6 + - Blast identity < 1.0 : 1 +######################################################################################################## +# Convert a biom file into tsv file (biom_to_tsv.py version : 3.2.3) +Command: + biom_to_tsv.py --input-biom res_3.2.3/1622731017.9484577_1874_impacted.biom --input-fasta res_3.2.3/04-filters.fasta --output-tsv res_3.2.3/07-impacted_OTU_deleted.tsv --output-multi-affi res_3.2.3/07-impacted_OTU_deleted_multihit.tsv --log-file res_3.2.3/1622731017.9484577_1874_impacted.biom2tsv.log + +Execution: + start: 03 Jun 2021 16:36:58 + end: 03 Jun 2021 16:36:58 + +######################################################################################################## +# Updates fasta file based on sequence in biom file. (biomFastaUpdate.py version : 1.0.1) +Command: + biomFastaUpdate.py --input-biom res_3.2.3/07-affiliation_deleted.biom --input-fasta res_3.2.3/04-filters.fasta --output-file res_3.2.3/07-affiliation_deleted.fasta --log res_3.2.3/1622731017.9484577_1874_update_fasta_log.txt + +Execution: + start: 03 Jun 2021 16:36:58 + end: 03 Jun 2021 16:36:58 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/07-affiliation_filter_maskMode.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,17 @@ +## Application +Software: affiliation_filters.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/affiliation_filters.py --input-biom res_3.2.3/06-affiliation.biom --input-fasta res_3.2.3/04-filters.fasta --output-biom res_3.2.3/07-affiliation_masked.biom --summary res_3.2.3/07-affiliation_masked.html --impacted res_3.2.3/07-impacted_OTU_masked.tsv --impacted-multihit res_3.2.3/07-impacted_OTU_masked_multihit.tsv --log-file res_3.2.3/07-affiliation_filter_maskMode.log --min-rdp-bootstrap Species:0.8 --min-blast-length 150 --min-blast-identity 1.0 --min-blast-coverage 1.0 --max-blast-evalue 1e-150 --ignore-blast-taxa "g__Sarcodon" "s__Trichoderma" --mask --taxonomic-ranks Domain Phylum Class Order Family Genus Species + +Identify OTU with : + - Blast evalue > 1e-150 : 30 + - Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma : 6 + - Blast identity < 1.0 : 1 +######################################################################################################## +# Convert a biom file into tsv file (biom_to_tsv.py version : 3.2.3) +Command: + biom_to_tsv.py --input-biom res_3.2.3/1622731017.3433716_1857_impacted.biom --input-fasta res_3.2.3/04-filters.fasta --output-tsv res_3.2.3/07-impacted_OTU_masked.tsv --output-multi-affi res_3.2.3/07-impacted_OTU_masked_multihit.tsv --log-file res_3.2.3/1622731017.3433716_1857_impacted.biom2tsv.log + +Execution: + start: 03 Jun 2021 16:36:57 + end: 03 Jun 2021 16:36:57 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/08-affiliation_postprocessed.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,31 @@ +## Application +Software: affiliation_postprocess.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/affiliation_postprocess.py --input-biom res_3.2.3/06-affiliation.biom --input-fasta res_3.2.3/04-filters.fasta --reference data/Unite_extract_ITS1.fasta --output-biom res_3.2.3/08-affiliation_postprocessed.biom --output-compo res_3.2.3/08-affiliation_postprocessed.compo.tsv --output-fasta res_3.2.3/08-affiliation_postprocessed.fasta --log-file res_3.2.3/08-affiliation_postprocessed.log + +######################################################################################################## +# Select smallest reference as affiliation. (select_inclusive_amplicon.py version : 1.0) +Command: + select_inclusive_amplicon.py --ITS-reference data/Unite_extract_ITS1.fasta -b res_3.2.3/06-affiliation.biom -o res_3.2.3/1622731018.5907402_1893_06-affiliation.biom_resolve_inclusiv_its.biom --log-file res_3.2.3/1622731018.5907402_1893_06-affiliation.biom_resolve_inclusiv_its.log + +Execution: + start: 03 Jun 2021 16:36:58 + end: 03 Jun 2021 16:36:58 + + # nb OTU : 55 + # nb OTU with multiaffiliations : 0 + # nb OTU with multiaffiliations resolved : 0 + # nb multiaffiliations removed : 0 + +######################################################################################################## +# Aggregate OTU that share taxonomic affiliation with at least I% identity and C% coverage (aggregate_affiliated_otus.py version : 1.0.0) +Command: + aggregate_affiliated_otus.py -b res_3.2.3/1622731018.5907402_1893_06-affiliation.biom_resolve_inclusiv_its.biom -f res_3.2.3/04-filters.fasta --identity 99.0 --coverage 99.0 --output-biom res_3.2.3/08-affiliation_postprocessed.biom --output-compo res_3.2.3/08-affiliation_postprocessed.compo.tsv --output-fasta res_3.2.3/08-affiliation_postprocessed.fasta --log-file res_3.2.3/1622731018.5907402_1893_06-affiliation.biom_aggregation.log + +Execution: + start: 03 Jun 2021 16:36:58 + end: 03 Jun 2021 16:36:58 + + # nb OTU in : 55 + # nb OTU out : 55 + # nb OTU aggregated : 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/09-normalisation.