PplacerException Error

[kevinmyers]

Additional comments

I am running GTDBTk on 123 bacterial MAGs using GTDB-Tk v1.5.1 (installed via Anaconda, see below) and release202 using the following commands:

export GTDBTK_DATA_PATH=/mnt/bigdata/processed_data/kmyers/GTDB/release202
~/anaconda3/bin/gtdbtk classify_wf --genome_dir ./ --out_dir ./GTDBTk_out/ -x fasta --cpus 16

It runs fine until step 6 of 9: Pulling Exponents when I get the following error (also in the LOG file, attached):

`[2021-10-04 15:58:06] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
==> Step 6 of 9: Pulling exponents. Process Process-137:
Traceback (most recent call last):
File "/home/GLBRCORG/kmyers/anaconda3/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/home/GLBRCORG/kmyers/anaconda3/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/home/GLBRCORG/kmyers/anaconda3/lib/python3.6/site-packages/gtdbtk/external/pplacer.py", line 126, in _worker
'file: {}'.format(pplacer_out))
gtdbtk.exceptions.PplacerException: An error was encountered while running pplacer, check the log file: ./GTDBTk_out/classify/intermediate_results/pplacer/pplacer.bac120.out
[2021-10-04 16:27:29] ERROR: Controlled exit resulting from an unrecoverable error or warning.

================================================================================
EXCEPTION: PplacerException
MESSAGE: An error was encountered while running pplacer.

---

Traceback (most recent call last):
File "/home/GLBRCORG/kmyers/anaconda3/lib/python3.6/site-packages/gtdbtk/main.py", line 95, in main
gt_parser.parse_options(args)
File "/home/GLBRCORG/kmyers/anaconda3/lib/python3.6/site-packages/gtdbtk/main.py", line 737, in parse_options
self.classify(options)
File "/home/GLBRCORG/kmyers/anaconda3/lib/python3.6/site-packages/gtdbtk/main.py", line 462, in classify
options.split_tree)
File "/home/GLBRCORG/kmyers/anaconda3/lib/python3.6/site-packages/gtdbtk/classify.py", line 448, in run
scratch_dir)
File "/home/GLBRCORG/kmyers/anaconda3/lib/python3.6/site-packages/gtdbtk/classify.py", line 241, in place_genomes
user_msa_file, pplacer_out, pplacer_mmap_file)
File "/home/GLBRCORG/kmyers/anaconda3/lib/python3.6/site-packages/gtdbtk/external/pplacer.py", line 93, in run
'An error was encountered while running pplacer.')
gtdbtk.exceptions.PplacerException: An error was encountered while running pplacer.
`
Here is what is in placer.bac120.out:

Running pplacer v1.1.alpha19-0-g807f6f3 analysis on ./GTDBTk_dRep/align/gtdbtk.bac120.user_msa.fasta...
Didn't find any reference sequences in given alignment file. Using supplied reference alignment.
Pre-masking sequences... sequence length cut from 5037 to 5037.
Determining figs... figs disabled.
Allocating memory for internal nodes... done.
Caching likelihood information on reference tree...

I've successfully run GTDBTk before and as far as I know, nothing as changed on the server side (I'm running this on a shared server cluster). I've included the Environment and CPU/OS information below. Any help would be greatly appreciated. Thanks!!

Environment

• Using a conda environment (include the output of conda list && conda list --revisions)

