compmetagen/micca

micca - MICrobial Community Analysis

micca's Issues

Error: a bytes-like object is required, not 'str' when runnning merge!

When running merge on latest version of Ubuntu the Error: a bytes-like object is required, not 'str' occur!
Any idea what is wrong and how to fix it?

Thanks

Micca assumes DataFrames are saved with the index on the first column

Hello,

I found out that micca reads csv files from DataFrames with the index on the first column: table = pd.read_csv(input_fn, sep='\t', index_col=0) (line 12, micca/table.py file).

If the user isn't aware (as me), saving a csv without the index will result in the drop of the first sample when calculating table summaries and plotting the rarefaction curve.

Best regards.

micca otu error

Hi,

I am running this command:

micca otu -m denovo_unoise -i filtered.fasta -o denovo_unoise_otus -t 4 -c

It creates an empty folder, but then I got this error message:

Error: vsearch v2.7.1_linux_x86_64, 3.7GB RAM, 8 cores
https://github.com/torognes/vsearch

Reading file filtered.fasta 100%
2254993018 nt in 15386761 seqs, min 51, max 399, avg 147

Can someone help me?

Thank you

FutureWarning: order is deprecated, use sort_values(...) in micca tablebar

Use pandas Series and DataFrame methods sort_values() instead of order() and sort() (deprecated since pandas 0.17).

tobiome error

upon running:
micca tobiom -i denovo_greedy_otus/otutable.txt -o denovo_greedy_otus/tables.biom -t denovo_greedy_otus/taxa.txt -s sampledata.txt

the following errors occurs:
Error: 492 is not JSON serializable

Qiime2 to downstream analysis

Hi,

there is some error in micca installation on iMac, could you please advice how to fix it?
admins-imac-3:~ ygupta$ sudo pip install micca
Password:
The directory '/Users/ygupta/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/ygupta/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Collecting micca
Downloading https://files.pythonhosted.org/packages/8a/79/fc77ff9a93ad5053a32b2c83dd9eda606dcb342ae1a3f3587a59f266280e/micca-1.7.2.tar.gz (2.1MB)
100% |████████████████████████████████| 2.1MB 798kB/s
Requirement already satisfied: numpy>=1.8.0 in ./miniconda2/lib/python2.7/site-packages (from micca)
Requirement already satisfied: scipy>=0.14.0 in ./miniconda2/lib/python2.7/site-packages (from micca)
Requirement already satisfied: matplotlib>=1.3.0 in ./miniconda2/lib/python2.7/site-packages (from micca)
Requirement already satisfied: pandas>=0.17.0 in ./miniconda2/lib/python2.7/site-packages (from micca)
Collecting biopython>=1.50 (from micca)
Downloading https://files.pythonhosted.org/packages/55/fe/3c1ecd4fa3a4ac1c981ebf948a189d702b77aa842bf879ab460eaaa934ce/biopython-1.75-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (2.4MB)
100% |████████████████████████████████| 2.4MB 685kB/s
Collecting cutadapt>=1.9 (from micca)
Downloading https://files.pythonhosted.org/packages/fd/4d/3ac2947d36e2d56ce1513dc4a53d3a45e520d7ccfb43af9ba85408e44c69/cutadapt-1.18.tar.gz (342kB)
100% |████████████████████████████████| 348kB 4.8MB/s
Requirement already satisfied: biom-format>=1.3.1 in ./miniconda2/lib/python2.7/site-packages (from micca)
Requirement already satisfied: six>=1.10 in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: python-dateutil>=2.0 in ./miniconda2/lib/python2.7/site-packages/python_dateutil-2.3-py2.7.egg (from matplotlib>=1.3.0->micca)
Requirement already satisfied: backports.functools_lru_cache in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: subprocess32 in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: pytz in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: cycler>=0.10 in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Collecting xopen>=0.3.2 (from cutadapt>=1.9->micca)
Downloading https://files.pythonhosted.org/packages/73/e9/bc35fd93cb6af3a011e44463db468914448825aa659f7636e836b8488b03/xopen-0.8.4-py2.py3-none-any.whl
Requirement already satisfied: click in ./miniconda2/lib/python2.7/site-packages (from biom-format>=1.3.1->micca)
Requirement already satisfied: future>=0.16.0 in ./miniconda2/lib/python2.7/site-packages (from biom-format>=1.3.1->micca)
Requirement already satisfied: pyqi in ./miniconda2/lib/python2.7/site-packages (from biom-format>=1.3.1->micca)
Collecting bz2file; python_version == "2.7" (from xopen>=0.3.2->cutadapt>=1.9->micca)
Downloading https://files.pythonhosted.org/packages/61/39/122222b5e85cd41c391b68a99ee296584b2a2d1d233e7ee32b4532384f2d/bz2file-0.98.tar.gz
Installing collected packages: biopython, bz2file, xopen, cutadapt, micca
Running setup.py install for bz2file ... done
Running setup.py install for cutadapt ... done
Running setup.py install for micca ... error
Complete output from command /Users/ygupta/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/tmp/pip-build-rZUyQD/micca/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-foXnJD-record/install-record.txt --single-version-externally-managed --compile:
Building VSEARCH...
./autogen.sh: line 2: autoreconf: command not found