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,34 @@ +## Application +Software: normalisation.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/normalisation.py -n 100 --input-biom res_3.2.3/08-affiliation_postprocessed.biom --input-fasta res_3.2.3/08-affiliation_postprocessed.fasta --output-biom res_3.2.3/09-normalisation.biom --output-fasta res_3.2.3/09-normalisation.fasta --summary res_3.2.3/09-normalisation.html --log-file res_3.2.3/09-normalisation.log + +Application start: 03 Jun 2021 16:36:59 + +#Normalisation calculation + start: 03 Jun 2021 16:36:59 +######################################################################################################## +# Random sampling in each sample. (biomTools.py version : 0.10.1) +Command: + biomTools.py sampling --nb-sampled 100 --input-file res_3.2.3/08-affiliation_postprocessed.biom --output-file res_3.2.3/09-normalisation.biom + +Execution: + start: 03 Jun 2021 16:36:59 + end: 03 Jun 2021 16:36:59 + + end: 03 Jun 2021 16:36:59 + +######################################################################################################## +# Update fasta file based on sequence in biom file (biomFastaUpdate.py version : 1.0.1) +Command: + biomFastaUpdate.py --input-biom res_3.2.3/09-normalisation.biom --input-fasta res_3.2.3/08-affiliation_postprocessed.fasta --output-file res_3.2.3/09-normalisation.fasta --log res_3.2.3/1622731019.036019_1904_tmp_fasta_update.log + +Execution: + start: 03 Jun 2021 16:36:59 + end: 03 Jun 2021 16:36:59 + + +#Summarise + start: 03 Jun 2021 16:36:59 + end: 03 Jun 2021 16:36:59 + +Application end: 03 Jun 2021 16:36:59
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/10-clustersStat.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,22 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/clusters_stat.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/clusters_stat.py --input-biom res_3.2.3/09-normalisation.biom --output-file res_3.2.3/10-clustersStat.html --log-file res_3.2.3/10-clustersStat.log + +######################################################################################################## +# Hierarchical classification on observation proportions. (biomTools.py version : 0.10.1) +Command: + biomTools.py hclassification --distance-method braycurtis --linkage-method average --input-file res_3.2.3/09-normalisation.biom --output-file res_3.2.3/1622731019.5516963_1914_HClassif.newick > res_3.2.3/1622731019.5516963_1914_HClassif_log.txt + +Execution: + start: 03 Jun 2021 16:36:59 + end: 03 Jun 2021 16:37:00 + +######################################################################################################## +# Writes by abundance the number of clusters. (biomTools.py version : 0.10.1) +Command: + biomTools.py obsdepth --input-file res_3.2.3/09-normalisation.biom --output-file res_3.2.3/1622731019.5516963_1914_depths.tsv + +Execution: + start: 03 Jun 2021 16:37:01 + end: 03 Jun 2021 16:37:01 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/11-affiliationsStat.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,22 @@ +## Application +Software: affiliations_stat.py (version: 3.2.3) +Command: /home/maria/miniconda3/envs/frogs@3.2.3/bin/affiliations_stat.py --input-biom res_3.2.3/09-normalisation.biom --output-file res_3.2.3/11-affiliationsStat.html --log-file res_3.2.3/11-affiliationsStat.log --tax-consensus-tag blast_taxonomy --identity-tag perc_identity --coverage-tag perc_query_coverage --multiple-tag blast_affiliations --rarefaction-ranks Family Genus Species --taxonomic-ranks Domain Phylum Class Order Family Genus Species + +######################################################################################################## +# Writes by sample the rarefaction data for rank(s) 4, 5, 6. (biomTools.py version : 0.10.1) +Command: + biomTools.py rarefaction --input-file res_3.2.3/09-normalisation.biom --output-file-pattern res_3.2.3/1622731021.3618112_1925_rarefaction_rank_##RANK##.tsv --taxonomy-key "blast_taxonomy" --step-size 2 --ranks 4 5 6 + +Execution: + start: 03 Jun 2021 16:37:01 + end: 03 Jun 2021 16:37:01 + +######################################################################################################## +# Produces a taxonomy tree with counts by sample. (biomTools.py version : 0.10.1) +Command: + biomTools.py treeCount --input-file res_3.2.3/09-normalisation.biom --taxonomy-key "blast_taxonomy" --output-enewick res_3.2.3/1622731021.3618112_1925_taxCount.enewick --output-samples res_3.2.3/1622731021.3618112_1925_taxCount_ids.tsv + +Execution: + start: 03 Jun 2021 16:37:01 + end: 03 Jun 2021 16:37:01 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/12-biom2tsv.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,22 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/biom_to_tsv.