https://github.com/collinschwantes/pcm-eukaryotes-

Analysis code created for manuscript "Antarctic biodiversity predictions through substrate qualities and environmental DNA"

https://github.com/collinschwantes/pcm-eukaryotes-

Repository

Analysis code created for manuscript "Antarctic biodiversity predictions through substrate qualities and environmental DNA"

https://github.com/collinschwantes/pcm-eukaryotes-/blob/master/

# Analysing 18S data from **Prince Charles Mountains**

Paul Czechowski 2011-2021, Material released with
Creative Commons Attribution 4.0 International Public License as per
`https://creativecommons.org/licenses/by/4.0/legalcode`

## Progress notes
* **12.02.2020** - adjusting repository for analysis restart
  * commit `4e8dccdaa9ac0501b6bf0655bef4b5d2fe91ae3d` in GitHub folder
  * commit `0ec21a12a03aa416ffd159cd3020f46a9437e510` in Transport folder.
  * removing `x` flags in Github and Transport folders
  * erasing unneeded file in project tree or marking them `red`.
  * collating sequence metadata
    * `cp /Users/paul/Archive/PhD_Thesis/07_agrf_library_prep/140319_AGRF_plate_layout_actual_pooling.xlsx /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/200212_18S_pooling.xlsx`
    * `cp /Users/paul/Archive/PhD_Thesis/06_sequence_runs/phd_140401_Illumina_run_18S_Antarctic_pools/140401_barcode_and_primer_info/*  /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/`
  * finding 18S sequnece data - merged reads are available at `/Users/paul/Sequences/Raw/140401_18S_Illumina_Adelaide`
    * `/Users/paul/Sequences/Raw/140401_18S_Illumina_Adelaide/18S3_PC_merged.Index.fastq.gz`
    * `/Users/paul/Sequences/Raw/140401_18S_Illumina_Adelaide/18S3_PC_merged.Read.fastq.gz
    * `/Users/paul/Sequences/Raw/140401_18S_Illumina_Adelaide/18S4_PC_merged.Index.fastq.gz
    * `/Users/paul/Sequences/Raw/140401_18S_Illumina_Adelaide/18S4_PC_merged.Read.fastq.gz
  * find old Qiime mapping file - **pending**
  * find predictor data - formatted or unformatted **pending**
  * commit `4e8dccdaa9ac0501b6bf0655bef4b5d2fe91ae3d`
* **13.02.2020** - adjusting repository for analysis restart
  * `cp /Users/paul/Archive/PhD_Thesis/09_pcm_2011_sample_information/150901_PCM_data_with_ages.xlsm /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Predictors/200213_PCM_predictors.xlsm`
  * edited file to have stable hashes (hashes not generated in sheet anymore by VBA function, but saved within:)
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Predictors/200213_PCM_predictors.xlsx`
  * started R script - **pending**
    * to read in `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Predictors/200213_PCM_predictors.xlsx`
    * import function doesn't handle column names correctly, needs correction
    * check `set_names()` function in script context, as a starting point
* **14.04.2020** - re-start sequencing processing
  * continuing on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/05_join_predictors.R` - **aborted**
  * mapping file drafts already available at
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Predictors/200213_PCM_predictors.xlsx`
  * moving to scratch folder
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/05_join_predictors.R`
  * getting sequence data to MacbookPro
    * sequence data is at:
      * `/Users/paul/Sequences/Raw/140401_18S_Illumina_Adelaide/18S3_PC_merged.Index.fastq.gz`
      * `/Users/paul/Sequences/Raw/140401_18S_Illumina_Adelaide/18S3_PC_merged.Read.fastq.gz`
      * `/Users/paul/Sequences/Raw/140401_18S_Illumina_Adelaide/18S4_PC_merged.Index.fastq.gz`
      * `/Users/paul/Sequences/Raw/140401_18S_Illumina_Adelaide/18S4_PC_merged.Read.fastq.gz`
  * adjusting scripts at `/Users/paul/Documents/OU_pcm_eukaryotes/Github`
    * adjusting `/Users/paul/Documents/OU_pcm_eukaryotes/Github/020_check_fastq_files.sh`  - **aborted**
       * check commit for earlier version
    * moving files to scratch
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/020_check_fastq_files.sh`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/025_collate_qc_reports.sh`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/030_parse_fastqc_logs.sh`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/035_create_manifests.sh`
    * adjusting and running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/040_imp_qiime.sh`
  * still not working - checking old files
  * obtained original analysis files from 2016 and earlier, from:
    * `/Volumes/Macintosh HD-1/Users/paul/Archive/Papers/Czechowski_et_al_2017/analyses/5_mapping_files`
    * `/Volumes/Macintosh HD-1/Users/paul/Archive/Papers/Czechowski_et_al_2017/analyses`
  * copied to 
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Scratch/160127_data_analysis_1a_18S.sh`
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Manifest/160202_18S_MF.txt`
  * restoring from commit `4e8dccdaa9ac0501b6bf0655bef4b5d2fe91ae3d`
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/040_imp_qiime.sh`
  * moving all script to `scratch` folder
  * commit `ed26ec6e134a61ee0bb64c620e825d99d2fe43e0`
  * adjusting `/Users/paul/Documents/OU_pcm_eukaryotes/Github/050_imp_qiime.sh` - **ok**