----------------------------------------

Command "/Users/ygupta/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/tmp/pip-build-rZUyQD/micca/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-foXnJD-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/tmp/pip-build-rZUyQD/micca/
You are using pip version 9.0.1, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
thanks
Yogesh

various vsearch errors in mergepairs and otu

micca v1.7.2 run via docker on a mac.
We had been working through the default paired-end workflow but realized or 'R2' files had forward primer and vice-versa so we changed the i,p&e flags in micca mergepairs as follows: -i <path>/*_R2*.fastq -p _R2 -e _R1 and got the following error:
VSEARCH error: vsearch v 2.7.1 Fatal error: Invalid line 172 in FastQ Illegal character ' '
However, the analysis continued to run and produced a merged fastq around the expected size and this was used in successful trim, filterstats, and filter commands subsequently. However, at the micca otu stage, we again encountered a VSEARCH error:

root@7edcd6962efa:/micca# micca otu -i filtered_R2ASforward.fasta -o Masstreat_otus -d 0.97 -c -t 4
Error: vsearch v2.7.1_linux_x86_64, 2.0GB RAM, 4 cores
https://github.com/torognes/vsearch
Reading file filtered_R2ASforward.fasta

This command produced a folder, but no files. I note that the vsearch errors started appearing when we changed up the forward pattern and my colleague wonders if she might be running into storage/processing limitations of her machine. What do you think? Have you heard of this before? The input filtered.fasta file looks similar to others we have used successfully. Thanks

Add quality filtering strategies page in docs

question about Mergepairs command

Hi,
When I use

micca mergepairs -i _R1.fastq -o Merged.fastq

it automatically recognize the R2 file? or I have to repeat the same command with R2 and then merge the two file sets?
thank you for the attention

core_set?

Hello,

Great tool, I recommend it for everyone here at our lab! Hadn't run myself in some time but was helping some other folks out and discovered that this link from the latest documentation no longer works.
wget ftp://ftp.fmach.it/metagenomics/micca/dbs/core_set.tar.gz

No such directory ‘metagenomics/micca/dbs’.

Also found this qiime issue from 2014.

Thoughts?

'Filter' returns only FASTA, not FASTQ

Hello!
I tried to filter sequences according to the maximum allowed expected error rate and specified the output file to be FASTQ. However, the result appears to be FASTA.
I used the following command:

micca filter \
 -i tst.fastq \
 -o tst_filter.fastq \
 -e 1 -m 200

micca v.1.6.0, installed using Docker in Ubuntu.
Did I miss something, or it is a bug?
Thank you for your help!
Vladimir

micca tree :: FastTree error

Hello while testing micca I encounter the following problem.

see:

