q2-itsxpress bbmerge error 2

Good day to you Dr Rivers
I am a beginner with qiime2 and I am trying to analyse ITS 1 and 2 for a read from a sequencing facility (MRDNA USA). I have a paired-end-demux.qza file.
I followed this tutorial for my reads. I tried to trim the qza file and get this error message:

qiime itsxpress trim-pair-output-unmerged \

--i-per-sample-sequences demux-full.qza
--p-region ALL
--p-taxa F
--o-trimmed trimmed.qza
Plugin error from itsxpress:

Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-21xz919x/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R1_001.fastq.gz', 'in2=/tmp/qiime2-archive-21xz919x/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R2_001.fastq.gz', 'out=/tmp/itsxpress_o0oh31fp/seq.fq.gz', 't=1', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-lb1gyl7a.log

Can you please help with this?
Do I have to install bbmerge and HMMsearch on qiime2? How do I go about it?

Have you seen this topic, @bettya ? It looks very similar to your error, and might help get you on the right track before @Adam_Rivers gets a chance to look your question over. The :mag: search tool is mighty mighty! :muscle:

Side note - if you ever find yourself posting a question about an error message with a debugging logfile, please consider sharing that file's contents in your post. They're often useful in figuring out what's going on. :slight_smile:

1 Like

Thanks for your help
I did tried all the suggestions in the searched topic, I still get the same error:

qiime itsxpress trim-pair-output-unmerged \

--i-per-sample-sequences demux-full.qza
--p-region ALL
--p-taxa F
--o-trimmed trimmed.qza
Plugin error from itsxpress:

Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-_jy02pke/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R1_001.fastq.gz', 'in2=/tmp/qiime2-archive-_jy02pke/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R2_001.fastq.gz', 'out=/tmp/itsxpress_z_hyqqni/seq.fq.gz', 't=1', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-_bw_d929.log

How do I get the error debug file on qiime2?
Please note that I am working with a virtual box and I am a beginner.
Can someone please help me with a step by step suggestion?

/tmp/qiime2-q2cli-err-lb1gyl7a.log is an absolute file path to the log file. Working from the command line, you can use any text editor to open it. e.g.
nano /tmp/qiime2-q2cli-err-lb1gyl7a.log

Notes:

  • Temp files are usually removed automatically shortly after they are created. If you get a file not found error, try re-running the command and then opening it immediately.
  • VirtualBox may handle temp files differently than the systems I'm used to. If that doesn't work, you may have to google how to open a temp file in virtualbox, or even how to change where the guest operating system you're running (e.g. Ubuntu) saves temp files so that they don't get automatically removed.

Let us know how that goes!
CK

1 Like

Hi Chris
Just like you described. The error log file:

ERROR:root:Could not perform read merging with BBmerge. Error from BBmerge was>
java -Djava.library.path=/home/qiime2/miniconda/envs/qiime2-2020.11/opt/bbma>
Executing jgi.BBMerge [in=/tmp/qiime2-archive-zd8zpdnx/8e2eaab4-8c65-44cf-abac>
Version 38.18

Set threads to 1
Exception in thread "main" java.lang.RuntimeException: Unknown parameter maxmi>
at jgi.BBMerge.(BBMerge.java:644)
at jgi.BBMerge.main(BBMerge.java:49)
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
p1.check_returncode()
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/subprocess.py>
self.stderr)
subprocess.CalledProcessError: Command '['bbmerge.sh', 'in=/tmp/qiime2-archive>
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
results = action(**arguments)
File "", line 2, in trim_pair_output_unmerged
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
[ Read 37 lines ]
Thank you for your help.

Within your Qiime2 conda environment run

conda list

Anything named bbtools or bbmap should be removed with conda (assuming that was how it was installed)

Run

conda remove bbmap

if present, also run

conda remove bbtools

Then reinstall the latest version of bbtools (under the package name bbmap)

conda install -c bioconda bbmap

Why this is happening:

It appears that newer versions of qiime2 are installing an older version of bbtools that is not compatible with Itsxpress. I need to test out installing Itsxpress on these newer versions and see if I can modify my bioconda manifest file in a way that is compatible with the new Qiime2 conda environment. There is a conflict with the way we specify dependencies.