    * check documentation for further information `http://qiime.org/scripts/split_libraries_fastq.html`
    * uses Qiime 1 code and mapping files
    * writes Fastq's
* **15.04.2020** - re-start sequencing processing
  * running and adjusting:
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/050_q1_demultiplex.sh`
      * syntax corrections  
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/060_q1_split_samples.sh`
      * creation and running
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/070_bash_check_quality.sh`
      * creating and running
      * update `Zenodo/Manifest/fastqc_adapter_reference.tsv`
  * commit `41d2a297a6bc5eb3404fc4328550e8222c2fde5f`
  * erasing all files in `/Users/paul/Sequences/Raw/`
  * compressing imports:
    * `pigz /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/050_plate_1/seqs.*`
    * `pigz /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/050_plate_2/seqs.*`
    * `pigz /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/050_plate_1/*.fastq`
    * `pigz /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/050_plate_2/*.fastq`
  * script `/Users/paul/Documents/OU_pcm_eukaryotes/Github/080_bash_cutadapt.sh`
    * creating
    * checking primers in Geneious
  *  commit `b7ac2c2b37e06ee238349673b3432854e84084cc`
  * checked DADA2 - too complicated - adjusting old Qiime2 scripts
  * created and ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/090_q2_create_manifests.sh`
  * installing Qiime 2019-10 for cluster compatibility
  * adjusting and running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/100_q2_import.sh` - **pending**
  * commit `9caed66a0551c4268e24d9640ee48e6ac8b8e68c`
  * adjusting and running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/100_q2_import.sh` - **ok**
  * also re-created valid manifest file
  * commit `cd88ed0e0836bb26c3aae2a185ed6890e2db0438`
* **16.04.2020** - re-start sequencing processing
  * adjusted `/Users/paul/Documents/OU_pcm_eukaryotes/Github/110_q2_denoise.sh`
  * commit `fbf6117688023906d86ca83fd7a308f052500620`
  * denoising started after syntax corrections, finishes quite soon
    * using Qiime 2019-10 to stay compatible with Cornell cluster
  * adjusted and ran:
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/115_gnu_plot_denoise_plate1.gnu`
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/115_gnu_plot_denoise_plate2.gnu`
    * results in `svgs` look well
  * wrote and ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/120_q2_merge.sh`
  * wrote and ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/130_q2_summary.sh`
  * commit `fb06ccb18f8f00c936e6a5ca4728f5f5970266e3`
  * exporting sequences for BLAST taxonomy annotation on cluster
    * `qiime tools export --input-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/120_18S_merged-seq.qza --output-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/120_18S_merged-seq.fasta`
    * `pigz /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/120_18S_merged-seq.fasta`
    * file names are:
     * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/140_18S_merged-seq.fasta`
     * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/140_18S_merged-seq.fasta.gz`
  * copying environmental definition file for BLAST script
    * `cp ~/Documents/CU_combined/Zenodo/Blast/190718_gi_list_environmental.txt ../Zenodo/Blast/`
  * preparing blast on cluster by reviewing
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Transport/050_sync_ncbi_nt_to_scratch.sh`
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/140_bash_fasta_blast.sh`
  * blast taxonomy assignment ongoing on cluster - finished after 6 h **ok**
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/110_18S_merged-seq_blast-noenv.xml.gz`
* **17.04.2020** - sequence processing - get taxonomy table
  * get `.tsv` from Blast results 
    * at `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/140_18S_merged-seq.fasta.gz`
    * column headers are:
     * `#OTUID`, `taxonomy`, `confidence`
    * example taxonomy table at  `/Users/paul/Documents/CU_combined/Zenodo/Qiime/180_18S_eDNA_samples_clustered99_tab_Eukaryote-shallow_qiime_artefacts_non_phylogenetic/taxonomy.tsv`
    * starting to work on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r`
      * installed all packages
      * updated paths to database on external external drive
      * waiting for `.xml` input to finish (since 15:15)
    * commit ` 8a5d9d565cb7f0f5398e2d1a0308c9b3d78cf9eb`
* **18.04.2020** - getting taxonomy table
  * progressed passed `.xml` import as indicated in script
  * commit `e657584f98d43f73e715b2eb7c0bd4968c64`
  * taxonomy table now available at
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.tsv` 
  * commit `dc91a5f4d69bdfa1e3219293774d654aaff38a8`
* **19.04.2020** - combining metadata for Qiime import
  * script `/Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
  * mapping file `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/160202_18S_MF.txt`
  * predictor source `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/200213_PCM_predictors.xlsx`
    * exported predictors `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/200419_pcm_atp.csv`
