Data were produced in Minknow. Fastq files generated using guppy basecalling (using "Accurate" mode) and demultiplexed (12 barcodes)
To launch notebook:
conda activate nanopore
jupyter lab
nanopore is the name I chose for my environment. Can be whatever you named it
# once inside notebook, activate again
conda activate nanopore
(nanopore)
Install Nanoplot from https://github.com/wdecoster/NanoPlot.
Reference for Nanoplot
#pip install Nanoplot
Collecting Nanoplot
Using cached NanoPlot-1.41.0.tar.gz (31 kB)
Preparing metadata (setup.py) ... done
Collecting biopython
Downloading biopython-1.80-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
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Collecting pysam>0.10.0.0
Downloading pysam-0.20.0.tar.gz (4.0 MB)
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Collecting numpy>=1.16.5
Downloading numpy-1.24.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
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Collecting scipy
Downloading scipy-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.1 MB)
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Requirement already satisfied: python-dateutil in /home/esuter/miniconda3/envs/nanopore/lib/python3.11/site-packages (from Nanoplot) (2.8.2)
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Using cached nanoget-1.18.1.tar.gz (24 kB)
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Using cached plotly-5.13.0-py2.py3-none-any.whl (15.2 MB)
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Building wheels for collected packages: Nanoplot, nanoget, nanomath, pysam, Python-Deprecated
Building wheel for Nanoplot (setup.py) ... done
Created wheel for Nanoplot: filename=NanoPlot-1.41.0-py3-none-any.whl size=34448 sha256=ec7739b39f2e9a01f06f36bd72c4d14977eb168d83f447b1a72db7b9ab2c0fc8
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Created wheel for pysam: filename=pysam-0.20.0-cp311-cp311-linux_x86_64.whl size=3253429 sha256=3a4ed6cc8c7896fa44e1677a24e0275d5df982a2300f5ac97bfc6655d1a7aad1
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Stored in directory: /home/esuter/.cache/pip/wheels/4b/3d/f8/4ee55d20d479ba1bd9ef02e0ab72a618eb59d8727defb4a770
Successfully built Nanoplot nanoget nanomath pysam Python-Deprecated
Installing collected packages: Python-Deprecated, pysam, kaleido, tenacity, numpy, scipy, pyarrow, plotly, pandas, biopython, nanomath, nanoget, Nanoplot
Successfully installed Nanoplot-1.41.0 Python-Deprecated-1.1.0 biopython-1.80 kaleido-0.2.1 nanoget-1.18.1 nanomath-1.2.1 numpy-1.24.2 pandas-1.5.3 plotly-5.13.0 pyarrow-11.0.0 pysam-0.20.0 scipy-1.10.0 tenacity-8.2.0
Note: you may need to restart the kernel to use updated packages.
# NanoPlot --summary raw_data/sequencing_summary.txt --loglength -o summary-plots-log-transformed
The above outputs a bunch of figures in summary-plots-log-transformed/.
For example:
The above shows most of my reads are around 4.2kB as expected and the average quality is about 13-14. There is a peak of reads at ~8.4kB, twice the amplicone length, so these are probablly chimeras. Same for ~12.6kB. Use Nanofilt to trim.
Nanofilt is available from here
Note- Nanofilt soon will be replaced with chopper? Keep checking
# pip install nanofilt
Collecting nanofilt Using cached NanoFilt-2.8.0.tar.gz (7.4 kB) Preparing metadata (setup.py) ... done Requirement already satisfied: biopython in /home/esuter/miniconda3/lib/python3.10/site-packages (from nanofilt) (1.80) Requirement already satisfied: pandas>=0.22.0 in /home/esuter/miniconda3/lib/python3.10/site-packages (from nanofilt) (1.5.3) Requirement already satisfied: python-dateutil>=2.8.1 in /home/esuter/miniconda3/lib/python3.10/site-packages (from pandas>=0.22.0->nanofilt) (2.8.2) Requirement already satisfied: numpy>=1.21.0 in /home/esuter/miniconda3/lib/python3.10/site-packages (from pandas>=0.22.0->nanofilt) (1.24.2) Requirement already satisfied: pytz>=2020.1 in /home/esuter/miniconda3/lib/python3.10/site-packages (from pandas>=0.22.0->nanofilt) (2022.7.1) Requirement already satisfied: six>=1.5 in /home/esuter/miniconda3/lib/python3.10/site-packages (from python-dateutil>=2.8.1->pandas>=0.22.0->nanofilt) (1.16.0) Building wheels for collected packages: nanofilt Building wheel for nanofilt (setup.py) ... done Created wheel for nanofilt: filename=NanoFilt-2.8.0-py3-none-any.whl size=8781 sha256=1b46647c8e6d7187cff40a0717aca06c26027dd257ed76342f0865b478b97e24 Stored in directory: /home/esuter/.cache/pip/wheels/53/4b/76/3e301955a8a693c62837d0be92909b33d93e40f5de21555e0b Successfully built nanofilt Installing collected packages: nanofilt Successfully installed nanofilt-2.8.0
# First concatenate all samples from same barcode into one fastq file
# concatenate content of all fastq files (I think each represents one pore) within each folder into one fastq file per sample/barcode
cd raw_data/barcode01
cat *.fastq.gz > b01.fq.gz
cd ..
cd barcode02
cat *.fastq.gz > b02.fq.gz
cd ..
cd barcode03
cat *.fastq.gz > b03.fq.gz
cd ..
cd barcode04
cat *.fastq.gz > b04.fq.gz
cd ..
cd barcode05
cat *.fastq.gz > b05.fq.gz
cd ..
cd barcode06
cat *.fastq.gz > b06.fq.gz
cd ..
cd barcode07
cat *.fastq.gz > b07.fq.gz
cd ..
cd barcode08
cat *.fastq.gz > b08.fq.gz
cd ..
cd barcode09
cat *.fastq.gz > b09.fq.gz
cd ..
cd barcode10
cat *.fastq.gz > b10.fq.gz
cd ..
cd barcode11
cat *.fastq.gz > b11.fq.gz
cd ..
cd barcode12
cat *.fastq.gz > b12.fq.gz
cd ..