/tmp/micca2/bin/micca tree -i ~tests/datas/micca/sample_data -o tree.tree  --fasttree-gtr
Error:   FastTree protein_alignment > tree
  FastTree < protein_alignment > tree
  FastTree -out tree protein_alignment
  FastTree -nt nucleotide_alignment > tree
  FastTree -nt -gtr < nucleotide_alignment > tree
  FastTree < nucleotide_alignment > tree
FastTree accepts alignments in fasta or phylip interleaved formats

while looking at tp/_fasttree.py, noticed that when FastTree specific options is provided via
--fasttree-gtr or --fasttree-fastest, the relevant option for FatsTree is APPENDED to the command line.
thus generate something like that

fasttree -nt alignementfile -gtr

but fasttree is pretty picky with the order of options // argument. -gtr or -fastest option must precede inputfile
should be something like that

fasttree -nt -gtr alignementfile
 fasttree -gtr -nt alignementfile

changing tp/_fasttree.py
from

    params = ["-nt", input_fn]
    if gtr:
        params.append("-gtr")
    if fastest:
        params.append("-fastest")

to

    params = ["-nt", input_fn]
    if gtr:
        params.insert(0, "-gtr")
    if fastest:
        params.insert(0, "-fastest")

solved the problem

regards

Eric

Regarding setup.py installation

I am trying to install micca from source code using
sudo python setup.py install

But gives me at the end error entitled
File "/tmp/easy_install-Ir3wOg/scipy-1.10.1/setup.py", line 27, in
'Environment :: Console',
ImportError: No module named tools.version_utils
(That is the end of the error) and I searched for this module to install with no results
Is there a solution ?

Missing sampledata.txt for the paired-end tutorial data

Missing sampledata.txt for the paired-end tutorial data.

Add the commands APIs in the documentation

Add the commands (Python) APIs (micca.api module) in the documentation.

Merge error

Upon running "micca merge -i fastq/*.fastq -o merged.fastq" the following error arises:

" Error: a bytes-like object is required, not 'str' "

use external tools if available

Hello,

I would like to install micca on our cluster.
we already have all the requirement tools (swarm, muscle, VSearch, etc...) installed and available.

unfortunatly micca have hardcoded path for those tools.

why vsearch, fasttree, swarm and muscle have hardcoded path while cutadapt and rdp are searched externaly ?

can you please provide an installation method that will allow us to use already installed tools.
or just use simple system calls that relies on the user path to run muscle, vsearch, ...

regards

Eric

problem with micca classify command

Hello,
I have been following the single end sequencing tutorial of micca for my 16s rrna samples and generated the otus.fasta and otu table files but I am stuck at micca classify ommand following is the command I am using and it gives the error,
micca classify -m rdp --rdp-gene 16srrna -i otus.fasta -o taxa.txt
Error: Error: RDPPATH environment variable is not set

I have rdp classifier sudo installed but I am unable to understand how to resolve this problem, Kindly help.

Best Regards,
Faizan Saleem

TypeError: write() argument must be str, not bytes

Hello, when I do: python setup.py install,
I obtain the following error:
`Building VSEARCH...
Building MUSCLE...

Traceback (most recent call last):
File "setup.py", line 120, in
_build_muscle()
File "setup.py", line 71, in _build_muscle
_system_call(["make"])
File "setup.py", line 44, in _system_call
sys.stderr.write(proc_stderr)
TypeError: write() argument must be str, not bytes`

I'm working on Python 3.8.1, Can you help me ?
Thanks for your time.

micca/tp/_cutadapt.py :: CutadaptError :: inactive

as code in micca/tp/_cutadapt.py for CutadaptError is just

class CutadaptError(Exception):
    pass

when cutadapt is not found by distutils find_executable, this code don't do nothing.

def _cutadapt_cmd(params):
    cutadapt_bin = find_executable("cutadapt")
    if cutadapt_bin is None:
        CutadaptError("Error: cutadapt is not installed\n")

should be at least

def _cutadapt_cmd(params):
    cutadapt_bin = find_executable("cutadapt")
    if cutadapt_bin is None:
        raise CutadaptError("Error: cutadapt is not installed\n")

regards

Eric

Resource Temporarily Unavailable; Connection Timed Out; Connection Refused for core set from ftp site

Hi @davidealbanese ,

Issue #29 seems to be not fully resolved. I tried wget ftp://ftp.fmach.it/metagenomics/micca/dbs/core_set.tar.gz from a couple of different machines this morning. The connection refused issue may be a separate gov firewall issue on our end, but I got 'Resource Temporarily Unavailable' and 'Connection Timed Out' when attempting from computers that should not have been subject to the firewall.