1 Like

Hi Dr Rivers
I tried your suggestion and this is what I got:

qiime itsxpress trim-pair-output-unmerged \

--i-per-sample-sequences demux-full.qza
--p-region ALL
--p-taxa F
--o-trimmed trimmed.qza
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/click/type.py", line 112, in _convert_input
result = qiime2.sdk.Result.load(value)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/result.py", line 66, in load
archiver = archive.Archiver.load(filepath)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/core/archive/archiver.py", line 307, in load
return cls(path, Format(rec))
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/core/archive/format/v1.py", line 29, in init
super().init(archive_record)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/core/archive/format/v0.py", line 73, in init
self.format = sdk.parse_format(format)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/util.py", line 88, in parse_format
pm = qiime2.sdk.PluginManager()
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 54, in new
self._init(add_plugins=add_plugins)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init
plugin = entry_point.load()
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/pkg_resources/init.py", line 2471, in load
self.require(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/pkg_resources/init.py", line 2494, in require
items = working_set.resolve(reqs, env, installer, extras=self.extras)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/pkg_resources/init.py", line 785, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'itsxpress>=1.8.0' distribution was not found and is required by the application

There was a problem loading demux-full.qza as a QIIME 2 Result:

The 'itsxpress>=1.8.0' distribution was not found and is required by the application

See above for debug info.

Still an error, kindly help.

Regards.

Hi Dr Rivers

I am still waiting for your reply on my last post/reply.

Kindly reply.
Regards.

Currently, itsxpress and q2-itsxpress are two packages, that will be changing in version 2 because it is confusing. You can make sure both are installed with these commands

conda install -c bioconda itsxpress
pip install q2-itsxpress

1 Like

Thank you, Dr Rivers for your response.
I tried all your suggestions and more.
I have errors again. This is the error and the error log:

Plugin error from itsxpress:

Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-svmsfmkj/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R1_001.fastq.gz', 'in2=/tmp/qiime2-archive-svmsfmkj/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R2_001.fastq.gz', 'out=/tmp/itsxpress_5ny3brkf/seq.fq.gz', 't=1', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1.

Error log:
GNU nano 4.8 /tmp/qiime2-q2cli-err-rat58zqb.log
ERROR:root:Could not perform read merging with BBmerge. Error from BBmerge was>
java -Djava.library.path=/home/qiime2/miniconda/envs/qiime2-2020.11/opt/bbma>
Executing jgi.BBMerge [in=/tmp/qiime2-archive-qstqyua0/8e2eaab4-8c65-44cf-abac>
Version 38.18

Set threads to 1
Exception in thread "main" java.lang.RuntimeException: Unknown parameter maxmi>
at jgi.BBMerge.(BBMerge.java:644)
at jgi.BBMerge.main(BBMerge.java:49)
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
p1.check_returncode()
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/subprocess.py>
self.stderr)
subprocess.CalledProcessError: Command '['bbmerge.sh', 'in=/tmp/qiime2-archive>
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
results = action(**arguments)
File "", line 2, in trim_pair_output_unmerged
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
cluster_id=cluster_id)

Please, help.

Regards.

I can see from there error log they it is still running too old a version of bbmerge, 38.18.

Maybe you have an old version of bbtools high in your Bash $PATH list?

Can you run conda list within the your qiime2 conda environment and paste in the output?

Also run which bbmerge.sh within your qiime2 environment to see where bbtools is.