# move concatenated files up to raw_data directory
cd ..
mv raw_data/barcode*/b* raw_data
# make directory for trimmed sequences
mkdir trimmed_data
# For each barcode, unzip, trim reads with quality score less than 10, make keep lengths +/- 20% of expected length (3360-5040).
# Trim first 50 bp which are likely primer + tail
# Rezip and put into trimmed_data directory
gunzip -c raw_data/b01.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b01.fq.gz
gunzip -c raw_data/b02.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b02.fq.gz
gunzip -c raw_data/b03.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b03.fq.gz
gunzip -c raw_data/b04.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b04.fq.gz
gunzip -c raw_data/b05.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b05.fq.gz
gunzip -c raw_data/b06.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b06.fq.gz
gunzip -c raw_data/b07.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b07.fq.gz
gunzip -c raw_data/b08.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b08.fq.gz
gunzip -c raw_data/b09.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b09.fq.gz
gunzip -c raw_data/b10.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b10.fq.gz
gunzip -c raw_data/b11.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b11.fq.gz
gunzip -c raw_data/b12.fq.gz | NanoFilt -q 10 -l 3360 --maxlength 5040 --headcrop 50 | gzip > trimmed_data/b12.fq.gz
# Use Nanoplot again to visualize reads now. No longer can use summary file (that was output from Minknow). Instead use fastq files directly:
NanoPlot -t 2 --fastq trimmed_data/*.fq.gz --plots hex dot
WARNING: hex as part of --plots has been deprecated and will be ignored. To get the hex output, rerun with --legacy hex.
# Move output from above into a directory
mkdir trimmed_data_summary-plots
mv *.html trimmed_data_summary-plots/
mv *.png trimmed_data_summary-plots/
mv *.log trimmed_data_summary-plots/
mv NanoStats.txt trimmed_data_summary-plots/
mv: cannot stat '*.html': No such file or directory mv: cannot stat '*.png': No such file or directory mv: cannot stat '*.log': No such file or directory
Look at plots again:
# Install ncbi toolkit
# run in terminal because need to put in password
## sudo apt-get install ncbi-blast+
[sudo] password for esuter:
# check
blastn -h
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-entrez_query entrez_query]
[-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
[-subject subject_input_file] [-subject_loc range] [-query input_file]
[-out output_file] [-evalue evalue] [-word_size int_value]
[-gapopen open_penalty] [-gapextend extend_penalty]
[-perc_identity float_value] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-version]
DESCRIPTION
Nucleotide-Nucleotide BLAST 2.6.0+
Use '-help' to print detailed descriptions of command line arguments
According to this, the blastn sudo-apt hasn't been updated since version 2.5 in 2017 and leads to errors (which I began having below).
Update to latest, v2.13.0
# conda install blast=2.13.0
blastn -version
blastn: 2.13.0+ Package: blast 2.13.0, build Jul 18 2022 22:49:37 (nanopore)
# make new directory for fasta files
# mkdir trimmed_fasta
# unzip fq files for input to fasta
#gunzip trimmed_data/*.fq.gz trimmed_data/*.fq
install pyfastx for handling fastq files
# pip install pyfastx
# convert fastq to fasta files
pyfastx fq2fa -o trimmed_fasta/b01.fa trimmed_data/b01.fq
pyfastx fq2fa -o trimmed_fasta/b02.fa trimmed_data/b02.fq
pyfastx fq2fa -o trimmed_fasta/b03.fa trimmed_data/b03.fq
pyfastx fq2fa -o trimmed_fasta/b04.fa trimmed_data/b04.fq
pyfastx fq2fa -o trimmed_fasta/b05.fa trimmed_data/b05.fq
pyfastx fq2fa -o trimmed_fasta/b06.fa trimmed_data/b06.fq
pyfastx fq2fa -o trimmed_fasta/b07.fa trimmed_data/b07.fq
pyfastx fq2fa -o trimmed_fasta/b08.fa trimmed_data/b08.fq
pyfastx fq2fa -o trimmed_fasta/b09.fa trimmed_data/b09.fq
pyfastx fq2fa -o trimmed_fasta/b10.fa trimmed_data/b10.fq
pyfastx fq2fa -o trimmed_fasta/b11.fa trimmed_data/b11.fq
pyfastx fq2fa -o trimmed_fasta/b12.fa trimmed_data/b12.fq
Test blast tools for annotation. Start with smallest file first, b11
Ibironke et al. use discontinuous mega-blast (dc-megablast from the blast docs) but this is depracated. Seems to be incorporated into blastn?