Add swarm denovo clustering protocol

Add swarm (https://github.com/torognes/swarm) denovo clustering protocol into the otu command in micca.

micca installation

Hi

I am trying to install micca but it is showing some error, could you please with it?

admins-imac-3:~ ygupta$ docker pull compmetagen/micca
Using default tag: latest
latest: Pulling from compmetagen/micca
55cbf04beb70: Pull complete
c1a62a31988d: Pull complete
c09866308940: Pull complete
688b2d2ab034: Pull complete
Digest: sha256:0001cef1ff7f16033f1052b376b19e4d862d03541047837a247381861375e565
Status: Downloaded newer image for compmetagen/micca:latest
docker.io/compmetagen/micca:latest
admins-imac-3:~ ygupta$
admins-imac-3:~ ygupta$ pwd
/Users/ygupta
admins-imac-3:~ ygupta$ docker run --rm -ti --user $(id -u):$(id -g) -v /Users/ygupta/micca:/micca -w /micca compmetagen/micca /bin/bash

I have no name!@30b323bdb055:/micca$

thanks
yogeshgupt

issues installing micca from source

We have been trying to install micca from source but have been unable to.
I have installed all of the dependencies required according to the installation page installed either using pip install or from source. I also installed, from source, the MUSCLE 3 package (MUSCLE v3.8.31) independently. However if I pip install micca or install from source using 'python setup.py install' I get this error code:

Building VSEARCH...
Building MUSCLE...
strip: 'muscle': No such file
ls: cannot access muscle: No such file or directory
sum: muscle: No such file or directory
make: *** [muscle] Error 1

Have you seen this error and do you know what might be preventing the installation of micca?

issue about installing micca

Hi:

Is micca no longer maintained/updated? I keep getting the error installing on Linux:

sudo apt-get update
sudo apt-get install build-essential python-numpy gcc gfortran python-dev libblas-dev liblapack-dev cython pkg-config libfreetype6 libfreetype6-dev libpng-dev
pip install --upgrade pip
pip install 'setuptools >=14.0'
pip install micca

So I try to install micca from source, but it also does work:

sudo pip install 'scipy >=0.13.0' 'pandas >=0.17.0' 'matplotlib >=1.3.0' 'biopython >= 1.50' 'cutadapt >=1.9' 'biom-format >=1.3.1'
tar -zxvf micca-1.7.2.tar.gz
sudo python setup.py install
error: Setup script exited with Python 2.7 is no longer supported

Then, I build a python 2.7 environment:
conda create -n envpython27 python=2.7 -y
conda activate envpython27

Then perform the above installation, still error.

Running setup.py install for micca ... error

Hi,
During the instillation of micca, following error message appeared.
Can you help me how to solve it.

Collecting micca

Downloading https://files.pythonhosted.org/packages/8a/79/fc77ff9a93ad5053a32b2c83dd9eda606dcb342ae1a3f3587a59f266280e/micca-1.7.2.tar.gz (2.1MB)

100% |████████████████████████████████| 2.1MB 372kB/s

Requirement already satisfied: numpy>=1.8.0 in /usr/lib/python3/dist-packages (from micca)

Requirement already satisfied: scipy>=0.14.0 in /usr/local/lib/python3.6/dist-packages (from micca)

Requirement already satisfied: matplotlib>=1.3.0 in /usr/local/lib/python3.6/dist-packages (from micca)

Requirement already satisfied: pandas>=0.17.0 in /usr/local/lib/python3.6/dist-packages (from micca)

Requirement already satisfied: biopython>=1.50 in /usr/local/lib/python3.6/dist-packages (from micca)

Requirement already satisfied: cutadapt>=1.9 in /usr/local/lib/python3.6/dist-packages (from micca)

Requirement already satisfied: biom-format>=1.3.1 in /usr/local/lib/python3.6/dist-packages (from micca)

Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=1.3.0->micca)

Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=1.3.0->micca)

Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=1.3.0->micca)

Requirement already satisfied: python-dateutil>=2.1 in /usr/lib/python3/dist-packages (from matplotlib>=1.3.0->micca)

Requirement already satisfied: pytz>=2017.2 in /usr/lib/python3/dist-packages (from pandas>=0.17.0->micca)