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/biom_to_tsv.py --input-biom res_3.2.3/09-normalisation.biom --input-fasta res_3.2.3/09-normalisation.fasta --output-tsv res_3.2.3/12-biom2tsv.tsv --output-multi-affi res_3.2.3/12-biom2tsv-affiliation_multihit.tsv --log-file res_3.2.3/12-biom2tsv.log + +######################################################################################################## +# Converts a BIOM file in TSV file. (biom2tsv.py version : 1.5.0) +Command: + biom2tsv.py --input-file res_3.2.3/09-normalisation.biom --input-fasta res_3.2.3/09-normalisation.fasta --output-file res_3.2.3/12-biom2tsv.tsv --fields 'comment' '@rdp_tax_and_bootstrap' 'blast_taxonomy' '@blast_subject' '@blast_perc_identity' '@blast_perc_query_coverage' '@blast_evalue' '@blast_aln_length' 'seed_id' '@seed_sequence' '@observation_name' '@observation_sum' '@sample_count' + +Execution: + start: 03 Jun 2021 16:37:01 + end: 03 Jun 2021 16:37:02 + +######################################################################################################## +# Extracts multi-affiliations data from a FROGS BIOM file. (multiAffiFromBiom.py version : 1.3.0) +Command: + multiAffiFromBiom.py --input-file res_3.2.3/09-normalisation.biom --output-file res_3.2.3/12-biom2tsv-affiliation_multihit.tsv + +Execution: + start: 03 Jun 2021 16:37:02 + end: 03 Jun 2021 16:37:02 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/13-biom2stdbiom.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,4 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/biom_to_stdBiom.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/biom_to_stdBiom.py --input-biom res_3.2.3/09-normalisation.biom --output-biom res_3.2.3/13-affiliation_std.biom --output-metadata res_3.2.3/13-affiliation_multihit.tsv --log-file res_3.2.3/13-biom2stdbiom.log +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/14-tsv2biom.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,13 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/tsv_to_biom.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/tsv_to_biom.py --input-tsv res_3.2.3/12-biom2tsv.tsv --input-multi-affi res_3.2.3/12-biom2tsv-affiliation_multihit.tsv --output-biom res_3.2.3/14-tsv2biom.biom --output-fasta res_3.2.3/14-tsv2biom.fasta --log-file res_3.2.3/14-tsv2biom.log + +######################################################################################################## +# Converts a TSV file in Biom. (tsv2biom.py version : 1.2.0) +Command: + tsv2biom.py --input-file res_3.2.3/12-biom2tsv.tsv --input-multihits res_3.2.3/12-biom2tsv-affiliation_multihit.tsv --output-file res_3.2.3/14-tsv2biom.biom --output-fasta res_3.2.3/14-tsv2biom.fasta --fields comment rdp_tax_and_bootstrap blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length seed_id seed_sequence observation_name --samples-names 01_subsample 02_subsample 03_subsample + +Execution: + start: 03 Jun 2021 16:37:02 + end: 03 Jun 2021 16:37:02 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/15-tree-mafft.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,33 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/tree.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/tree.py --nb-cpus 2 --input-sequences res_3.2.3/09-normalisation.fasta --biom-file res_3.2.3/09-normalisation.biom --out-tree res_3.2.3/15-tree-mafft.nwk --html res_3.2.3/15-tree-mafft.html --log-file res_3.2.3/15-tree-mafft.log + +Number of input OTUs sequences: 52 + +######################################################################################################## +# Mafft multiple alignment. (mafft version : v7.407) +Command: + mafft --maxiterate 1000 --globalpair --thread 2 res_3.2.3/09-normalisation.fasta > res_3.2.3/1622731022.8104277_1957_mafft_aligned.fasta 2> res_3.2.3/1622731022.8104277_1957_mafft.stderr + +Execution: + start: 03 Jun 2021 16:37:02 + end: 03 Jun 2021 16:37:10 + +######################################################################################################## +# reconstruction a phylogenetic tree (FastTree version : 2.1.9) +Command: + FastTree -nt -gtr res_3.2.3/1622731022.8104277_1957_mafft_aligned.fasta > res_3.2.3/1622731022.8104277_1957_fasttree.nwk 2> res_3.2.3/1622731022.8104277_1957_fasttree.stderr + +Execution: + start: 03 Jun 2021 16:37:10 + end: 03 Jun 2021 16:37:12 + +######################################################################################################## +# root newick tree with phangorn R package midpoint function. (root_tree.R version : 1.1.0 [R : 4.0.5; phangorn : 2.7.0]) +Command: + root_tree.R res_3.2.3/1622731022.8104277_1957_fasttree.nwk res_3.2.3/15-tree-mafft.nwk + +Execution: + start: 03 Jun 2021 16:37:16 + end: 03 Jun 2021 16:37:19 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/16-phylo_import.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,15 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_import_data.