$ conda list && conda list --revisions
packages in environment at /opt/bifxapps/miniconda3:
Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
blas 1.0 mkl
boost 1.74.0 py37h429e714_0 conda-forge
boost-cpp 1.74.0 h9359b55_0 conda-forge
bottleneck 1.3.2 py37heb32a55_1
brotlipy 0.7.0 py37h27cfd23_1003
bzip2 1.0.8 h7b6447c_0
ca-certificates 2021.7.5 h06a4308_1
cairo 1.16.0 h3fc0475_1005 conda-forge
certifi 2021.5.30 py37h06a4308_0
cffi 1.14.6 py37h400218f_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
conda 4.10.3 py37h06a4308_0
conda-package-handling 1.7.3 py37h27cfd23_1
cryptography 3.4.7 py37hd23ed53_0
fontconfig 2.13.1 h1056068_1002 conda-forge
freetype 2.10.4 h5ab3b9f_0
glib 2.69.1 h5202010_0
icu 67.1 he1b5a44_0 conda-forge
idna 3.2 pyhd3eb1b0_0
intel-openmp 2021.3.0 h06a4308_3350
jpeg 9b h024ee3a_2
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.35.1 h7274673_9
libedit 3.1.20210714 h7f8727e_0
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgomp 9.3.0 h5101ec6_17
libiconv 1.16 h516909a_0 conda-forge
libpng 1.6.37 hbc83047_0
libstdcxx-ng 9.3.0 hd4cf53a_17
libtiff 4.2.0 h85742a9_0
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp-base 1.2.0 h27cfd23_0
libxcb 1.14 h7b6447c_0
libxml2 2.9.10 h68273f3_2 conda-forge
lz4-c 1.9.3 h295c915_1
mkl 2021.3.0 h06a4308_520
mkl-service 2.4.0 py37h7f8727e_0
mkl_fft 1.3.0 py37h42c9631_2
mkl_random 1.2.2 py37h51133e4_0
ncurses 6.2 he6710b0_1
numexpr 2.7.3 py37h22e1b3c_1
numpy 1.20.3 py37hf144106_0
numpy-base 1.20.3 py37h74d4b33_0
olefile 0.46 py37_0
openjpeg 2.4.0 h3ad879b_0
openssl 1.1.1k h27cfd23_0
pandas 1.3.2 py37h8c16a72_0
pcre 8.45 h295c915_0
pillow 8.3.1 py37h2c7a002_0
pip 21.0.1 py37h06a4308_0
pixman 0.38.0 h516909a_1003 conda-forge
pycairo 1.19.1 py37h708ec4a_0
pycosat 0.6.3 py37h27cfd23_0
pycparser 2.20 py_2
pyopenssl 20.0.1 pyhd3eb1b0_1
pysocks 1.7.1 py37_1
python 3.7.6 h0371630_2
python-dateutil 2.8.2 pyhd3eb1b0_0
python_abi 3.7 1_cp37m conda-forge
pytz 2021.1 pyhd3eb1b0_0
rdkit 2020.03.6 py37h0c252aa_0 conda-forge
readline 7.0 h7b6447c_5
requests 2.26.0 pyhd3eb1b0_0
ruamel_yaml 0.15.100 py37h27cfd23_0
setuptools 52.0.0 py37h06a4308_0
six 1.16.0 pyhd3eb1b0_0
sqlite 3.33.0 h62c20be_0
tk 8.6.10 hbc83047_0
tqdm 4.62.1 pyhd3eb1b0_1
urllib3 1.26.6 pyhd3eb1b0_1
wheel 0.37.0 pyhd3eb1b0_0
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-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxrender 0.9.10 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 h27cfd23_1007
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h7b6447c_0
zlib 1.2.11 h7b6447c_3
zstd 1.4.9 haebb681_0
2019-10-24 19:27:50 (rev 0)
+_libgcc_mutex-0.1
+asn1crypto-1.2.0
+ca-certificates-2019.10.16
+certifi-2019.9.11
+cffi-1.13.0
+chardet-3.0.4
+conda-4.7.12
+conda-package-handling-1.6.0
+cryptography-2.8
+idna-2.8
+libedit-3.1.20181209
+libffi-3.2.1
+libgcc-ng-9.1.0
+libstdcxx-ng-9.1.0
+ncurses-6.1
+openssl-1.1.1d
+pip-19.3.1
+pycosat-0.6.3
+pycparser-2.19
+pyopenssl-19.0.0
+pysocks-1.7.1
+python-3.7.4
+readline-7.0
+requests-2.22.0
+ruamel_yaml-0.15.46
+setuptools-41.4.0
+six-1.12.0
+sqlite-3.30.0
+tk-8.6.8
+tqdm-4.36.1
+urllib3-1.24.2
+wheel-0.33.6
+xz-5.2.4
+yaml-0.1.7
+zlib-1.2.11