Requirement already satisfied: dnaio~=0.4.2 in /usr/local/lib/python3.6/dist-packages (from cutadapt>=1.9->micca)

Requirement already satisfied: xopen~=0.8.4 in /usr/local/lib/python3.6/dist-packages (from cutadapt>=1.9->micca)

Requirement already satisfied: click in /usr/local/lib/python3.6/dist-packages (from biom-format>=1.3.1->micca)

Requirement already satisfied: cython in ./.local/lib/python3.6/site-packages (from biom-format>=1.3.1->micca)

Requirement already satisfied: future>=0.16.0 in /usr/local/lib/python3.6/dist-packages (from biom-format>=1.3.1->micca)

Requirement already satisfied: h5py in /usr/local/lib/python3.6/dist-packages (from biom-format>=1.3.1->micca)

Requirement already satisfied: six>=1.10.0 in /usr/lib/python3/dist-packages (from biom-format>=1.3.1->micca)

Installing collected packages: micca

Running setup.py install for micca ... error

Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-xazzw28s/micca/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-6fh62fud-record/install-record.txt --single-version-externally-managed --compile:

Building VSEARCH...

Traceback (most recent call last):

File "", line 1, in

File "/tmp/pip-build-xazzw28s/micca/setup.py", line 119, in

_build_vsearch()

File "/tmp/pip-build-xazzw28s/micca/setup.py", line 54, in _build_vsearch

_system_call(["./autogen.sh"])

File "/tmp/pip-build-xazzw28s/micca/setup.py", line 44, in _system_call

sys.stderr.write(proc_stderr)

TypeError: write() argument must be str, not bytes

---

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-xazzw28s/micca/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-6fh62fud-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-xazzw28s/micca/

Merge paired-end sequences in micca

Hello,
I am using micca, my file name is P1_1.fq and P1_2.fq. When I used "micca mergepairs -i fastq/P1_1.fastq -o merged.fastq -l 100 -d 30" command, "P1_1.fastq: unable to find pattern '_R1', SKIP" error come up. I changed the file name as P1_R1.fq and P1_R2.fq and same error occurred.
Can you help me how can I solve the problem.
Thanks in advance
Best wishes

Fix micca tablebar when --raw

micca tablebar: Y-scale should be free and not fixed to 0-1 when --raw

micca installation error on iMac

Hi,

I was trying to installed micca on iMac but there is some error at the end, could you please advice how to fix it?

admins-imac-3:~ ygupta$ sudo pip install micca
Password:
The directory '/Users/ygupta/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/ygupta/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Collecting micca
Downloading https://files.pythonhosted.org/packages/8a/79/fc77ff9a93ad5053a32b2c83dd9eda606dcb342ae1a3f3587a59f266280e/micca-1.7.2.tar.gz (2.1MB)
100% |████████████████████████████████| 2.1MB 798kB/s
Requirement already satisfied: numpy>=1.8.0 in ./miniconda2/lib/python2.7/site-packages (from micca)
Requirement already satisfied: scipy>=0.14.0 in ./miniconda2/lib/python2.7/site-packages (from micca)
Requirement already satisfied: matplotlib>=1.3.0 in ./miniconda2/lib/python2.7/site-packages (from micca)
Requirement already satisfied: pandas>=0.17.0 in ./miniconda2/lib/python2.7/site-packages (from micca)
Collecting biopython>=1.50 (from micca)
Downloading https://files.pythonhosted.org/packages/55/fe/3c1ecd4fa3a4ac1c981ebf948a189d702b77aa842bf879ab460eaaa934ce/biopython-1.75-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (2.4MB)
100% |████████████████████████████████| 2.4MB 685kB/s
Collecting cutadapt>=1.9 (from micca)
Downloading https://files.pythonhosted.org/packages/fd/4d/3ac2947d36e2d56ce1513dc4a53d3a45e520d7ccfb43af9ba85408e44c69/cutadapt-1.18.tar.gz (342kB)
100% |████████████████████████████████| 348kB 4.8MB/s
Requirement already satisfied: biom-format>=1.3.1 in ./miniconda2/lib/python2.7/site-packages (from micca)
Requirement already satisfied: six>=1.10 in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: python-dateutil>=2.0 in ./miniconda2/lib/python2.7/site-packages/python_dateutil-2.3-py2.7.egg (from matplotlib>=1.3.0->micca)
Requirement already satisfied: backports.functools_lru_cache in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: subprocess32 in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: pytz in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: cycler>=0.10 in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./miniconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->micca)
Collecting xopen>=0.3.2 (from cutadapt>=1.9->micca)
Downloading https://files.pythonhosted.org/packages/73/e9/bc35fd93cb6af3a011e44463db468914448825aa659f7636e836b8488b03/xopen-0.8.4-py2.py3-none-any.whl
Requirement already satisfied: click in ./miniconda2/lib/python2.7/site-packages (from biom-format>=1.3.1->micca)
Requirement already satisfied: future>=0.16.0 in ./miniconda2/lib/python2.7/site-packages (from biom-format>=1.3.1->micca)
Requirement already satisfied: pyqi in ./miniconda2/lib/python2.7/site-packages (from biom-format>=1.3.1->micca)
Collecting bz2file; python_version == "2.7" (from xopen>=0.3.2->cutadapt>=1.9->micca)
Downloading https://files.pythonhosted.org/packages/61/39/122222b5e85cd41c391b68a99ee296584b2a2d1d233e7ee32b4532384f2d/bz2file-0.98.tar.gz
Installing collected packages: biopython, bz2file, xopen, cutadapt, micca
Running setup.py install for bz2file ... done
Running setup.py install for cutadapt ... done
Running setup.py install for micca ... error
Complete output from command /Users/ygupta/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/tmp/pip-build-rZUyQD/micca/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-foXnJD-record/install-record.txt --single-version-externally-managed --compile:
Building VSEARCH...
./autogen.sh: line 2: autoreconf: command not found