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_import_data.py --biomfile data/chaillou.biom --samplefile data/sample_metadata.tsv --treefile data/tree.nwk --rdata res_3.2.3/16-phylo_import.Rdata --html res_3.2.3/16-phylo_import.nb.html --log-file res_3.2.3/16-phylo_import.log + +######################################################################################################## +# Run r_import_data.Rmd (Rscript version : [1] "R version 4.0.5 (2021-03-31)" +[1] "Rmarkdown version: 2.8" +[1] "Phyloseq version: 1.34.0") +Command: + Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_import_data.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.nb.html', params=list(biomfile='/home/maria/workspace/FROGS_dev/test/data/chaillou.biom', samplefile='/home/maria/workspace/FROGS_dev/test/data/sample_metadata.tsv', treefile='/home/maria/workspace/FROGS_dev/test/data/tree.nwk', normalisation=FALSE, outputRdata='/home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.Rdata', ranks='Kingdom Phylum Class Order Family Genus Species', libdir ='/home/maria/miniconda3/envs/frogs@3.2.3/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.3')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731039.8180652_2170_rmarkdown.stderr + +Execution: + start: 03 Jun 2021 16:37:30 + end: 03 Jun 2021 16:37:48 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/17-phylo_composition.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,15 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_composition.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_composition.py --varExp EnvType --taxaRank1 Kingdom --taxaSet1 Bacteria --taxaRank2 Phylum --numberOfTaxa 9 --rdata res_3.2.3/16-phylo_import.Rdata --html res_3.2.3/17-phylo_composition.nb.html --log-file res_3.2.3/17-phylo_composition.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 4.0.5 (2021-03-31)" +[1] "Rmarkdown version: 2.8" +[1] "Phyloseq version: 1.34.0") +Command: + Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_composition.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.3/17-phylo_composition.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.Rdata', varExp='EnvType',taxaRank1='Kingdom',taxaSet1='Bacteria',taxaRank2='Phylum',numberOfTaxa=9, libdir ='/home/maria/miniconda3/envs/frogs@3.2.3/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.3')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731068.6720974_2243_rmarkdown.stderr + +Execution: + start: 03 Jun 2021 16:37:59 + end: 03 Jun 2021 16:38:20 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/18-phylo_alpha_div.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,15 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_alpha_diversity.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_alpha_diversity.py --varExp EnvType --rdata res_3.2.3/16-phylo_import.Rdata --alpha-measures Observed Chao1 Shannon --alpha-out res_3.2.3/18-phylo_alpha_div.tsv --html res_3.2.3/18-phylo_alpha_div.nb.html --log-file res_3.2.3/18-phylo_alpha_div.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 4.0.5 (2021-03-31)" +[1] "Rmarkdown version: 2.8" +[1] "Phyloseq version: 1.34.0") +Command: + Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_alpha_diversity.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.3/18-phylo_alpha_div.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.Rdata', measures='Observed,Chao1,Shannon', varExp='EnvType',fileAlpha='/home/maria/workspace/FROGS_dev/test/res_3.2.3/18-phylo_alpha_div.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.3/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.3')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731101.0754166_2320_rmarkdown.stderr + +Execution: + start: 03 Jun 2021 16:38:31 + end: 03 Jun 2021 16:39:11 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/19-phylo_beta_div.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,15 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_beta_diversity.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_beta_diversity.py --varExp EnvType --distance-methods cc,unifrac --rdata res_3.2.3/16-phylo_import.Rdata --matrix-outdir res_3.2.3 --html res_3.2.3/19-phylo_beta_div.nb.html --log-file res_3.2.3/19-phylo_beta_div.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 4.0.5 (2021-03-31)" +[1] "Rmarkdown version: 2.8" +[1] "Phyloseq version: 1.34.0") +Command: + Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_beta_diversity.Rmd',knit_root_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.3',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.3/19-phylo_beta_div.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.Rdata', varExp='EnvType', methods='cc,unifrac', libdir ='/home/maria/miniconda3/envs/frogs@3.2.3/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.3')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731151.2391036_2392_rmarkdown.stderr + +Execution: + start: 03 Jun 2021 16:39:21 + end: 03 Jun 2021 16:39:37 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/20-phylo_structure.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,15 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_structure.