Hi Dr Rivers

(qiime2-2020.11) [email protected]:/media/sf_Desktop/qiime2-ITS1$ conda list

packages in environment at /home/qiime2/miniconda/envs/qiime2-2020.11:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
arb-bio-tools 6.0.6 haa8b8d8_8 bioconda
argon2-cffi 20.1.0 py36h1d69622_2 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 20.3.0 pyhd3deb0d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
bbmap 38.18 0 bioconda
bibtexparser 1.1.0 py_0 conda-forge
binutils_impl_linux-64 2.35.1 h17ad2fc_0 conda-forge
binutils_linux-64 2.35 hc3fd857_29 conda-forge
bioconductor-biobase 2.50.0 r40h037d062_0 bioconda
bioconductor-biocgenerics 0.36.0 r40_0 bioconda
bioconductor-biocparallel 1.24.0 r40h5f743cb_0 bioconda
bioconductor-biostrings 2.58.0 r40h037d062_0 bioconda
bioconductor-dada2 1.18.0 r40h5f743cb_0 bioconda
bioconductor-delayedarray 0.16.0 r40h037d062_0 bioconda
bioconductor-genomeinfodb 1.26.0 r40_0 bioconda
bioconductor-genomeinfodbdata 1.2.4 r40_0 bioconda
bioconductor-genomicalignments 1.26.0 r40h037d062_0 bioconda
bioconductor-genomicranges 1.42.0 r40h037d062_0 bioconda
bioconductor-iranges 2.24.0 r40h037d062_0 bioconda
bioconductor-matrixgenerics 1.2.0 r40_0 bioconda
bioconductor-rhtslib 1.22.0 r40h037d062_0 bioconda
bioconductor-rsamtools 2.6.0 r40h5f743cb_0 bioconda
bioconductor-s4vectors 0.28.0 r40h037d062_0 bioconda
bioconductor-shortread 1.48.0 r40h5f743cb_0 bioconda
bioconductor-summarizedexperiment 1.20.0 r40_0 bioconda
bioconductor-xvector 0.30.0 r40h037d062_0 bioconda
bioconductor-zlibbioc 1.36.0 r40h037d062_0 bioconda
biom-format 2.1.10 py36ha112f06_0 conda-forge
biopython 1.79 pypi_0 pypi
blas 2.17 openblas conda-forge
blast 2.10.1 pl526he19e7b1_3 bioconda
bleach 3.2.1 pyh9f0ad1d_0 conda-forge
bokeh 2.2.3 py36h5fab9bb_0 conda-forge
boost-cpp 1.70.0 h7b93d67_3 conda-forge
bowtie2 2.4.2 py36h5202f60_1 bioconda
brotlipy 0.7.0 py36he6145b8_1001 conda-forge
bwidget 1.9.14 ha770c72_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h36c2ea0_0 conda-forge
ca-certificates 2021.7.5 h06a4308_1
cachecontrol 0.12.6 py_0 conda-forge
cairo 1.16.0 h9f066cc_1006 conda-forge
certifi 2021.5.30 py36h06a4308_0
cffi 1.14.4 py36hc120d54_1 conda-forge
chardet 3.0.4 py36h9880bd3_1008 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
cryptography 3.3.1 py36h0a59100_0 conda-forge
curl 7.71.1 he644dc0_8 conda-forge
cutadapt 3.1 py36h4c5857e_0 bioconda
cycler 0.10.0 py_2 conda-forge
cython 0.29.21 py36ha357f81_1 conda-forge
deblur 1.1.0 py_2 bioconda
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
dendropy 4.5.1 pyh3252c3a_0 bioconda
dnaio 0.4.4 py36h4c5857e_0 bioconda
emperor 1.0.1 py36h5fab9bb_1 conda-forge
entrez-direct 13.9 pl526h375a9b1_0 bioconda
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
fastcluster 1.1.26 py36h7c3b610_2 conda-forge
fasttree 2.1.10 0 bioconda
flask 1.1.2 pypi_0 pypi
fontconfig 2.13.1 h7e3eb15_1002 conda-forge
freetype 2.10.4 h7ca028e_0 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