----------------------------------------

Command "/Users/ygupta/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/tmp/pip-build-rZUyQD/micca/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-foXnJD-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/tmp/pip-build-rZUyQD/micca/
You are using pip version 9.0.1, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Error when connecting to ftp.fmach.it link

Using MICCA to process 16S data and when I go to generate a phylogenetic tree I discovered that the following link from the latest documentation no longer works:
wget ftp://ftp.fmach.it/metagenomics/micca/dbs/core_set.tar.gz

I get the following error:
Connecting to ftp.fmach.it (ftp.fmach.it)|77.72.197.176|:21... failed: Connection refused.

Thoughts?

micca/tp/_cutadapt.py :: CutadaptError :: inactive

as code in micca/tp/_cutadapt.py for CutadaptError is just

class CutadaptError(Exception):
    pass

when cutadapt is not found by distutils find_executable, this code don't do nothing.

def _cutadapt_cmd(params):
    cutadapt_bin = find_executable("cutadapt")
    if cutadapt_bin is None:
        CutadaptError("Error: cutadapt is not installed\n")

should be at least

def _cutadapt_cmd(params):
    cutadapt_bin = find_executable("cutadapt")
    if cutadapt_bin is None:
        raise CutadaptError("Error: cutadapt is not installed\n")

regards

Eric

mergepairs error: add the filename in the output message

When I ran this command
micca mergepairs -i fastq/*_R1.fastq -o merged.fastq -l 100 -d 32
I got this error
`Merging reads 100% RCH error: Merging reads 0%

Fatal error: Invalid line 2213255 in FASTQ file: Unexpected end of file
, SKIP`

What could be the possible cause of this error?

Add the "hits" output for the NAST alignment in micca msa

Add the TAB-delimited "hits" output file for the NAST alignment in micca msa with the query sequence id, the template sequence id and the identity.

Error: a bytes-like object is required, not 'str'

Hello,
I just installed micca on my ubuntu 18 installed in virtual box. I also downloaded the garda file to make an exercise. After entering following command, an error occurred.
(base) arne@arne-:~/garda$ micca mergepairs -i fastq/_R1.fastq -o merged.fastq -l 100 -d 30
Error: a bytes-like object is required, not 'str'
Can you help me to solve the problem?
Best wishes,
Arne

Error: 'DataFrame' object has no attribute 'as_matrix'

Hello,

As micca install any version of pandas (>=0.17.0), currently, the latest pandas version has replaced 'as_matrix' by 'values'.

Best regards.