mkdir results
The headings of the output table will be the following parameters from NCBI:
According to this task-blastn should be used for finding different species, task-megablast should be used for finding differents within the same species (and thus is faster), but seems like I should be using regular blastn
# test blastn on small subset i copied from b12 (pos ctl)
blastn -query trimmed_fasta/test.fa \
-db nt \
-out results/test_blast.txt \
-remote \
-max_target_seqs 1 \
-task dc-megablast \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
(nanopore) (nanopore) Warning: [blastn] Examining 5 or more matches is recommended (nanopore)
After running the test file, I see there are multiple species output for one input sequence. It seems like it gives the top 2-3 hits. Need to do some post filtering to get one-for-one in species table. Not sure why it's doing this because I set max target seqs to 1
The warning about 5 or more matches is related to the -max_target_seqs, I think
# barcode 1
blastn -query trimmed_fasta/b01.fa \
-db nt \
-out results/b01.txt \
-remote \
-max_target_seqs 1 \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
Warning: [blastn] Examining 5 or more matches is recommended (nanopore)
blastn -query trimmed_fasta/b02.fa \
-db nt \
-out results/b02.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b03.fa \
-db nt \
-out results/b03.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b04.fa \
-db nt \
-out results/b04.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b05.fa \
-db nt \
-out results/b05.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b06.fa \
-db nt \
-out results/b06.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b07.fa \
-db nt \
-out results/b07.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b08.fa \
-db nt \
-out results/b08.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b09.fa \
-db nt \
-out results/b09.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b10.fa \
-db nt \
-out results/b10.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b11.fa \
-db nt \
-out results/b11.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
blastn -query trimmed_fasta/b12.fa \
-db nt \
-out results/b12.txt \
-remote \
-max_target_seqs 1 \
-task-blastn \
-outfmt "6 qseqid sseqid pident length mismatch evalue bitscore staxids stitle"
Abandon BLAST for now. Found this relatively new pub
Follow instructions for use from github repo and website
conda install numpy
Collecting numpy Using cached https://files.pythonhosted.org/packages/3a/5f/47e578b3ae79e2624e205445ab77a1848acdaa2929a00eeef6b16eaaeb20/numpy-1.16.6-cp27-cp27mu-manylinux1_x86_64.whl Installing collected packages: numpy Successfully installed numpy-1.16.6 (nanopore2)
## had to make new environment to get these installs to work
# conda create --name nanopore2
# conda activate nanopore2
## For dependencies
# conda install -c bioconda minimap2 # long-read mapper
# conda install -c bioconda krona rename # Krona plot
pip install pandas matplotlib # Stacked bar plot
minimap2 --version
ktImportTaxonomy # just check one of Krona functions
(nanopore2)
(nanopore2)
(nanopore2)
(nanopore2)
(nanopore2)
(nanopore2)
(nanopore2)
(nanopore2)
Collecting pandas
Using cached pandas-1.5.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.0 MB)
Collecting matplotlib
Downloading matplotlib-3.6.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.8 MB)
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Collecting python-dateutil>=2.8.1
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting pytz>=2020.1
Using cached pytz-2022.7.1-py2.py3-none-any.whl (499 kB)
Requirement already satisfied: numpy>=1.21.0 in /home/esuter/miniconda3/envs/nanopore2/lib/python3.11/site-packages (from pandas) (1.24.2)
Collecting contourpy>=1.0.1
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Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
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Successfully installed contourpy-1.0.7 cycler-0.11.0 fonttools-4.38.0 kiwisolver-1.4.4 matplotlib-3.6.3 packaging-23.0 pandas-1.5.3 pillow-9.4.0 pyparsing-3.0.9 python-dateutil-2.8.2 pytz-2022.7.1 six-1.16.0
(nanopore2)
(nanopore2)
2.24-r1122
(nanopore2)
_____________________________________
______________________________________/ KronaTools 2.7.1 - ktImportTaxonomy \___
Creates a Krona chart based on taxonomy IDs and, optionally, magnitudes and
scores. Taxonomy IDs corresponding to a rank of "no rank" in the database will
be assigned to their parents to make the hierarchy less cluttered (e.g.
"Cellular organisms" will be assigned to "root").
_______
____________________________________________________________________/ Usage \___
ktImportTaxonomy \
[options] \
taxonomy_1[:magnitudes_1][,name_1] \
[taxonomy_2[:magnitudes_2][,name_2]] \
...
taxonomy Tab-delimited file with taxonomy IDs and (optionally) query
IDs, magnitudes and scores. By default, query IDs, taxonomy IDs
and scores will be taken from columns 1, 2 and 3, respectively
(see -q, -t, -s, and -m). Lines beginning with "#" will be
ignored. By default, separate datasets will be created for each
input (see [-c]).
magnitudes Optional file listing query IDs with magnitudes, separated by
tabs. This can be used to account for read length or contig
depth to obtain a more accurate representation of abundance. By
default, query sequences without specified magnitudes will be
assigned a magnitude of 1. Magnitude files for assemblies in ACE
format can be created with ktGetContigMagnitudes.
name A name to show in the list of datasets in the Krona chart (if
multiple input files are present and [-c] is not specified). By
default, the basename of the file will be used.
_________
__________________________________________________________________/ Options \___
[-o <string>] Output file name. [Default: 'taxonomy.krona.html']
[-n <string>] Name of the highest level. [Default: 'Root']
[-i] Include a wedge for queries with no hits.
[-c] Combine data from each file, rather than creating separate
datasets within the chart.
[-q <integer>] Column of input files to use as query ID. Required if
magnitude files are specified. [Default: '1']
[-t <integer>] Column of input files to use as taxonomy ID. [Default:
'2']
[-s <integer>] Column of input files to use as score. [Default: '3']
[-m <integer>] Column of input files to use as magnitude. If magnitude
files are specified, their magnitudes will override those
in this column.
[-d <integer>] Maximum depth of wedges to include in the chart.
[-k] Show the "cellular organisms" taxon (collapsed by
default).
[-K] Collapse assignments to taxa with ranks labeled "no rank"
by moving up to parent.
[-x <integer>] Hue (0-360) for "bad" scores. [Default: '0']
[-y <integer>] Hue (0-360) for "good" scores. [Default: '120']
[-u <string>] URL of Krona resources to use instead of bundling them
with the chart (e.g. "http://krona.sourceforge.net").
Reduces size of charts and allows updates, though charts
will not work without access to this URL.
[-qp <string>] Url to send query IDs to (instead of listing them) for
each wedge. The query IDs will be sent as a comma separated
list in the POST variable "queries", with the current
dataset index (from 0) in the POST variable "dataset". The
url can include additional variables encoded via GET.