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_structure.py --varExp EnvType --ordination-method MDS --rdata res_3.2.3/16-phylo_import.Rdata --distance-matrix res_3.2.3/unifrac.tsv --html res_3.2.3/20-phylo_structure.nb.html --log-file res_3.2.3/20-phylo_structure.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 4.0.5 (2021-03-31)" +[1] "Rmarkdown version: 2.8" +[1] "Phyloseq version: 1.34.0") +Command: + Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_structure.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.3/20-phylo_structure.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.Rdata', varExp='EnvType',method='MDS',distance='/home/maria/workspace/FROGS_dev/test/res_3.2.3/unifrac.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.3/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.3')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731178.3899164_2466_rmarkdown.stderr + +Execution: + start: 03 Jun 2021 16:39:48 + end: 03 Jun 2021 16:40:09 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/21-phylo_clustering.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,15 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_clustering.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_clustering.py --varExp EnvType --rdata res_3.2.3/16-phylo_import.Rdata --distance-matrix res_3.2.3/unifrac.tsv --html res_3.2.3/21-phylo_clustering.nb.html --log-file res_3.2.3/21-phylo_clustering.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 4.0.5 (2021-03-31)" +[1] "Rmarkdown version: 2.8" +[1] "Phyloseq version: 1.34.0") +Command: + Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_clustering.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.3/21-phylo_clustering.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/FROGS_dev/test/res_3.2.3/unifrac.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.3/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.3')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731209.4272215_2548_rmarkdown.stderr + +Execution: + start: 03 Jun 2021 16:40:20 + end: 03 Jun 2021 16:40:33 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/22-phylo_manova.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,15 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_manova.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_manova.py --varExp "EnvType" --rdata res_3.2.3/16-phylo_import.Rdata --distance-matrix res_3.2.3/unifrac.tsv --html res_3.2.3/22-phylo_manova.nb.html --log-file res_3.2.3/22-phylo_manova.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 4.0.5 (2021-03-31)" +[1] "Rmarkdown version: 2.8" +[1] "Phyloseq version: 1.34.0") +Command: + Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.3/bin/phyloseq_manova.Rmd', output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.3/22-phylo_manova.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/FROGS_dev/test/res_3.2.3/unifrac.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.3/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.3')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731233.551139_2625_rmarkdown.stderr + +Execution: + start: 03 Jun 2021 16:40:43 + end: 03 Jun 2021 16:40:56 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/23-deseq2_preprocess.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,13 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/deseq2_preprocess.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/deseq2_preprocess.py --data res_3.2.3/16-phylo_import.Rdata --log-file res_3.2.3/23-deseq2_preprocess.log --out-Rdata res_3.2.3/23-deseq2_preprocess.Rdata --var EnvType + +######################################################################################################## +# Construc DESeq2 object from a Phyloseq one. (deseq2_preprocess.R version : 1.1.0 [R : 4.0.5; DESeq2 : 1.30.1; Phyloseq : 1.34.0]) +Command: + deseq2_preprocess.R --inRdata /home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.Rdata --var EnvType --outRdata /home/maria/workspace/FROGS_dev/test/res_3.2.3/23-deseq2_preprocess.Rdata 2> /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731256.7432642_2686_R.stderr + +Execution: + start: 03 Jun 2021 16:41:16 + end: 03 Jun 2021 16:41:41 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/24-deseq2_visualisation.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,14 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/deseq2_visualisation.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/deseq2_visualisation.py --phyloseqData res_3.2.3/16-phylo_import.Rdata --dds res_3.2.3/23-deseq2_preprocess.Rdata --log-file res_3.2.3/24-deseq2_visualisation.log --html res_3.2.3/24-deseq2_visualisation.nb.html --var EnvType --mod1 BoeufHache --mod2 SaumonFume + +######################################################################################################## +# Run deseq2_visualisation.Rmd (Rscript version : [1] "R version 4.0.5 (2021-03-31)" +[1] "DESeq2 version: 1.30.