future 0.18.2 py36h5fab9bb_2 conda-forge
gcc_impl_linux-64 7.5.0 hd9e1a51_17 conda-forge
gcc_linux-64 7.5.0 he2a3fca_29 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
gevent 20.9.0 pypi_0 pypi
gfortran_impl_linux-64 7.5.0 hfca37b7_17 conda-forge
gfortran_linux-64 7.5.0 ha081f1e_29 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
glib 2.66.3 h9c3ff4c_1 conda-forge
gneiss 0.4.6 py_0 bioconda
graphite2 1.3.13 h58526e2_1001 conda-forge
greenlet 0.4.17 pypi_0 pypi
gsl 2.6 he838d99_1 conda-forge
gxx_impl_linux-64 7.5.0 h7ea4de1_17 conda-forge
gxx_linux-64 7.5.0 h547f3ba_29 conda-forge
h5py 2.10.0 nompi_py36h513d04c_102 conda-forge
harfbuzz 2.7.2 ha5b49bf_1 conda-forge
hdf5 1.10.5 nompi_h7c3c948_1111 conda-forge
hdmedians 0.14.1 py36h68bb277_1 conda-forge
hmmer 3.1b2 3 bioconda
htslib 1.11 hd3b49d5_1 bioconda
icu 67.1 he1b5a44_0 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
ijson 3.1.3 pyhd3deb0d_0 conda-forge
importlib-metadata 3.1.1 pyhd8ed1ab_0 conda-forge
importlib_metadata 3.1.1 hd8ed1ab_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipykernel 5.3.4 py36he448a4c_1 conda-forge
ipython 7.16.1 py36h95af2a2_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 pyh9f0ad1d_1 conda-forge
iqtree 2.0.3 h176a8bc_0 bioconda
isa-l 2.30.0 h36c2ea0_0 conda-forge
itsdangerous 1.1.0 pypi_0 pypi
itsxpress 1.8.0 pypi_0 pypi
jedi 0.17.2 py36h5fab9bb_1 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
joblib 0.17.0 py_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
jsonschema 3.2.0 py_2 conda-forge
jupyter_client 6.1.7 py_0 conda-forge
jupyter_core 4.7.0 py36h5fab9bb_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge
kiwisolver 1.3.1 py36h51d7077_0 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
lcms2 2.11 hcbb858e_1 conda-forge
ld_impl_linux-64 2.35.1 hed1e6ac_0 conda-forge
libarbdb 6.0.6 haa8b8d8_8 bioconda
libblas 3.8.0 17_openblas conda-forge
libcblas 3.8.0 17_openblas conda-forge
libcurl 7.71.1 hcdd3856_8 conda-forge
libdeflate 1.6 h516909a_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-devel_linux-64 7.5.0 h42c25f5_17 conda-forge
libgcc-ng 9.3.0 h5dbcf3e_17 conda-forge
libgfortran-ng 7.5.0 hae1eefd_17 conda-forge
libgfortran4 7.5.0 hae1eefd_17 conda-forge
libglib 2.66.3 h1f3bc88_1 conda-forge
libgomp 9.3.0 h5dbcf3e_17 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.8.0 17_openblas conda-forge
liblapacke 3.8.0 17_openblas conda-forge
libnghttp2 1.41.0 h8cfc5f6_2 conda-forge
libopenblas 0.3.10 pthreads_hb3c22a3_5 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.9.0 hab1572f_5 conda-forge
libstdcxx-devel_linux-64 7.5.0 h4084dd6_17 conda-forge
libstdcxx-ng 9.3.0 h2ae2ef3_17 conda-forge
libtiff 4.1.0 h4f3a223_6 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.1.0 h36c2ea0_3 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.10 h68273f3_2 conda-forge
llvm-openmp 11.0.0 hfc4b9b4_1 conda-forge
lockfile 0.12.2 py_1 conda-forge