[-tax <string>] Path to directory containing a taxonomy database to use.
[Default:
'/home/esuter/miniconda3/envs/nanopore2/opt/krona/taxonomy']
(nanopore2)
## Getting Started
# git clone https://github.com/seoldh/MIrROR.git
# cd MIrROR
# ./MIrROR.py -h
(nanopore2)
Cloning into 'MIrROR'...
remote: Enumerating objects: 49, done.
remote: Counting objects: 100% (3/3), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 49 (delta 0), reused 3 (delta 0), pack-reused 46
Receiving objects: 100% (49/49), 49.31 MiB | 3.26 MiB/s, done.
Resolving deltas: 100% (9/9), done.
(nanopore2)
(nanopore2)
Usage: MIrROR.py [options] (-d DBDIR) INPUTFILE
MIrROR: a tool for metataxonomics with 16S-23S rRNA operon region.
INPUTFILE: FASTA/FASTQ/PAF | SAMPLELIST
Options:
-d DBDIR, --db_dir=DBDIR
directory containing MIrROR database [required]
-o OUTDIR, --output_dir=OUTDIR
specify directory to output files (default : ./Result)
-t INT, --threads=INT
number of threads (default : 4)
Mapping option:
this option control for Mapping
-M NUM, --minibatch=NUM
number of query bases loaded to the memory at once.
K/M/G/k/m/g suffix is accepted. (default : 500M)
Threshold options:
these options control for Threshold
-m INT, --residuemaches=INT
number of residue matches (default : 2500)
-b INT, --blocklength=INT
alignment block length (default : 3500)
-n, --Normalization
normalize by 16S-23S rRNA operon copy number
Visualization options:
these options control for Visualization
-K, --Krona create a Krona plot. Requires KronaTools to be
installed
-S, --Stackedplot create a stacked bar plot. Requires Python packages to
be installed
-V, --visualized perform all visualization tasks (Same as: -K -S)
Help:
-h, --help show this help message and exit
-v, --version show version number and exit
(nanopore2)
## Download 16S-23S rRNA operon database
#mkdir DBDIR
#wget -P DBDIR http://mirror.egnome.co.kr/media/ToolsDatabase/2021_06/MIrROR_DB_r01.mmi
#wget -P DBDIR http://mirror.egnome.co.kr/media/ToolsDatabase/2021_06/MIrROR_DB_r01.tsv
(nanopore2) (nanopore2) --2023-02-10 12:30:09-- http://mirror.egnome.co.kr/media/ToolsDatabase/2021_06/MIrROR_DB_r01.mmi Resolving mirror.egnome.co.kr (mirror.egnome.co.kr)... 147.47.67.225 Connecting to mirror.egnome.co.kr (mirror.egnome.co.kr)|147.47.67.225|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 846091773 (807M) [application/octet-stream] Saving to: ‘DBDIR/MIrROR_DB_r01.mmi’ MIrROR_DB_r01.mmi 100%[===================>] 806.90M 224KB/s in 1h 46m 2023-02-10 14:16:17 (130 KB/s) - ‘DBDIR/MIrROR_DB_r01.mmi’ saved [846091773/846091773] (nanopore2) --2023-02-10 14:16:17-- http://mirror.egnome.co.kr/media/ToolsDatabase/2021_06/MIrROR_DB_r01.tsv Resolving mirror.egnome.co.kr (mirror.egnome.co.kr)... 147.47.67.225 Connecting to mirror.egnome.co.kr (mirror.egnome.co.kr)|147.47.67.225|:80... connected. HTTP request sent, awaiting response... 302 Found Location: http://mirror.egnome.co.kr/003892724856/media/ToolsDatabase/2021_06/MIrROR_DB_r01.tsv [following] --2023-02-10 14:16:18-- http://mirror.egnome.co.kr/003892724856/media/ToolsDatabase/2021_06/MIrROR_DB_r01.tsv Connecting to mirror.egnome.co.kr (mirror.egnome.co.kr)|147.47.67.225|:80... connected. HTTP request sent, awaiting response... 302 Found Location: http://mirror.egnome.co.kr/media/ToolsDatabase/2021_06/MIrROR_DB_r01.tsv [following] --2023-02-10 14:16:18-- http://mirror.egnome.co.kr/media/ToolsDatabase/2021_06/MIrROR_DB_r01.tsv Connecting to mirror.egnome.co.kr (mirror.egnome.co.kr)|147.47.67.225|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 5127809 (4.9M) [text/tab-separated-values] Saving to: ‘DBDIR/MIrROR_DB_r01.tsv’ MIrROR_DB_r01.tsv 100%[===================>] 4.89M 104KB/s in 77s 2023-02-10 14:17:37 (64.7 KB/s) - ‘DBDIR/MIrROR_DB_r01.tsv’ saved [5127809/5127809] (nanopore2)
# Try on test data
./MIrROR.py -V -d DBDIR -o ../results/test ../trimmed_fasta/test.fa
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/test ../trimmed_fasta/test.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/test.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-10 15:08:26] INFO : MIrROR analysis Start
[2023-02-10 15:08:26] INFO : filecheck STEP START
[2023-02-10 15:08:26] INFO : 1 sample proceeding
[2023-02-10 15:08:26] INFO : mapping STEP START
[2023-02-10 15:08:26] INFO : 1 / 1 Mapping...
[2023-02-10 15:08:29] INFO : classification STEP START
[2023-02-10 15:08:29] INFO : 1 / 1 Annotatioin...