      * reviewed for import - **ok**
    * exported predictors `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/200419_pcm_geog.csv`
       * reviewed for import - **ok**   
    * exported predictors `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/200419_pcm_xrd.csv`
      * reviewed for import - **ok**    
    * exported predictors `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/200419_pcm_csbp.csv`
       * reviewed for import - **ok** 
* **20.04.2020** - data verification
  * checking number formats in above `csv` files - **ok**
  * checking hash formats via `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/200420_hash_correction.xlsm`
    * exporting new mapping files with checked hash keys
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200420_18S_MF_corrected.txt`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200420_18S_MF_corrected.xlsx`
    * checking all data files mentioned above for correct hash keys - **ok**
    * re-insert hash character in `#SmpleID`
  * in `* script /Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
    * table import is done
    * commit `f836ff3f885c6172720ffad4cf167930e4d32566`
* **20.04.2020** - data merging finished
  * finished `/Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
    * writes to `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/210421_18S_MF_merged.txt`
    * created `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/210421_18S_MF_merged_q2.txt`
      * added `#` version for Qiime
* **20.04.2020** - data merging finished
  * finished `/Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
    * writes to `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/210421_18S_MF_merged.txt`
    * created `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/210421_18S_MF_merged_q2.txt`
      * added `#` version for Qiime`
  * commit `6bc9dd6dfb530aa4634f6ad08b29af39dd207a10`
  * started to add code for transformations in `/Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
    * **unfinished, see todo**
* **24.04.2020** - correct data errors and implement transformation
  * worked on script `/Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
    * duplicate hash values in input tables have been resolved by going back to source tables
    * implemented `clr` transformation for xrd data
    * commit `fa9ffdd3ba20b9bfe8abae9f1c4947d1aca0b8cd`
* **01.05.2020** - working on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
  * preprocessing completed as in Czchowski 2016 RSOCOS
  * **ok** - introduced plotting code
  * **ok** - writing intermediate object for Michel de Lange
  * **ok** - writing final object object as `.tsv` for Qiime import
  * commit `62951db4d44e135c7fea62a4ebd765bac5066359`
* **02.05.2020** - working on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
  * save backup copy for later processing
  * simplifying script and export
  * rewrote `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200501_18S_MF_merged.txt`
  * adjusted `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200501_18S_MF_merged_q2_import.txt`
  * importing taxonomy file:
        `qiime tools import \
           --input-path  "/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.tsv" \
           --output-path "/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.qza" \
           --type 'FeatureData[Taxonomy]' \
           --input-format HeaderlessTSVTaxonomyFormat || { echo 'Taxonomy import failed' ; exit 1; }`
  * adjusting `/Users/paul/Documents/OU_pcm_eukaryotes/Github/170_q2_summary.sh`
    * working, but Blast files incomplete:
      * some ids in `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/140_18S_merged-seq.fasta`
      * are not in `~/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.tsv`
      * converting `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/110_18S_merged-seq_blast-noenv.xml`
      * for further inspection as `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/110_18S_merged-seq_blast-noenv.txt`
      * sequence counts:
        * 12399 in `.fasta` file `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/140_18S_merged-seq.fasta`
        * 11675 in `.xml`:  (`awk '{print $1}'  /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/110_18S_merged-seq_blast-noenv.txt | sort | uniq | wc -l`)
        * 11675 in q2 tax table: `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.tsv`
  * commit `dea8784c3aa3004a7794a87ac79bf2629c14b699`
* **03.05.2020** - extending taxonomy table with dropped blast hits
  * working on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r`
  * re-wrote `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.tsv`
  * rewrote `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.qza` manually as above
  * now working: `/Users/paul/Documents/OU_pcm_eukaryotes/Github/170_q2_summary.sh`
  * taxonomy table corrected **ok**
  * commit ` f8c36917a67326ee5bddc2f288025ffbf6d0ae05`
  * started working on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * commit `63ff7efbe3caaa8f05bf077cb4e39108f90b05fa`
* **04.05.2020** - testing `qiime2R`
  * `qiime2R` import function (`qza_to_phyloseq()`) is buggy.