lz4 3.1.1 py36hbb6ea5d_0 conda-forge
lz4-c 1.9.2 he1b5a44_3 conda-forge
mafft 7.475 h516909a_0 bioconda
make 4.3 hd18ef5c_1 conda-forge
markupsafe 1.1.1 py36he6145b8_2 conda-forge
matplotlib 3.2.2 1 conda-forge
matplotlib-base 3.2.2 py36h5fdd944_1 conda-forge
mistune 0.8.4 py36h1d69622_1002 conda-forge
more-itertools 8.6.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.0 py36h51d7077_2 conda-forge
natsort 7.1.0 pyhd8ed1ab_0 conda-forge
nbclient 0.5.1 py_0 conda-forge
nbconvert 6.0.7 py36h5fab9bb_3 conda-forge
nbformat 5.0.8 py_0 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
nest-asyncio 1.4.3 pyhd8ed1ab_0 conda-forge
networkx 2.5 py_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 6.1.5 py36h5fab9bb_0 conda-forge
numpy 1.19.4 py36h8732dcd_1 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openjdk 11.0.8 hacce0ff_0 conda-forge
openssl 1.1.1k h27cfd23_0
packaging 20.7 pyhd3deb0d_0 conda-forge
pandas 1.1.5 py36h284efc9_0 conda-forge
pandoc 2.11.2 h36c2ea0_0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
pango 1.42.4 h69149e4_5 conda-forge
parso 0.7.1 pyh9f0ad1d_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pcre2 10.35 h032f7d1_2 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
perl-app-cpanminus 1.7044 pl526_1 bioconda
perl-archive-tar 2.32 pl526_0 bioconda
perl-base 2.23 pl526_1 bioconda
perl-business-isbn 3.004 pl526_0 bioconda
perl-business-isbn-data 20140910.003 pl526_0 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda
perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda
perl-constant 1.33 pl526_1 bioconda
perl-data-dumper 2.173 pl526_0 bioconda
perl-digest-hmac 1.03 pl526_3 bioconda
perl-digest-md5 2.55 pl526_0 bioconda
perl-encode 2.88 pl526_1 bioconda
perl-encode-locale 1.05 pl526_6 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.36 pl526_1 bioconda
perl-file-listing 6.04 pl526_1 bioconda
perl-file-path 2.16 pl526_0 bioconda
perl-file-temp 0.2304 pl526_2 bioconda
perl-html-parser 3.72 pl526h6bb024c_5 bioconda
perl-html-tagset 3.20 pl526_3 bioconda
perl-html-tree 5.07 pl526_1 bioconda
perl-http-cookies 6.04 pl526_0 bioconda
perl-http-daemon 6.01 pl526_1 bioconda
perl-http-date 6.02 pl526_3 bioconda
perl-http-message 6.18 pl526_0 bioconda
perl-http-negotiate 6.01 pl526_3 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-html 1.001 pl526_2 bioconda
perl-io-socket-ssl 2.066 pl526_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
perl-libwww-perl 6.39 pl526_0 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-lwp-mediatypes 6.04 pl526_0 bioconda
perl-lwp-protocol-https 6.07 pl526_4 bioconda
perl-mime-base64 3.15 pl526_1 bioconda
perl-mozilla-ca 20180117 pl526_1 bioconda
perl-net-http 6.19 pl526_0 bioconda
perl-net-ssleay 1.88 pl526h90d6eec_0 bioconda
perl-ntlm 1.09 pl526_4 bioconda
perl-parent 0.236 pl526_1 bioconda
perl-pathtools 3.75 pl526h14c3975_1 bioconda
perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda
perl-socket 2.027 pl526_1 bioconda