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.3/bin/deseq2_visualisation.Rmd', output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.3/24-deseq2_visualisation.nb.html', params=list(phyloseq_data='/home/maria/workspace/FROGS_dev/test/res_3.2.3/16-phylo_import.Rdata', dds='/home/maria/workspace/FROGS_dev/test/res_3.2.3/23-deseq2_preprocess.Rdata', var='EnvType', mod1='BoeufHache', mod2='SaumonFume', padj=0.05), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.3')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.3/1622731301.4988678_2720_R.stderr + +Execution: + start: 03 Jun 2021 16:41:53 + end: 03 Jun 2021 16:42:17 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/demultiplex.log Mon Jun 21 14:09:38 2021 +0000 @@ -0,0 +1,237 @@ +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/demultiplex.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/demultiplex.py --input-R1 data/demultiplex_test2_R1.fq.gz --input-R2 data/demultiplex_test2_R2.fq.gz --input-barcode data/demultiplex_barcode.txt --mismatches 1 --end both --output-demultiplexed res_3.2.3/demultiplexed.tar.gz --output-excluded res_3.2.3/undemultiplexed.tar.gz --log-file res_3.2.3/demultiplex.log --summary res_3.2.3/demultiplex_summary.txt + + +#Demultiplexing demultiplex_test2_R1.fq.gz and demultiplex_test2_R2.fq.gz with forward_bc in bol strand +######################################################################################################## +# Demultiplex reads. (splitbc.pl version : unknown) +Command: + splitbc.pl data/demultiplex_test2_R1.fq.gz data/demultiplex_test2_R2.fq.gz --bol --bcfile res_3.2.3/forward_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.3/1622730423.397978_32533_tmp/1622730423.4106433_32533/%_R1.fastq --prefix-r2 res_3.2.3/1622730423.397978_32533_tmp/1622730423.4106433_32533/%_R2.fastq >> res_3.2.3/1622730423.397978_32533_Demult.log + +Execution: + start: 03 Jun 2021 16:27:03 + end: 03 Jun 2021 16:27:04 + +Results : + nb seq before demultiplexing : 10.0 + nb seq after process matched : 9.0 + nb seq after process non-ambiguous : 8.0 + +#Demultiplexing ACAGCGT_R1.fastq and ACAGCGT_R2.fastq with ACAGCGT_reverse_bc in eol strand +######################################################################################################## +# Demultiplex reads. (splitbc.pl version : unknown) +Command: + splitbc.pl res_3.2.3/1622730423.397978_32533_tmp/1622730423.4106433_32533/ACAGCGT_R1.fastq res_3.2.3/1622730423.397978_32533_tmp/1622730423.4106433_32533/ACAGCGT_R2.fastq --eol --bcfile res_3.2.3/ACAGCGT_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.3/1622730423.397978_32533_tmp/1622730424.2060387_32533/%_R1.fastq --prefix-r2 res_3.2.3/1622730423.397978_32533_tmp/1622730424.2060387_32533/%_R2.fastq >> res_3.2.3/1622730423.397978_32533_Demult.log + +Execution: + start: 03 Jun 2021 16:27:04 + end: 03 Jun 2021 16:27:04 + +Results : + nb seq before demultiplexing : 4.0 + nb seq after process matched : 0.0 + nb seq after process non-ambiguous : 0.0 + +#Demultiplexing ACAGTAG_R1.fastq and ACAGTAG_R2.fastq with ACAGTAG_reverse_bc in eol strand +######################################################################################################## +# Demultiplex reads. (splitbc.pl version : unknown) +Command: + splitbc.pl res_3.2.3/1622730423.397978_32533_tmp/1622730423.4106433_32533/ACAGTAG_R1.fastq res_3.2.3/1622730423.397978_32533_tmp/1622730423.4106433_32533/ACAGTAG_R2.fastq --eol --bcfile res_3.2.3/ACAGTAG_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.3/1622730423.397978_32533_tmp/1622730424.3845317_32533/%_R1.fastq --prefix-r2 res_3.2.3/1622730423.397978_32533_tmp/1622730424.3845317_32533/%_R2.fastq >> res_3.2.3/1622730423.397978_32533_Demult.log + +Execution: + start: 03 Jun 2021 16:27:04 + end: 03 Jun 2021 16:27:04 + +Results : + nb seq before demultiplexing : 4.0 + nb seq after process matched : 0.0 + nb seq after process non-ambiguous : 0.0 + +#Summarising result + +#Concatenation of undemultiplexed files 1 + +#Concatenation of undemultiplexed files 2 + +#Archive demultiplexed R1 and R2 files +######################################################################################################## +# Archives files. (tar version : unknown) +Command: + tar -zcf res_3.2.3/demultiplexed.tar.gz -C res_3.2.3/1622730424.539783_32533 MgArd0001_A_R1.fastq MgArd0002_R1.fastq MgArd0003_R1.fastq MgArd0004_R1.fastq MgArd0009_R1.fastq MgArd0010_R1.fastq MgArd0011_R1.fastq MgArd0012_R1.fastq MgArd0001_A_R2.fastq MgArd0002_R2.fastq MgArd0003_R2.fastq MgArd0004_R2.fastq MgArd0009_R2.fastq MgArd0010_R2.fastq MgArd0011_R2.fastq MgArd0012_R2.fastq + +Execution: + start: 03 Jun 2021 16:27:04 + end: 03 Jun 2021 16:27:04 + + +#Archive undemultiplexed R1 and R2 files +######################################################################################################## +# Archives files. (tar version : unknown) +Command: + tar -zcf res_3.2.3/undemultiplexed.tar.gz -C res_3.2.3/1622730424.6438384_32533 demultiplex_test2_R1.fq.gz_excluded_demult demultiplex_test2_R2.fq.gz_excluded_demult + +Execution: + start: 03 Jun 2021 16:27:04 + end: 03 Jun 2021 16:27:04 + + +#Removing temporary files +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/demultiplex.