  * `150_r_get_q2_tax-tab.r` should be yesterday's state. 
  * commit `61ecbb94869d87ecea2779db68368467628c5033`
* **05.05.2020** - creating Phyloseqs objects
  * working on `~/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * using bash based conversion, as implemented in `/Users/paul/Documents/OU_pcm_eukaryotes/Github/190_q2_export_objects.sh`
  * got long format for MdL
  * created Phyloseq object
  * rudimentary version working - create tape archive for Mdl
        `gtar -cf /Users/paul/Documents/OU_pcm_eukaryotes/Tarballs/200_r_get_phyloseq.results.tar.gz \
           /Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r \
           /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/200_all_data_long_export.Rdata \
           /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/200_all_data_psob_export.Rdata \
           /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/R/200_all_data_psob_export-image.Rdata \
           /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/R/200_all_data_psob_import-image.Rdata \
           /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/R/200_all_data_psob_import.Rdata`
  * commit `8ae070056cc00c5f61b98a9929c840f166cfe30d`
* **06.05.2020** - creating Phyloseqs objects
  * checking `~/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
* **07.05.2020** - working on obtaining trees
  * creating and running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/175_q2_seq_align.sh`  
  * creating and running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/177_q2_mask_align.sh`
  * creating and running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/180_q2_get_fastree.sh`
* **29.06.2020** -  in `200_r_get_phyloseq.r` implement filtering
  * done: `160 Samples (88 %) and 8448 Taxa (68 %) retained`
  * writing new output files as described in script (check commit history for details)
  * commit `9de24b18ae4ef7b5a9d803390b9e8650285fd6a7`
* **17.07.2020** -  in `200_r_get_phyloseq.r` started to add visualisation code
  * code for summary counts is now there
  * ASV summary counts are summed up across all samples.
  * removed low coverage phyla - **ok**
  * unfinished - see todo
  * `591721c79d7a02df556c1bcb4ae8136ff214ce5b`
* **20.07.2020** -  in `200_r_get_phyloseq.r` started re-code and new decontamination
  * continue in line 255: `# ---- continue here after 20-Jul-2020 -----` - **aborted**
* **27.07.2020** - 
  * create hitherto unused file `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200727_18S_MF.xlsx`
  * updated todo list
  * commit before further changes
  * commmit `72403c340a5ac9bea5a848d9f7b763b026c454b` 
  * drafted `decontam` usage and minor adjustments in `200_r_get_phyloseq.r`
  * commit `ae762b6201f0b1128cf4477d247572d21c39d34`
  * starting re-processing
    * **ok** - added post-PCR library and pool concentrations to `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200727_18S_MF.xlsx`
* **28.07.2020** - restarting processing
  * mapping file validation went through without errors
  * re-running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/050_q1_demultiplex.sh`
    * minimum Phred score `25`
    * new mapping file `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200727_18S_MF.txt`
* **29.07.2020** - continuing processing
  * running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/060_q1_split_samples.sh` - **ok**
  * running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/070_bash_check_quality.sh`  - **ok**
  * compressing files in place 
    * `pigz /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/050_plate_1/*.fastq` - **ok**
    * `pigz /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/050_plate_2/*.fastq` - **ok**
  * running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/080_bash_cutadapt.sh` - **ok**
  * running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/090_bash_create_manifests.sh` - **ok**
  * running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/100_q2_import.sh` - **ok**
* **30.07.2020** - denoising on Cornell cluster
  * commit `fcfee3b1b773976424e21c77c4712e6c91376cd8`
  * uploading to cluster - **completed**
* **03.08.2020** - denoising on Cornell cluster
  * denoising with `ee=1` finished quickly
    * output files do not indicate ee treshhold
  * re-running with more ee settings
    * `ee=2` specified in output file names
    * `ee=3` specified in output file names
  * exporting summary stats files to `tsv`
    * `qiime tools export --input-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_1.qza  --output-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_1.tsv`
    * `qiime tools export --input-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_2.qza  --output-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_2.tsv`
    * `qiime tools export --input-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_1_ee2.qza --output-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_1_ee2.tsv`
    * `qiime tools export --input-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_2_ee2.qza --output-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_2_ee2.tsv`
    * `qiime tools export --input-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_1_ee3.qza --output-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_1_ee3.tsv`
    * `qiime tools export --input-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_2_ee3.qza --output-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/110_18S_denoised-stt_run_2_ee3.tsv`
    * bumb in Qiime version added percentage column - erased those in converted `.txt` files so as to no need to edit the gnuplot scripts.