2020-01-22 11:01:30 (rev 1)
asn1crypto {1.2.0 -> 1.3.0}
ca-certificates {2019.10.16 -> 2019.11.27}
certifi {2019.9.11 -> 2019.11.28}
cffi {1.13.0 -> 1.13.2}
conda {4.7.12 -> 4.8.1}
pycosat {0.6.3 -> 0.6.3}
pyopenssl {19.0.0 -> 19.1.0}
python {3.7.4 -> 3.7.6}
requests {2.22.0 -> 2.22.0}
ruamel_yaml {0.15.46 -> 0.15.87}
setuptools {41.4.0 -> 44.0.0}
six {1.12.0 -> 1.13.0}
sqlite {3.30.0 -> 3.30.1}
tqdm {4.36.1 -> 4.41.1}
urllib3 {1.24.2 -> 1.25.7}
+ld_impl_linux-64-2.33.1

2020-03-09 12:25:21 (rev 2)
_libgcc_mutex {0.1 -> 0.1 (defaults/linux-64)}
asn1crypto {1.3.0 -> 1.3.0 (defaults/linux-64)}
ca-certificates {2019.11.27 -> 2020.1.1 (defaults/linux-64)}
certifi {2019.11.28 -> 2019.11.28 (defaults/linux-64)}
cffi {1.13.2 -> 1.14.0 (defaults/linux-64)}
chardet {3.0.4 -> 3.0.4 (defaults/linux-64)}
conda {4.8.1 -> 4.8.2 (defaults/linux-64)}
conda-package-handling {1.6.0 -> 1.6.0 (defaults/linux-64)}
cryptography {2.8 -> 2.8 (defaults/linux-64)}
idna {2.8 -> 2.8 (defaults/linux-64)}
ld_impl_linux-64 {2.33.1 -> 2.33.1 (defaults/linux-64)}
libedit {3.1.20181209 -> 3.1.20181209 (defaults/linux-64)}
libffi {3.2.1 -> 3.2.1 (defaults/linux-64)}
libgcc-ng {9.1.0 -> 9.1.0 (defaults/linux-64)}
libstdcxx-ng {9.1.0 -> 9.1.0 (defaults/linux-64)}
ncurses {6.1 -> 6.2 (defaults/linux-64)}
openssl {1.1.1d -> 1.1.1d (defaults/linux-64)}
pip {19.3.1 -> 20.0.2 (defaults/linux-64)}
pycosat {0.6.3 -> 0.6.3 (defaults/linux-64)}
pycparser {2.19 -> 2.19 (defaults/linux-64)}
pyopenssl {19.1.0 -> 19.1.0 (defaults/linux-64)}
pysocks {1.7.1 -> 1.7.1 (defaults/linux-64)}
python {3.7.6 -> 3.7.6 (defaults/linux-64)}
readline {7.0 -> 7.0 (defaults/linux-64)}
requests {2.22.0 -> 2.22.0 (defaults/linux-64)}
ruamel_yaml {0.15.87 -> 0.15.87 (defaults/linux-64)}
setuptools {44.0.0 -> 45.2.0 (defaults/linux-64)}
six {1.13.0 -> 1.14.0 (defaults/linux-64)}
sqlite {3.30.1 -> 3.31.1 (defaults/linux-64)}
tk {8.6.8 -> 8.6.8 (defaults/linux-64)}
tqdm {4.41.1 -> 4.42.1 (defaults/noarch)}
urllib3 {1.25.7 -> 1.25.8 (defaults/linux-64)}
wheel {0.33.6 -> 0.34.2 (defaults/linux-64)}
xz {5.2.4 -> 5.2.4 (defaults/linux-64)}
yaml {0.1.7 -> 0.1.7 (defaults/linux-64)}
zlib {1.2.11 -> 1.2.11 (defaults/linux-64)}