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/demultiplex.py --input-R1 data/demultiplex_test2_R1.fq.gz --input-R2 data/demultiplex_test2_R2.fq.gz --input-barcode data/demultiplex_barcode.txt --mismatches 1 --end both --output-demultiplexed res_3.2.3/demultiplexed.tar.gz --output-excluded res_3.2.3/undemultiplexed.tar.gz --log-file res_3.2.3/demultiplex.log --summary res_3.2.3/demultiplex_summary.txt + + +#Demultiplexing demultiplex_test2_R1.fq.gz and demultiplex_test2_R2.fq.gz with forward_bc in bol strand +######################################################################################################## +# Demultiplex reads. (splitbc.pl version : unknown) +Command: + splitbc.pl data/demultiplex_test2_R1.fq.gz data/demultiplex_test2_R2.fq.gz --bol --bcfile res_3.2.3/forward_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.3/1622730557.7274978_32591_tmp/1622730557.7278774_32591/%_R1.fastq --prefix-r2 res_3.2.3/1622730557.7274978_32591_tmp/1622730557.7278774_32591/%_R2.fastq >> res_3.2.3/1622730557.7274978_32591_Demult.log + +Execution: + start: 03 Jun 2021 16:29:17 + end: 03 Jun 2021 16:29:17 + +Results : + nb seq before demultiplexing : 10.0 + nb seq after process matched : 9.0 + nb seq after process non-ambiguous : 8.0 + +#Demultiplexing ACAGCGT_R1.fastq and ACAGCGT_R2.fastq with ACAGCGT_reverse_bc in eol strand +######################################################################################################## +# Demultiplex reads. (splitbc.pl version : unknown) +Command: + splitbc.pl res_3.2.3/1622730557.7274978_32591_tmp/1622730557.7278774_32591/ACAGCGT_R1.fastq res_3.2.3/1622730557.7274978_32591_tmp/1622730557.7278774_32591/ACAGCGT_R2.fastq --eol --bcfile res_3.2.3/ACAGCGT_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.3/1622730557.7274978_32591_tmp/1622730557.8559873_32591/%_R1.fastq --prefix-r2 res_3.2.3/1622730557.7274978_32591_tmp/1622730557.8559873_32591/%_R2.fastq >> res_3.2.3/1622730557.7274978_32591_Demult.log + +Execution: + start: 03 Jun 2021 16:29:17 + end: 03 Jun 2021 16:29:17 + +Results : + nb seq before demultiplexing : 4.0 + nb seq after process matched : 0.0 + nb seq after process non-ambiguous : 0.0 + +#Demultiplexing ACAGTAG_R1.fastq and ACAGTAG_R2.fastq with ACAGTAG_reverse_bc in eol strand +######################################################################################################## +# Demultiplex reads. (splitbc.pl version : unknown) +Command: + splitbc.pl res_3.2.3/1622730557.7274978_32591_tmp/1622730557.7278774_32591/ACAGTAG_R1.fastq res_3.2.3/1622730557.7274978_32591_tmp/1622730557.7278774_32591/ACAGTAG_R2.fastq --eol --bcfile res_3.2.3/ACAGTAG_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.3/1622730557.7274978_32591_tmp/1622730557.9832373_32591/%_R1.fastq --prefix-r2 res_3.2.3/1622730557.7274978_32591_tmp/1622730557.9832373_32591/%_R2.fastq >> res_3.2.3/1622730557.7274978_32591_Demult.log + +Execution: + start: 03 Jun 2021 16:29:17 + end: 03 Jun 2021 16:29:18 + +Results : + nb seq before demultiplexing : 4.0 + nb seq after process matched : 0.0 + nb seq after process non-ambiguous : 0.0 + +#Summarising result + +#Concatenation of undemultiplexed files 1 + +#Concatenation of undemultiplexed files 2 + +#Archive demultiplexed R1 and R2 files +######################################################################################################## +# Archives files. (tar version : unknown) +Command: + tar -zcf res_3.2.3/demultiplexed.tar.gz -C res_3.2.3/1622730558.1170962_32591 MgArd0001_A_R1.fastq MgArd0002_R1.fastq MgArd0003_R1.fastq MgArd0004_R1.fastq MgArd0009_R1.fastq MgArd0010_R1.fastq MgArd0011_R1.fastq MgArd0012_R1.fastq MgArd0001_A_R2.fastq MgArd0002_R2.fastq MgArd0003_R2.fastq MgArd0004_R2.fastq MgArd0009_R2.fastq MgArd0010_R2.fastq MgArd0011_R2.fastq MgArd0012_R2.fastq + +Execution: + start: 03 Jun 2021 16:29:18 + end: 03 Jun 2021 16:29:18 + + +#Archive undemultiplexed R1 and R2 files +######################################################################################################## +# Archives files. (tar version : unknown) +Command: + tar -zcf res_3.2.3/undemultiplexed.tar.gz -C res_3.2.3/1622730558.1235144_32591 demultiplex_test2_R1.fq.gz_excluded_demult demultiplex_test2_R2.fq.gz_excluded_demult + +Execution: + start: 03 Jun 2021 16:29:18 + end: 03 Jun 2021 16:29:18 + + +#Removing temporary files +## Application +Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/demultiplex.py (version : 3.2.3) +Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/demultiplex.py --input-R1 data/demultiplex_test2_R1.fq.gz --input-R2 