    * ran only for `ee=1`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/115_gnu_plot_denoise_plate1.gnu`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/115_gnu_plot_denoise_plate2.gnu`
    * ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/120_q2_merge.sh` 
    * ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/130_q2_summary.sh`
  * exporting sequences for BLAST taxonomy annotation on cluster
    * `qiime tools export --input-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/120_18S_merged-seq.qza --output-path /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/120_18S_merged-seq.fasta`
    * `pigz /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/120_18S_merged-seq.fasta`
    * file names are:
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/120_18S_merged-seq.fasta
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/120_18S_merged-seq.fasta.gz
    * copying environmental definition file for BLAST script
      * `cp ~/Documents/CU_combined/Zenodo/Blast/190718_gi_list_environmental.txt ../Zenodo/Blast/`
    * preparing blast on cluster by reviewing
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Transport/050_sync_ncbi_nt_to_scratch.sh`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/140_bash_fasta_blast.sh`
    * commit `316577910262d8d0811f362c85863cca9fa77825`
    * files arrived on cluster - copying database to scratch
    * erasing outdated files for simplicity: `find . ! -newermt 2020-06-01 ! -type d -delete`
    * blast started sucessfully at 2020-Aug-3 16:30 - finished 17:30 - expecting only few hits
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/140_18S_merged-seq_blast-noenv.xml`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/140_18S_merged-seq_blast-noenv.xml.gz`
    * start working on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r` - **unfinished**
      * waiting for `furrr::future_map()` to finish
      * contains no data 
      * re-BLast with less stringent settings (not `-evalue 1e-5`, nor `-evalue 1e-50`,  but `-evalue 1e-10` ) - **pending**
        * readily adjusted `~/Documents/OU_pcm_eukaryotes/Github/140_bash_fasta_blast.sh`
      * commit `1a75d8e79ec98d4982167c41f6138df10f15df2b`
      * erased
        * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/140_18S_merged-seq_blast-noenv.xml`
        * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_blast-noenv.Rdata`
      * pushed updated files to cluster
* **04.08.2020** - third blast on Cornell cluster
  * working on `cbsumm25` - files arriving ok
  * files blasted and back on local
  * continue 
    * reading in `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/140_18S_merged-seq_blast-noenv.xml`
    * with `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r`
* **06.08.2020** - read-in of 3rd Blast results
  * running through `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r`
* **07.08.2020** - read-in of 3rd Blast results
  * continue in line `37` - with `save()` call
* **10.08.2020** - continue processing of new Blast results
  * continue in line `80`with loading saved file
  * commit `260f6fe0a9816f2daf19ef0c0a94571d30275991`
  * finished running through `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r` - **ok**
    * re-wrote `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.tsv`
  * starting to run through `/Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
    * continued from line `21` - **ok**
    * finished script, saved output file `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200810_18S_MF_merged.txt`
* **10.08.2020** - continue re-processing - checking XRD values
  * working on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/160_r_prep_q2_predictor-tab.r`
    * as xrd values now using from `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/150901_PCM_data_with_ages_modified.xlsm`
      * original ratios values `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/200421_pcm_xrd.csv`
      * instead of raw vales `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Metadata/200421_pcm_xrd.csv`
    * in script now setting xrd values to absolute and recalculating ratios - better now - **ok**
  * commit `ec7daef26b90a15ecd9c91396c02838b788a6d55`
  * updating to qiime to `qiime2-2020.6`
  * importing taxonomy file:
      `qiime tools import \
        --input-path  "/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.tsv" \
        --output-path "/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast/150_18S_merged-seq_q2taxtable.qza" \
        --type 'FeatureData[Taxonomy]' \
        --input-format HeaderlessTSVTaxonomyFormat || { echo 'Taxonomy import failed' ; exit 1; }`