perl-storable 3.15 pl526h14c3975_0 bioconda
perl-test-requiresinternet 0.05 pl526_0 bioconda
perl-time-local 1.28 pl526_1 bioconda
perl-try-tiny 0.30 pl526_1 bioconda
perl-types-serialiser 1.0 pl526_2 bioconda
perl-uri 1.76 pl526_0 bioconda
perl-www-robotrules 6.02 pl526_3 bioconda
perl-xml-namespacesupport 1.12 pl526_0 bioconda
perl-xml-parser 2.44_01 pl526ha1d75be_1002 conda-forge
perl-xml-sax 1.02 pl526_0 bioconda
perl-xml-sax-base 1.09 pl526_0 bioconda
perl-xml-sax-expat 0.51 pl526_3 bioconda
perl-xml-simple 2.25 pl526_1 bioconda
perl-xsloader 0.24 pl526_0 bioconda
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pickleshare 0.7.5 py_1003 conda-forge
pigz 2.3.4 hed695b0_1 conda-forge
pillow 8.0.1 py36h10ecd5c_0 conda-forge
pip 20.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pluggy 0.13.1 py36h9880bd3_3 conda-forge
prometheus_client 0.9.0 pyhd3deb0d_0 conda-forge
prompt-toolkit 3.0.8 pyha770c72_0 conda-forge
psutil 5.7.3 py36he6145b8_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
py 1.9.0 pyh9f0ad1d_0 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pygments 2.7.3 pyhd8ed1ab_0 conda-forge
pyopenssl 20.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyrsistent 0.17.3 py36h1d69622_1 conda-forge
pysocks 1.7.1 py36h9880bd3_2 conda-forge
pytest 6.1.2 py36h5fab9bb_0 conda-forge
python 3.6.12 hffdb5ce_0_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.6 1_cp36m conda-forge
pytz 2020.4 pyhd8ed1ab_0 conda-forge
pyyaml 5.3.1 py36he6145b8_1 conda-forge
pyzmq 20.0.0 py36h2b1bd32_1 conda-forge
q2-alignment 2020.11.1 py36_0 qiime2/label/r2020.11
q2-composition 2020.11.1 py36_0 qiime2/label/r2020.11
q2-cutadapt 2020.11.1 py36_0 qiime2/label/r2020.11
q2-dada2 2020.11.1 py36_0 qiime2/label/r2020.11
q2-deblur 2020.11.1 py36_0 qiime2/label/r2020.11
q2-demux 2020.11.1 py36_0 qiime2/label/r2020.11
q2-diversity 2020.11.1 py36_0 qiime2/label/r2020.11
q2-diversity-lib 2020.11.1 0 qiime2/label/r2020.11
q2-emperor 2020.11.1 py36_0 qiime2/label/r2020.11
q2-feature-classifier 2020.11.1 py36_0 qiime2/label/r2020.11
q2-feature-table 2020.11.1 py36_0 qiime2/label/r2020.11
q2-fragment-insertion 2020.11.1 py36_0 qiime2/label/r2020.11
q2-gneiss 2020.11.1 py36_0 qiime2/label/r2020.11
q2-itsxpress 1.8.0 pypi_0 pypi
q2-longitudinal 2020.11.1 py36_0 qiime2/label/r2020.11
q2-metadata 2020.11.1 py36_0 qiime2/label/r2020.11
q2-phylogeny 2020.11.1 py36_0 qiime2/label/r2020.11
q2-quality-control 2020.11.1 py36_0 qiime2/label/r2020.11
q2-quality-filter 2020.11.1 py36_0 qiime2/label/r2020.11
q2-sample-classifier 2020.11.1 py36_0 qiime2/label/r2020.11
q2-taxa 2020.11.1 py36_0 qiime2/label/r2020.11
q2-types 2020.11.1 py36_0 qiime2/label/r2020.11
q2-vsearch 2020.11.1 py36_0 qiime2/label/r2020.11
q2cli 2020.11.1 py36_0 qiime2/label/r2020.11
q2studio 2020.11.0 pypi_0 pypi
q2templates 2020.11.1 py36_0 qiime2/label/r2020.11
qiime2 2020.11.1 py36_0 qiime2/label/r2020.11
r-assertthat 0.2.1 r40h6115d3f_2 conda-forge
r-backports 1.2.1 r40hcfec24a_0 conda-forge