data/demultiplex_test2_R2.fq.gz --input-barcode data/demultiplex_barcode.txt --mismatches 1 --end both --output-demultiplexed res_3.2.3/demultiplexed.tar.gz --output-excluded res_3.2.3/undemultiplexed.tar.gz --log-file res_3.2.3/demultiplex.log --summary res_3.2.3/demultiplex_summary.txt + + +#Demultiplexing demultiplex_test2_R1.fq.gz and demultiplex_test2_R2.fq.gz with forward_bc in bol strand +######################################################################################################## +# Demultiplex reads. (splitbc.pl version : unknown) +Command: + splitbc.pl data/demultiplex_test2_R1.fq.gz data/demultiplex_test2_R2.fq.gz --bol --bcfile res_3.2.3/forward_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.3/1622730610.883609_32623_tmp/1622730610.8841264_32623/%_R1.fastq --prefix-r2 res_3.2.3/1622730610.883609_32623_tmp/1622730610.8841264_32623/%_R2.fastq >> res_3.2.3/1622730610.883609_32623_Demult.log + +Execution: + start: 03 Jun 2021 16:30:10 + end: 03 Jun 2021 16:30:11 + +Results : + nb seq before demultiplexing : 10.0 + nb seq after process matched : 9.0 + nb seq after process non-ambiguous : 8.0 + +#Demultiplexing ACAGCGT_R1.fastq and ACAGCGT_R2.fastq with ACAGCGT_reverse_bc in eol strand +######################################################################################################## +# Demultiplex reads. (splitbc.pl version : unknown) +Command: + splitbc.pl res_3.2.3/1622730610.883609_32623_tmp/1622730610.8841264_32623/ACAGCGT_R1.fastq res_3.2.3/1622730610.883609_32623_tmp/1622730610.8841264_32623/ACAGCGT_R2.fastq --eol --bcfile res_3.2.3/ACAGCGT_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.3/1622730610.883609_32623_tmp/1622730611.0380332_32623/%_R1.fastq --prefix-r2 res_3.2.3/1622730610.883609_32623_tmp/1622730611.0380332_32623/%_R2.fastq >> res_3.2.3/1622730610.883609_32623_Demult.log + +Execution: + start: 03 Jun 2021 16:30:11 + end: 03 Jun 2021 16:30:11 + +Results : + nb seq before demultiplexing : 4.0 + nb seq after process matched : 0.0 + nb seq after process non-ambiguous : 0.0 + +#Demultiplexing ACAGTAG_R1.fastq and ACAGTAG_R2.fastq with ACAGTAG_reverse_bc in eol strand +######################################################################################################## +# Demultiplex reads. (splitbc.pl version : unknown) +Command: + splitbc.pl res_3.2.3/1622730610.883609_32623_tmp/1622730610.8841264_32623/ACAGTAG_R1.fastq res_3.2.3/1622730610.883609_32623_tmp/1622730610.8841264_32623/ACAGTAG_R2.fastq --eol --bcfile res_3.2.3/ACAGTAG_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.3/1622730610.883609_32623_tmp/1622730611.1855626_32623/%_R1.fastq --prefix-r2 res_3.2.3/1622730610.883609_32623_tmp/1622730611.1855626_32623/%_R2.fastq >> res_3.2.3/1622730610.883609_32623_Demult.log + +Execution: + start: 03 Jun 2021 16:30:11 + end: 03 Jun 2021 16:30:11 + +Results : + nb seq before demultiplexing : 4.0 + nb seq after process matched : 0.0 + nb seq after process non-ambiguous : 0.0 + +#Summarising result + +#Concatenation of undemultiplexed files 1 + +#Concatenation of undemultiplexed files 2 + +#Archive demultiplexed R1 and R2 files +######################################################################################################## +# Archives files. (tar version : unknown) +Command: + tar -zcf res_3.2.3/demultiplexed.tar.gz -C res_3.2.3/1622730611.3448439_32623 MgArd0001_A_R1.fastq MgArd0002_R1.fastq MgArd0003_R1.fastq MgArd0004_R1.fastq MgArd0009_R1.fastq MgArd0010_R1.fastq MgArd0011_R1.fastq MgArd0012_R1.fastq MgArd0001_A_R2.fastq MgArd0002_R2.fastq MgArd0003_R2.fastq MgArd0004_R2.fastq MgArd0009_R2.fastq MgArd0010_R2.fastq MgArd0011_R2.fastq MgArd0012_R2.fastq + +Execution: + start: 03 Jun 2021 16:30:11 + end: 03 Jun 2021 16:30:11 + + +#Archive undemultiplexed R1 and R2 files +######################################################################################################## +# Archives files. (tar version : unknown) +Command: + tar -zcf res_3.2.3/undemultiplexed.tar.gz -C res_3.2.3/1622730611.354186_32623 demultiplex_test2_R1.fq.gz_excluded_demult demultiplex_test2_R2.fq.gz_excluded_demult + +Execution: + start: 03 Jun 2021 16:30:11 + end: 03 Jun 2021 16:30:11 + + +#Removing temporary files
--- a/tree.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/tree.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_Tree" name="FROGS Tree" version="3.2.3"> +<tool id="FROGS_Tree" name="FROGS Tree" version="3.2.3.1"> <description>Reconstruction of phylogenetic tree </description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>
--- a/tsv_to_biom.xml Fri Jun 04 11:09:35 2021 +0000 +++ b/tsv_to_biom.xml Mon Jun 21 14:09:38 2021 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="3.2.3"> +<tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="3.2.3.1"> <description>Converts a TSV file in a BIOM file.</description> <requirements> <requirement type="package" version="3.2.3">frogs</requirement>