  * continue with `/Users/paul/Documents/OU_pcm_eukaryotes/Github/170_q2_summary.sh`
    * `cp /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200810_18S_MF_merged.txt /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/200810_18S_MF_merged_q2_import.txt`
  * barplot:  `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/170_18S_merged-seq_barplot.qzv`
    * many bacterial reads - **keep in mind**
  * summary file: `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/170_18S_merged-tab.qz`
    * saved output files - **ok**
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/170_feature-frequency-detail.csv`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/170_sample-frequency-detail.csv`
  * ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/175_q2_seq_align.sh` - **ok, but check alignment if using file in tree**
  * ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/177_q2_mask_align.sh` - **ok, but check alignment if using file in tree**
  * ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/180_q2_get_fastree.sh` - **ok**
  * ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/190_q2_export_objects.sh` - **ok**
    * results in `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Processing/190_18S_merged-tab_q2_export`
  * checking and rerunning `~/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
    * continue  after line `215` (with `decontam`-filtered Phyloseq object)
    * script needs restructuring, otherwise `decontam` filtering dosen't make sense
  * commit `f8157bbfea9688f1ee3f1b7bc7b1f79e020bb6fd`
* **13.08.2020** - continue re-processing - checking XRD values
  * drafted revisions of `200_r_get_phyloseq.r` 
    * needs cleaning up from top two bottom
    * upper and lower section surrounding cleanup need to be adjusted
    * adjust output file names
  * commit `39f32a129888691d69d3cbc3887c93f297b1c31b`
    * continue at line 228
* **14.08.2020** - continue re-processing - 
  * finished revision of `200_r_get_phyloseq.r`
  * putative contamination / moss reads removed to largest extent possible
  * exclude Streptophyta in Discussion
    * commit `789a099b4e7aee0279f01b1fb4ef73ff008fcd28`
  * removing contamination by genera
    * commit `01d1bb7e83652c55cd5870b592e016e2ffff3df1`
  * mailing off files
  * checking roach discrepancy - other species in control then in samples
    * commit `9ead478d554c24573598eab21e70f0c3681ba69` - other species in control then in samples
* **15.08.2020** - checking extent of putative contamination or spurious hits
  * checked alignments in Megan - see `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Megan`
  * added code to `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
   * 84 samples contain one of "Streptophyta", "Insecta", or "Chordata".
    * 69 samples contain "Streptophyta"
    * 26 samples contain one of "Insecta", or "Chordata"
  * commit `f86106a8dd1618674d7f026fb9293a4d84f8629`
* **26.08.2020** - rerunning script for manuscript composition
  * re-running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * commit `eb5c5ebe894c9c68dae3d84079b24f27a4f8accd`
* **26.08.2020** - rerunning script for manuscript composition
  * adding to `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
    * adding code to export sample locations for QGis map to `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/200622_display_item_development/200828_coordinates_all_filtered_phyla_at_all_locations.xlsx`
  * commit `f86106a8dd1618674d7f026fb9293a4d84f8629f`
* **27.12.2020**
  * received results  from Michel de Lange and GitHub link
  * check `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript`
* **03.01.2020** - starting code revision for results section update
  * added Excel export code to `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * next continue updating results by updating `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * commit `ce4d0667d73c8fcdec60080c594f65e4993a1311`
* **04.01.2020** - continuing code revision for results section update
  * done with pass
  * commit `cd030c97b4663af6aa8229f1335eebf6fc6d6c41`
  * recoded figure 2 and updated README
  * commit `874b1d1cbf45b4b95ec820210bdd7a2378d264ef`
* **07.01.2020** - continued code revision for results section update
  * commit `04349baf0bf243ee3525757c1fac697a467cd97f`
* **01.02.2020** - started manuscript revision
  * to update statistics ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
* **09.02.2021** - attempting to read in climate data from Qgis restarts
  * created copy `/Users/paul/Documents/OU_pcm_eukaryotes/Github/165_r_prep_q2_predictor-tab_with-ratser.r`