r-base 4.0.2 he766273_1 conda-forge
r-bh 1.72.0_3 r40h6115d3f_1 conda-forge
r-bitops 1.0_6 r40hcdcec82_1004 conda-forge
r-brio 1.1.0 r40h9e2df91_1 conda-forge
r-callr 3.5.1 r40h142f84f_0 conda-forge
r-cli 2.2.0 r40hc72bb7e_0 conda-forge
r-cluster 2.1.0 r40h31ca83e_4 conda-forge
r-colorspace 2.0_0 r40h9e2df91_0 conda-forge
r-crayon 1.3.4 r40h6115d3f_1003 conda-forge
r-desc 1.2.0 r40h6115d3f_1003 conda-forge
r-diffobj 0.3.2 r40h9e2df91_1 conda-forge
r-digest 0.6.27 r40h1b71b39_0 conda-forge
r-ellipsis 0.3.1 r40hcdcec82_0 conda-forge
r-evaluate 0.14 r40h6115d3f_2 conda-forge
r-fansi 0.4.1 r40hcdcec82_1 conda-forge
r-farver 2.0.3 r40h0357c0b_1 conda-forge
r-formatr 1.7 r40h6115d3f_2 conda-forge
r-futile.logger 1.4.3 r40h6115d3f_1003 conda-forge
r-futile.options 1.0.1 r40h6115d3f_1002 conda-forge
r-ggplot2 3.3.2 r40hc72bb7e_1 conda-forge
r-glue 1.4.2 r40hcdcec82_0 conda-forge
r-gtable 0.3.0 r40h6115d3f_3 conda-forge
r-hwriter 1.3.2 r40h6115d3f_1003 conda-forge
r-isoband 0.2.3 r40h03ef668_0 conda-forge
r-jpeg 0.1_8.1 r40hcdcec82_1 conda-forge
r-jsonlite 1.7.2 r40hcfec24a_0 conda-forge
r-labeling 0.4.2 r40h142f84f_0 conda-forge
r-lambda.r 1.2.4 r40h6115d3f_1 conda-forge
r-lattice 0.20_41 r40hcdcec82_2 conda-forge
r-latticeextra 0.6_29 r40h6115d3f_1 conda-forge
r-lifecycle 0.2.0 r40h6115d3f_1 conda-forge
r-magrittr 2.0.1 r40h9e2df91_1 conda-forge
r-mass 7.3_53 r40hcdcec82_0 conda-forge
r-matrix 1.2_18 r40h7fa42b6_3 conda-forge
r-matrixstats 0.57.0 r40hcdcec82_0 conda-forge
r-mgcv 1.8_33 r40h7fa42b6_0 conda-forge
r-munsell 0.5.0 r40h6115d3f_1003 conda-forge
r-nlme 3.1_150 r40h31ca83e_0 conda-forge
r-permute 0.9_5 r40h6115d3f_3 conda-forge
r-pillar 1.4.7 r40hc72bb7e_0 conda-forge
r-pkgbuild 1.1.0 r40h6115d3f_0 conda-forge
r-pkgconfig 2.0.3 r40h6115d3f_1 conda-forge
r-pkgload 1.1.0 r40h0357c0b_0 conda-forge
r-plyr 1.8.6 r40h0357c0b_1 conda-forge
r-png 0.1_7 r40hcdcec82_1004 conda-forge
r-praise 1.0.0 r40h6115d3f_1004 conda-forge
r-prettyunits 1.1.1 r40h6115d3f_1 conda-forge
r-processx 3.4.5 r40hcfec24a_0 conda-forge
r-ps 1.5.0 r40hcfec24a_0 conda-forge
r-r6 2.5.0 r40hc72bb7e_0 conda-forge
r-rcolorbrewer 1.1_2 r40h6115d3f_1003 conda-forge
r-rcpp 1.0.5 r40he524a50_0 conda-forge
r-rcppparallel 5.0.2 r40h0357c0b_0 conda-forge
r-rcurl 1.98_1.2 r40hcdcec82_1 conda-forge
r-rematch2 2.1.2 r40h6115d3f_1 conda-forge
r-reshape2 1.4.4 r40h0357c0b_1 conda-forge
r-rlang 0.4.9 r40hcfec24a_0 conda-forge
r-rprojroot 2.0.2 r40hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r40hc72bb7e_0 conda-forge
r-scales 1.1.1 r40h6115d3f_0 conda-forge
r-snow 0.4_3 r40h6115d3f_1002 conda-forge
r-stringi 1.5.3 r40h604b29c_0 conda-forge
r-stringr 1.4.0 r40h6115d3f_2 conda-forge
r-testthat 3.0.0 r40he524a50_0 conda-forge
r-tibble 3.0.4 r40h0eb13af_0 conda-forge
r-utf8 1.1.4 r40hcdcec82_1003 conda-forge
r-vctrs 0.3.5 r40h9e2df91_0 conda-forge
r-vegan 2.5_6 r40hc3f0d1c_3 conda-forge
r-viridislite 0.3.0 r40h6115d3f_1003 conda-forge