[2023-02-10 15:08:29] INFO : OTUtable STEP START
[2023-02-10 15:08:29] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/OTUtable/OUTPUT_std.txt
[2023-02-10 15:08:29] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/OTUtable/OUTPUT_mpa.txt
[2023-02-10 15:08:29] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/OTUtable/OUTPUT_std_type2.txt
[2023-02-10 15:08:29] INFO : visualization STEP START
[2023-02-10 15:08:30] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/visualization/stacked_phylum.png
[2023-02-10 15:08:30] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/visualization/stacked_class.png
[2023-02-10 15:08:30] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/visualization/stacked_order.png
[2023-02-10 15:08:30] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/visualization/stacked_family.png
[2023-02-10 15:08:30] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/visualization/stacked_genus.png
[2023-02-10 15:08:30] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/visualization/stacked_species.png
[2023-02-10 15:08:30] INFO : Log from OTUsamples2krona
Writing krona/test.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-10 15:08:30] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/visualization/krona
[2023-02-10 15:08:30] INFO : MIrROR analysis Completed!
Total time used : 0:00:03.835219
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/test/test.log
(nanopore2)
Got it working. Run the samples. Still need to find out alignment quality- that is hidden somewhere in .paf file (output from minimap2). But at least generate tables for now
./MIrROR.py -V -d DBDIR -o ../results/b01 ../trimmed_fasta/b01.fa
./MIrROR.py -V -d DBDIR -o ../results/b02 ../trimmed_fasta/b02.fa
./MIrROR.py -V -d DBDIR -o ../results/b03 ../trimmed_fasta/b03.fa
./MIrROR.py -V -d DBDIR -o ../results/b04 ../trimmed_fasta/b04.fa
./MIrROR.py -V -d DBDIR -o ../results/b05 ../trimmed_fasta/b05.fa
./MIrROR.py -V -d DBDIR -o ../results/b06 ../trimmed_fasta/b06.fa
./MIrROR.py -V -d DBDIR -o ../results/b07 ../trimmed_fasta/b07.fa
./MIrROR.py -V -d DBDIR -o ../results/b08 ../trimmed_fasta/b08.fa
./MIrROR.py -V -d DBDIR -o ../results/b09 ../trimmed_fasta/b09.fa
./MIrROR.py -V -d DBDIR -o ../results/b10 ../trimmed_fasta/b10.fa
./MIrROR.py -V -d DBDIR -o ../results/b11 ../trimmed_fasta/b11.fa
./MIrROR.py -V -d DBDIR -o ../results/b12 ../trimmed_fasta/b12.fa
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b01 ../trimmed_fasta/b01.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b01.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-10 15:17:55] INFO : MIrROR analysis Start
[2023-02-10 15:17:55] INFO : filecheck STEP START
[2023-02-10 15:17:55] INFO : 1 sample proceeding
[2023-02-10 15:17:55] INFO : mapping STEP START
[2023-02-10 15:17:55] INFO : 1 / 1 Mapping...
[2023-02-10 16:36:01] INFO : classification STEP START
[2023-02-10 16:36:01] INFO : 1 / 1 Annotatioin...
[2023-02-10 16:36:01] INFO : OTUtable STEP START
[2023-02-10 16:36:01] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/OTUtable/OUTPUT_std.txt
[2023-02-10 16:36:01] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/OTUtable/OUTPUT_mpa.txt
[2023-02-10 16:36:01] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/OTUtable/OUTPUT_std_type2.txt
[2023-02-10 16:36:01] INFO : visualization STEP START
[2023-02-10 16:36:02] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/visualization/stacked_phylum.png
[2023-02-10 16:36:02] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/visualization/stacked_class.png
[2023-02-10 16:36:02] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/visualization/stacked_order.png
[2023-02-10 16:36:03] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/visualization/stacked_family.png
[2023-02-10 16:36:03] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/visualization/stacked_genus.png
[2023-02-10 16:36:04] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/visualization/stacked_species.png
[2023-02-10 16:36:04] INFO : Log from OTUsamples2krona
Writing krona/b01.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-10 16:36:04] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/visualization/krona
[2023-02-10 16:36:04] INFO : MIrROR analysis Completed!
Total time used : 1:18:08.778566
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b01/b01.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b02 ../trimmed_fasta/b02.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b02.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-10 16:36:04] INFO : MIrROR analysis Start
[2023-02-10 16:36:04] INFO : filecheck STEP START
[2023-02-10 16:36:04] INFO : 1 sample proceeding
[2023-02-10 16:36:04] INFO : mapping STEP START
[2023-02-10 16:36:04] INFO : 1 / 1 Mapping...
[2023-02-10 19:32:15] INFO : classification STEP START
[2023-02-10 19:32:15] INFO : 1 / 1 Annotatioin...
[2023-02-10 19:32:15] INFO : OTUtable STEP START
[2023-02-10 19:32:15] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/OTUtable/OUTPUT_std.txt
[2023-02-10 19:32:15] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/OTUtable/OUTPUT_mpa.txt
[2023-02-10 19:32:15] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/OTUtable/OUTPUT_std_type2.txt
[2023-02-10 19:32:15] INFO : visualization STEP START
[2023-02-10 19:32:16] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/visualization/stacked_phylum.png
[2023-02-10 19:32:16] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/visualization/stacked_class.png
[2023-02-10 19:32:17] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/visualization/stacked_order.png
[2023-02-10 19:32:19] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/visualization/stacked_family.png
[2023-02-10 19:32:22] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/visualization/stacked_genus.png
[2023-02-10 19:32:31] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/visualization/stacked_species.png
[2023-02-10 19:32:31] INFO : Log from OTUsamples2krona
Writing krona/b02.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-10 19:32:31] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/visualization/krona
[2023-02-10 19:32:31] INFO : MIrROR analysis Completed!
Total time used : 2:56:26.847421
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b02/b02.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b03 ../trimmed_fasta/b03.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b03.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-10 19:32:32] INFO : MIrROR analysis Start
[2023-02-10 19:32:32] INFO : filecheck STEP START
[2023-02-10 19:32:32] INFO : 1 sample proceeding
[2023-02-10 19:32:32] INFO : mapping STEP START
[2023-02-10 19:32:32] INFO : 1 / 1 Mapping...