  * to read in and interpolate data from rasters
    * see `/Users/paul/Quantarctica/Quantarctica3/Atmosphere/Van Wessem RACMO`
    * RACMO Average 10 m wind speed (35 km) - `/Users/paul/Quantarctica/Quantarctica3/Atmosphere/Van Wessem RACMO/RACMO_WindSpeed_10m_35km.tif`
    * RACMO Average 2 m Total precipitation (35 km) - `/Users/paul/Quantarctica/Quantarctica3/Atmosphere/Van Wessem RACMO/RACMO_Precipitation_35km.tif`
    * RACMO Average 2 m Temperature  (35 km) - `/Users/paul/Quantarctica/Quantarctica3/Atmosphere/Van Wessem RACMO/RACMO_Temperature_2m_35km.txt`
  * created script draft
    * using `raster::diaggregate()` only -  **possibly rework**
    * better use 
       * AreaToPointKriging (`https://link.springer.com/article/10.1007/s11004-019-09840-6`) - ****possibly rework****
       * `raster.downscale()` as per `https://rdrr.io/cran/spatialEco/man/raster.downscale.html` - ****possibly rework****
    * step through pipeline again - keep in mind new mapping file with new metadata - **pending**
* **09.02.2021** - starting to re-run pipeline with new climate data
  * commit `9a378dd2d7d3e12529d4e0cd56b88f094b9c03f8`
  * continue with `/Users/paul/Documents/OU_pcm_eukaryotes/Github/170_q2_summary.sh`
    * `cp /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/210209_18S_MF_merged.txt /Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Manifest/210209_18S_MF_merged_q2_import.txt`
    * using `qiime2-2020.11` after `qiime2-2020.06` on cluster for denoising
    * adjusting and running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/170_q2_summary.sh`
    * adjusting and running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/190_q2_export_objects.sh`
    * adjusting and running `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * commit `66fe31ba4437c3ee4c230f136eb636b7ed35c937`
* **16.02.2021** - working on manuscript submission
  * revised `/Users/paul/Documents/OU_pcm_eukaryotes/Github/165_r_prep_q2_predictor-tab_with-raster.r`
    * plot `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/ProcessingPlots/210209_RACMO_selection_disagr_data_extent.pdf`
    * now used in SI as `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/201230_supplemental_information/210216_RACMO_variables.pdf`
  * commit `18f66c05ce6be9041a32573a2ab090018c074147`
  * detected in-correct counts
    * in `/Users/paul/Documents/OU_pcm_eukaryotes/Github/165_r_prep_q2_predictor-tab_with-raster.r`
    * commit before moving code to `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
    * commit `08f3697b025a3e4e35ded69cfbb2523fe81084b0`
* revised scripts and committed:
  * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/165_r_prep_q2_predictor-tab_with-raster.r`
  * `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * commit `336efabd390d9615b576bc871fcb14907cb3e963`
* **03.03.2021** - working on manuscript submission
  * worked on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * **next**
    * in manuscript correct counts (lines 139ff) and figure 2 (using Qgis)
      * for this, in `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
        * read in MdL's object at line 705, re-extract counts (for text) and coordinates (for figure)
  * commit `b96dffb43f67aa704608073572c92c5fbbca07cf`
* **03.03.2021** - submitted manuscript
  * commit `4a340cafb1383c925a8f521090b61c173e0685a6`
* **20.04.2021** - checking springtail assignments for Mark
  * in `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * after line `614`
  * running `psob_molten %>% select(OTU, Sample, Location, LongDEC, LatDEC, phylum, class, order, family, genus, species) %>% filter(class == "Collembola") %>% print(n = Inf)`
  * commit `41bd1bc9348a969edce570ce5e745843e52706c3`
* **02.06.2021** - started to work on manuscript revsions
  * created and ran `/Users/paul/Documents/OU_pcm_eukaryotes/Github/000_r_in_silico_pcr.R`
    * not the usual results - aborted
  * commit `0ee59e1e85d88678f6ae14e92f58591a77c5122c`
* **11.06.2021** - continued to work on manuscript revsions
  * started reformatting supplemental materials
* **15.06.2021** - continued to work on manuscript revsions
  * continued reformatting supplemental materials
* **16.06.2021** - continued to work on manuscript revsions
  * continued reformatting supplemental materials
  * adding better histogram code and other modifications to `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * start re-tracing steps in `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r`
  * commit can't be copied anymore check date
* **17.06.2021** - continued to work on manuscript revsions
  * ammending `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