r-waldo 0.2.3 r40hc72bb7e_0 conda-forge
r-withr 2.3.0 r40h6115d3f_0 conda-forge
r-zeallot 0.1.0 r40h6115d3f_1002 conda-forge
raxml 8.2.12 h516909a_2 bioconda
readline 8.0 he28a2e2_2 conda-forge
requests 2.25.0 pyhd3deb0d_0 conda-forge
samtools 1.11 h6270b1f_0 bioconda
scikit-bio 0.5.6 py36ha112f06_4 conda-forge
scikit-learn 0.23.1 py36h0e1014b_0 conda-forge
scipy 1.5.3 py36h976291a_0 conda-forge
seaborn 0.11.0 ha770c72_1 conda-forge
seaborn-base 0.11.0 pyhd8ed1ab_1 conda-forge
sed 4.8 he412f7d_0 conda-forge
send2trash 1.5.0 py_0 conda-forge
sepp 4.3.10 py36heb1dbbb_2 bioconda
setuptools 49.6.0 py36h9880bd3_2 conda-forge
sina 1.7.1 h9aa86b4_0 bioconda
six 1.15.0 pyh9f0ad1d_0 conda-forge
sortmerna 2.0 he860b03_4 bioconda
sqlite 3.34.0 h74cdb3f_0 conda-forge
statsmodels 0.12.1 py36ha112f06_1 conda-forge
sysroot_linux-64 2.12 h77966d4_13 conda-forge
tbb 2020.2 hc9558a2_0 conda-forge
terminado 0.9.1 py36h5fab9bb_1 conda-forge
testpath 0.4.4 py_0 conda-forge
threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge
tk 8.6.10 hed695b0_1 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py36h1d69622_0 conda-forge
traitlets 4.3.3 py36h9f0ad1d_1 conda-forge
typing_extensions 3.7.4.3 py_0 conda-forge
tzlocal 2.1 pyh9f0ad1d_0 conda-forge
unifrac 0.20.1 py36h0e47c99_0 bioconda
urllib3 1.25.11 py_0 conda-forge
vsearch 2.7.0 1 bioconda
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
werkzeug 1.0.1 pypi_0 pypi
wheel 0.36.1 pyhd3deb0d_0 conda-forge
widgetsnbextension 3.5.1 py36h5fab9bb_4 conda-forge
xopen 1.0.1 py36h5fab9bb_1 conda-forge
xorg-fixesproto 5.0 h14c3975_1002 conda-forge
xorg-inputproto 2.3.2 h14c3975_1002 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.12 h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxfixes 5.0.3 h516909a_1004 conda-forge
xorg-libxi 1.7.10 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-libxtst 1.2.3 h516909a_1002 conda-forge
xorg-recordproto 1.14.2 h516909a_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h516909a_0 conda-forge
zeromq 4.3.3 h58526e2_3 conda-forge
zipp 3.4.0 py_0 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zope-event 4.5.0 pypi_0 pypi
zope-interface 5.2.0 pypi_0 pypi
zstd 1.4.5 h6597ccf_2 conda-forge

(qiime2-2020.11) [email protected]:/media/sf_Desktop/qiime2-ITS1$ which bbmerge.sh
/home/qiime2/miniconda/envs/qiime2-2020.11/bin/bbmerge.sh

Thanks.

Hi Dr Rivers
I am still for your reply.

Thanks and regards.

Betty

Hi @bettya !

Try: conda install -y -c bioconda bbmap==38.69 inside your conda environment.

Maybe it works with newer versions as well, but this is the version I used when I experienced the problem you describe.

Good luck with your research :slight_smile:

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Thanks a bunch.
The merging command I believed required a lot of space as my VM did not come up for hours after performing the command.

It eventually worked after restarting and I have proceeded.

Thanks a million.

1 Like