[2023-02-10 23:12:06] INFO : classification STEP START
[2023-02-10 23:12:06] INFO : 1 / 1 Annotatioin...
[2023-02-10 23:12:06] INFO : OTUtable STEP START
[2023-02-10 23:12:06] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/OTUtable/OUTPUT_std.txt
[2023-02-10 23:12:06] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/OTUtable/OUTPUT_mpa.txt
[2023-02-10 23:12:06] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/OTUtable/OUTPUT_std_type2.txt
[2023-02-10 23:12:06] INFO : visualization STEP START
[2023-02-10 23:12:07] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/visualization/stacked_phylum.png
[2023-02-10 23:12:07] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/visualization/stacked_class.png
[2023-02-10 23:12:07] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/visualization/stacked_order.png
[2023-02-10 23:12:08] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/visualization/stacked_family.png
[2023-02-10 23:12:08] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/visualization/stacked_genus.png
[2023-02-10 23:12:09] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/visualization/stacked_species.png
[2023-02-10 23:12:09] INFO : Log from OTUsamples2krona
Writing krona/b03.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-10 23:12:09] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/visualization/krona
[2023-02-10 23:12:09] INFO : MIrROR analysis Completed!
Total time used : 3:39:37.306994
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b03/b03.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b04 ../trimmed_fasta/b04.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b04.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-10 23:12:09] INFO : MIrROR analysis Start
[2023-02-10 23:12:09] INFO : filecheck STEP START
[2023-02-10 23:12:09] INFO : 1 sample proceeding
[2023-02-10 23:12:09] INFO : mapping STEP START
[2023-02-10 23:12:09] INFO : 1 / 1 Mapping...
[2023-02-11 02:04:34] INFO : classification STEP START
[2023-02-11 02:04:34] INFO : 1 / 1 Annotatioin...
[2023-02-11 02:04:34] INFO : OTUtable STEP START
[2023-02-11 02:04:34] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/OTUtable/OUTPUT_std.txt
[2023-02-11 02:04:34] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/OTUtable/OUTPUT_mpa.txt
[2023-02-11 02:04:34] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/OTUtable/OUTPUT_std_type2.txt
[2023-02-11 02:04:34] INFO : visualization STEP START
[2023-02-11 02:04:34] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/visualization/stacked_phylum.png
[2023-02-11 02:04:35] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/visualization/stacked_class.png
[2023-02-11 02:04:35] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/visualization/stacked_order.png
[2023-02-11 02:04:35] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/visualization/stacked_family.png
[2023-02-11 02:04:36] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/visualization/stacked_genus.png
[2023-02-11 02:04:37] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/visualization/stacked_species.png
[2023-02-11 02:04:37] INFO : Log from OTUsamples2krona
Writing krona/b04.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-11 02:04:37] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/visualization/krona
[2023-02-11 02:04:37] INFO : MIrROR analysis Completed!
Total time used : 2:52:27.597229
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b04/b04.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b05 ../trimmed_fasta/b05.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b05.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-11 02:04:37] INFO : MIrROR analysis Start
[2023-02-11 02:04:37] INFO : filecheck STEP START
[2023-02-11 02:04:37] INFO : 1 sample proceeding
[2023-02-11 02:04:37] INFO : mapping STEP START
[2023-02-11 02:04:37] INFO : 1 / 1 Mapping...
[2023-02-11 06:11:24] INFO : classification STEP START
[2023-02-11 06:11:24] INFO : 1 / 1 Annotatioin...
[2023-02-11 06:11:24] INFO : OTUtable STEP START
[2023-02-11 06:11:24] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/OTUtable/OUTPUT_std.txt
[2023-02-11 06:11:24] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/OTUtable/OUTPUT_mpa.txt
[2023-02-11 06:11:24] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/OTUtable/OUTPUT_std_type2.txt
[2023-02-11 06:11:24] INFO : visualization STEP START
[2023-02-11 06:11:25] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/visualization/stacked_phylum.png
[2023-02-11 06:11:25] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/visualization/stacked_class.png
[2023-02-11 06:11:25] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/visualization/stacked_order.png
[2023-02-11 06:11:26] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/visualization/stacked_family.png
[2023-02-11 06:11:26] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/visualization/stacked_genus.png
[2023-02-11 06:11:27] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/visualization/stacked_species.png
[2023-02-11 06:11:27] INFO : Log from OTUsamples2krona
Writing krona/b05.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-11 06:11:27] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/visualization/krona
[2023-02-11 06:11:27] INFO : MIrROR analysis Completed!
Total time used : 4:06:50.341560
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b05/b05.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b06 ../trimmed_fasta/b06.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b06.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-11 06:11:27] INFO : MIrROR analysis Start
[2023-02-11 06:11:27] INFO : filecheck STEP START
[2023-02-11 06:11:27] INFO : 1 sample proceeding
[2023-02-11 06:11:27] INFO : mapping STEP START
[2023-02-11 06:11:27] INFO : 1 / 1 Mapping...
[2023-02-11 10:12:48] INFO : classification STEP START
[2023-02-11 10:12:48] INFO : 1 / 1 Annotatioin...