    * saving distinct species to `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/SpeciesLists/200104_significant_species_unique.xlsx`
    * saving copy as `WebTable4`
    * saving copy to `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/R/200_uniq_sign_species.Rdata`
  * started to work through `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r`to describe taxonomy assignment process properly
  * creating `/Users/paul/Documents/OU_pcm_eukaryotes/Github/220_r_check_species_occurences.r`  for GBIF parsing
* **17.06.2021** - continued to work on manuscript revsions
  * continued working through `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r`
    * to describe taxonomy assignment process properly
    * saved workspace
    * updated all intermediate files at `/Users/paul/Documents/OU_pcm_eukaryotes/Zenodo/Blast`
    * **completed** describing taxonomy assignment process
    * commit `9bf9fc6a13b8fb58c08b8ee0d588a123798d303a`
  * continued  to work through `/Users/paul/Documents/OU_pcm_eukaryotes/Github/220_r_check_species_occurences.r`
    * to describe species occurrences
    * **unfinished** - see comments within
    * commit `92030a2dd12964ceba35e33a7b1792a7423f3447`
    * extended code somewhat - outlined next steps
* **23.06.2021** - continued to work on manuscript revsions
  * likely finished `/Users/paul/Documents/OU_pcm_eukaryotes/Github/220_r_check_species_occurences.r`
  * **no commit yet**
* **24.06.2021** - continued to work on manuscript revsions - updated manuscript files with regards to data completeness
  * worked on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/165_r_prep_q2_predictor-tab_with-raster.r`
    * updated `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/210602_supporting_material/WebFigure 4.docx`
    * created `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/210602_supporting_material/WebTable 7.xlsx`
  * commit `78b4f59c6753683732f67a340f7e4a70c344e7df`
* **25.06.2021** - continued to work on manuscript revsions - updated manuscript files with regards to data completeness
  * worked on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/165_r_prep_q2_predictor-tab_with-raster.r`
  * worked on `/Users/paul/Documents/OU_pcm_eukaryotes/Github/200_r_get_phyloseq.r`
  * commit `88a8468862b63d349e2024e09bfc4720e316770c`
* **28.06.2021** - continued to work on manuscript revsions
* **29.06.2021** - continued to work on manuscript revsions
* **30.06.2021** - finished manuscript revsions for review by coauthors - commit `cea3a7a393cb5de59783fe77bd7a0ce3d334f80d`
* **12.07.2021** - started finalizing revisions after receiving feedback
  * **next** 
    * add Blast confidences to
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/210602_supporting_material/WebTable 4.xlsx`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/210602_supporting_material/WebTable 5.xlsx`
      * `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/210602_supporting_material/WebTable 6.xlsx`
    * continue in text `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/210712_FEE21-0056_main_text.docx`
* **13.07.2021** - started finalizing revisions after receiving feedback  
  * use `/Users/paul/Documents/OU_pcm_eukaryotes/Github/150_r_get_q2_tax-tab.r`
  * as a template for `/Users/paul/Documents/OU_pcm_eukaryotes/Github/230_r_add_blast_scores_to_som.r`
  * finished `/Users/paul/Documents/OU_pcm_eukaryotes/Github/230_r_add_blast_scores_to_som.r`
  * finalising revisions
  * commit `a0dcc39ebc9546608944e925686ff8ca38571514`
* **10.11.2021** - starting revisions in version `FEE21-0056.R2`
  * see files:
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/211110_FEE21-0056.R1_responses.docx`
    * `/Users/paul/Documents/OU_pcm_eukaryotes/Manuscript/211110_FEE21-0056.R2_main_text.docx`
* **11.11.2021** - continuing revisions in version `FEE21-0056.R2`
* **12.11.2021** - continuing revisions in version `FEE21-0056.R2`
  * done with most - waiting fro MdL
  * commit `e8454abe7e6d4f57364d4ec5656abbe55f8e599b`
* **18.11.2021** - continuing revisions in version `FEE21-0056.R2`
  * uploading script folder to GitHub
  * releasing scripts on GitHub - crosslinking to Zenodo for doi minting
  * compressing  analysis files `tar -zcvf 211118_analysis_files.tar.gz Zenodo/` 
  * uploading files to Zenodo
  * erase archive to save local disk space
  * finalising revsion for co-authors
* **19.11.2021** - updating archives for GBIF licensing
  * getting derived data set for GBIF
  * creating new code commit past release version
  * creating new Zenodo version

  
 
  

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