[2023-02-11 10:12:48] INFO : OTUtable STEP START
[2023-02-11 10:12:48] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/OTUtable/OUTPUT_std.txt
[2023-02-11 10:12:48] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/OTUtable/OUTPUT_mpa.txt
[2023-02-11 10:12:48] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/OTUtable/OUTPUT_std_type2.txt
[2023-02-11 10:12:48] INFO : visualization STEP START
[2023-02-11 10:12:48] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/visualization/stacked_phylum.png
[2023-02-11 10:12:49] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/visualization/stacked_class.png
[2023-02-11 10:12:50] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/visualization/stacked_order.png
[2023-02-11 10:12:50] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/visualization/stacked_family.png
[2023-02-11 10:12:51] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/visualization/stacked_genus.png
[2023-02-11 10:12:53] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/visualization/stacked_species.png
[2023-02-11 10:12:53] INFO : Log from OTUsamples2krona
Writing krona/b06.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-11 10:12:53] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/visualization/krona
[2023-02-11 10:12:53] INFO : MIrROR analysis Completed!
Total time used : 4:01:26.101685
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b06/b06.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b07 ../trimmed_fasta/b07.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b07.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-11 10:12:54] INFO : MIrROR analysis Start
[2023-02-11 10:12:54] INFO : filecheck STEP START
[2023-02-11 10:12:54] INFO : 1 sample proceeding
[2023-02-11 10:12:54] INFO : mapping STEP START
[2023-02-11 10:12:54] INFO : 1 / 1 Mapping...
[2023-02-11 12:33:42] INFO : classification STEP START
[2023-02-11 12:33:42] INFO : 1 / 1 Annotatioin...
[2023-02-11 12:33:43] INFO : OTUtable STEP START
[2023-02-11 12:33:43] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/OTUtable/OUTPUT_std.txt
[2023-02-11 12:33:43] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/OTUtable/OUTPUT_mpa.txt
[2023-02-11 12:33:43] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/OTUtable/OUTPUT_std_type2.txt
[2023-02-11 12:33:43] INFO : visualization STEP START
[2023-02-11 12:33:43] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/visualization/stacked_phylum.png
[2023-02-11 12:33:43] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/visualization/stacked_class.png
[2023-02-11 12:33:44] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/visualization/stacked_order.png
[2023-02-11 12:33:44] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/visualization/stacked_family.png
[2023-02-11 12:33:45] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/visualization/stacked_genus.png
[2023-02-11 12:33:47] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/visualization/stacked_species.png
[2023-02-11 12:33:47] INFO : Log from OTUsamples2krona
Writing krona/b07.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-11 12:33:47] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/visualization/krona
[2023-02-11 12:33:47] INFO : MIrROR analysis Completed!
Total time used : 2:20:53.182012
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b07/b07.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b08 ../trimmed_fasta/b08.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b08.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-11 12:33:47] INFO : MIrROR analysis Start
[2023-02-11 12:33:47] INFO : filecheck STEP START
[2023-02-11 12:33:47] INFO : 1 sample proceeding
[2023-02-11 12:33:47] INFO : mapping STEP START
[2023-02-11 12:33:47] INFO : 1 / 1 Mapping...
[2023-02-11 18:32:51] INFO : classification STEP START
[2023-02-11 18:32:52] INFO : 1 / 1 Annotatioin...
[2023-02-11 18:32:52] INFO : OTUtable STEP START
[2023-02-11 18:32:52] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/OTUtable/OUTPUT_std.txt
[2023-02-11 18:32:52] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/OTUtable/OUTPUT_mpa.txt
[2023-02-11 18:32:52] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/OTUtable/OUTPUT_std_type2.txt
[2023-02-11 18:32:52] INFO : visualization STEP START
[2023-02-11 18:32:52] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/visualization/stacked_phylum.png
[2023-02-11 18:32:52] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/visualization/stacked_class.png
[2023-02-11 18:32:53] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/visualization/stacked_order.png
[2023-02-11 18:32:53] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/visualization/stacked_family.png
[2023-02-11 18:32:54] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/visualization/stacked_genus.png
[2023-02-11 18:32:55] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/visualization/stacked_species.png
[2023-02-11 18:32:55] INFO : Log from OTUsamples2krona
Writing krona/b08.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-11 18:32:55] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/visualization/krona
[2023-02-11 18:32:55] INFO : MIrROR analysis Completed!
Total time used : 5:59:07.611812
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b08/b08.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b09 ../trimmed_fasta/b09.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b09.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-11 18:32:55] INFO : MIrROR analysis Start
[2023-02-11 18:32:55] INFO : filecheck STEP START
[2023-02-11 18:32:55] INFO : 1 sample proceeding
[2023-02-11 18:32:55] INFO : mapping STEP START
[2023-02-11 18:32:55] INFO : 1 / 1 Mapping...
[2023-02-11 21:28:27] INFO : classification STEP START
[2023-02-11 21:28:27] INFO : 1 / 1 Annotatioin...
[2023-02-11 21:28:27] INFO : OTUtable STEP START
[2023-02-11 21:28:27] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/OTUtable/OUTPUT_std.txt
[2023-02-11 21:28:27] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/OTUtable/OUTPUT_mpa.txt
[2023-02-11 21:28:27] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/OTUtable/OUTPUT_std_type2.txt
[2023-02-11 21:28:27] INFO : visualization STEP START
[2023-02-11 21:28:28] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/visualization/stacked_phylum.png
[2023-02-11 21:28:28] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/visualization/stacked_class.png
[2023-02-11 21:28:28] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/visualization/stacked_order.png
[2023-02-11 21:28:28] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/visualization/stacked_family.png
[2023-02-11 21:28:29] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/visualization/stacked_genus.png
[2023-02-11 21:28:31] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/visualization/stacked_species.png
[2023-02-11 21:28:31] INFO : Log from OTUsamples2krona
Writing krona/b09.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-11 21:28:31] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/visualization/krona
[2023-02-11 21:28:31] INFO : MIrROR analysis Completed!
Total time used : 2:55:36.603314
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b09/b09.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b10 ../trimmed_fasta/b10.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b10.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-11 21:28:32] INFO : MIrROR analysis Start
[2023-02-11 21:28:32] INFO : filecheck STEP START
[2023-02-11 21:28:32] INFO : 1 sample proceeding
[2023-02-11 21:28:32] INFO : mapping STEP START
[2023-02-11 21:28:32] INFO : 1 / 1 Mapping...
[2023-02-11 23:17:17] INFO : classification STEP START
[2023-02-11 23:17:17] INFO : 1 / 1 Annotatioin...
[2023-02-11 23:17:17] INFO : OTUtable STEP START
[2023-02-11 23:17:17] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/OTUtable/OUTPUT_std.txt
[2023-02-11 23:17:17] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/OTUtable/OUTPUT_mpa.txt
[2023-02-11 23:17:17] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/OTUtable/OUTPUT_std_type2.txt
[2023-02-11 23:17:17] INFO : visualization STEP START
[2023-02-11 23:17:18] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/visualization/stacked_phylum.png
[2023-02-11 23:17:18] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/visualization/stacked_class.png
[2023-02-11 23:17:18] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/visualization/stacked_order.png
[2023-02-11 23:17:19] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/visualization/stacked_family.png
[2023-02-11 23:17:20] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/visualization/stacked_genus.png
[2023-02-11 23:17:21] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/visualization/stacked_species.png
[2023-02-11 23:17:21] INFO : Log from OTUsamples2krona
Writing krona/b10.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-11 23:17:21] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/visualization/krona
[2023-02-11 23:17:21] INFO : MIrROR analysis Completed!
Total time used : 1:48:49.596072
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b10/b10.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b11 ../trimmed_fasta/b11.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b11.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-11 23:17:21] INFO : MIrROR analysis Start
[2023-02-11 23:17:21] INFO : filecheck STEP START
[2023-02-11 23:17:21] INFO : 1 sample proceeding
[2023-02-11 23:17:21] INFO : mapping STEP START
[2023-02-11 23:17:21] INFO : 1 / 1 Mapping...
[2023-02-11 23:24:11] INFO : classification STEP START
[2023-02-11 23:24:11] INFO : 1 / 1 Annotatioin...
[2023-02-11 23:24:11] INFO : OTUtable STEP START
[2023-02-11 23:24:11] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/OTUtable/OUTPUT_std.txt
[2023-02-11 23:24:11] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/OTUtable/OUTPUT_mpa.txt
[2023-02-11 23:24:11] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/OTUtable/OUTPUT_std_type2.txt
[2023-02-11 23:24:11] INFO : visualization STEP START
[2023-02-11 23:24:11] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/visualization/stacked_phylum.png
[2023-02-11 23:24:12] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/visualization/stacked_class.png
[2023-02-11 23:24:12] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/visualization/stacked_order.png
[2023-02-11 23:24:13] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/visualization/stacked_family.png
[2023-02-11 23:24:13] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/visualization/stacked_genus.png
[2023-02-11 23:24:15] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/visualization/stacked_species.png
[2023-02-11 23:24:15] INFO : Log from OTUsamples2krona
Writing krona/b11.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-11 23:24:15] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/visualization/krona
[2023-02-11 23:24:15] INFO : MIrROR analysis Completed!
Total time used : 0:06:53.543496
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b11/b11.log
(nanopore2)
MIrROR analysis tool v1.0 Built on Apr 28 2022
Command : ./MIrROR.py -V -d DBDIR -o ../results/b12 ../trimmed_fasta/b12.fa
DataBase : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.mmi
/media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/MIrROR/DBDIR/MIrROR_DB_r01.tsv
Database release 01 (built Jan 21 2021)
Input Format : [FASTA] /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/trimmed_fasta/b12.fa
Group information : No
Read filtering threshold : Number of residue matches - 2500 bp, Alignment block length - 3500 bp
[2023-02-11 23:24:15] INFO : MIrROR analysis Start
[2023-02-11 23:24:15] INFO : filecheck STEP START
[2023-02-11 23:24:15] INFO : 1 sample proceeding
[2023-02-11 23:24:15] INFO : mapping STEP START
[2023-02-11 23:24:15] INFO : 1 / 1 Mapping...
[2023-02-12 08:06:14] INFO : classification STEP START
[2023-02-12 08:06:14] INFO : 1 / 1 Annotatioin...
[2023-02-12 08:06:15] INFO : OTUtable STEP START
[2023-02-12 08:06:15] INFO : Created OTU table (standard version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/OTUtable/OUTPUT_std.txt
[2023-02-12 08:06:15] INFO : (MetaPhlAn version) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/OTUtable/OUTPUT_mpa.txt
[2023-02-12 08:06:15] INFO : (for Krona plot) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/OTUtable/OUTPUT_std_type2.txt
[2023-02-12 08:06:15] INFO : visualization STEP START
[2023-02-12 08:06:15] INFO : Created Stacked bar plot (phylum) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/visualization/stacked_phylum.png
[2023-02-12 08:06:15] INFO : (class) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/visualization/stacked_class.png
[2023-02-12 08:06:15] INFO : (order) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/visualization/stacked_order.png
[2023-02-12 08:06:15] INFO : (family) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/visualization/stacked_family.png
[2023-02-12 08:06:16] INFO : (genus) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/visualization/stacked_genus.png
[2023-02-12 08:06:16] INFO : (species) : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/visualization/stacked_species.png
[2023-02-12 08:06:16] INFO : Log from OTUsamples2krona
Writing krona/b12.fa.tax.html...
Krona charts have been created in krona
Adios
[2023-02-12 08:06:16] INFO : Created Krona plot : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/visualization/krona
[2023-02-12 08:06:16] INFO : MIrROR analysis Completed!
Total time used : 8:42:00.571859
MIrROR analysis log file is created : /media/esuter/MyPassport/Oyster_Pathogen_WRI_Jupyter/results/b12/b12.log
(nanopore2)