2020-03-16 12:54:01 (rev 3)
requests {2.22.0 (defaults/linux-64) -> 2.23.0 (defaults/linux-64)}
setuptools {45.2.0 (defaults/linux-64) -> 46.0.0 (defaults/linux-64)}

2020-05-04 16:52:25 (rev 4)
certifi {2019.11.28 (defaults/linux-64) -> 2020.4.5.1 (defaults/linux-64)}
conda {4.8.2 (defaults/linux-64) -> 4.8.3 (defaults/linux-64)}
idna {2.8 (defaults/linux-64) -> 2.9 (defaults/noarch)}
ncurses {6.2 (defaults/linux-64) -> 6.2 (defaults/linux-64)}
openssl {1.1.1d (defaults/linux-64) -> 1.1.1g (defaults/linux-64)}
pycparser {2.19 (defaults/linux-64) -> 2.20 (defaults/noarch)}
setuptools {46.0.0 (defaults/linux-64) -> 46.1.3 (defaults/linux-64)}
sqlite {3.31.1 (defaults/linux-64) -> 3.31.1 (defaults/linux-64)}
tqdm {4.42.1 (defaults/noarch) -> 4.45.0 (defaults/noarch)}
xz {5.2.4 (defaults/linux-64) -> 5.2.5 (defaults/linux-64)}

2020-09-18 13:28:32 (rev 5)
ca-certificates {2020.1.1 (defaults/linux-64) -> 2020.7.22 (defaults/linux-64)}
certifi {2020.4.5.1 (defaults/linux-64) -> 2020.6.20 (defaults/linux-64)}
cffi {1.14.0 (defaults/linux-64) -> 1.14.2 (defaults/linux-64)}
conda {4.8.3 (defaults/linux-64) -> 4.8.4 (defaults/linux-64)}
conda-package-handling {1.6.0 (defaults/linux-64) -> 1.6.1 (defaults/linux-64)}
cryptography {2.8 (defaults/linux-64) -> 3.1 (defaults/linux-64)}
idna {2.9 (defaults/noarch) -> 2.10 (defaults/noarch)}
libedit {3.1.20181209 (defaults/linux-64) -> 3.1.20191231 (defaults/linux-64)}
libffi {3.2.1 (defaults/linux-64) -> 3.3 (defaults/linux-64)}
pip {20.0.2 (defaults/linux-64) -> 20.2.2 (defaults/linux-64)}
pycparser {2.20 (defaults/noarch) -> 2.20 (defaults/noarch)}
pyopenssl {19.1.0 (defaults/linux-64) -> 19.1.0 (defaults/noarch)}
pysocks {1.7.1 (defaults/linux-64) -> 1.7.1 (defaults/linux-64)}
requests {2.23.0 (defaults/linux-64) -> 2.24.0 (defaults/noarch)}
ruamel_yaml {0.15.87 (defaults/linux-64) -> 0.15.87 (defaults/linux-64)}
setuptools {46.1.3 (defaults/linux-64) -> 49.6.0 (defaults/linux-64)}
six {1.14.0 (defaults/linux-64) -> 1.15.0 (defaults/noarch)}
sqlite {3.31.1 (defaults/linux-64) -> 3.33.0 (defaults/linux-64)}
tk {8.6.8 (defaults/linux-64) -> 8.6.10 (defaults/linux-64)}
tqdm {4.45.0 (defaults/noarch) -> 4.48.2 (defaults/noarch)}
urllib3 {1.25.8 (defaults/linux-64) -> 1.25.10 (defaults/noarch)}
wheel {0.34.2 (defaults/linux-64) -> 0.35.1 (defaults/noarch)}
yaml {0.1.7 (defaults/linux-64) -> 0.2.5 (defaults/linux-64)}
-asn1crypto-1.3.0 (defaults/linux-64)
+brotlipy-0.7.0 (defaults/linux-64)

2020-09-22 11:24:29 (rev 6)
cffi {1.14.2 (defaults/linux-64) -> 1.14.3 (defaults/linux-64)}
conda {4.8.4 (defaults/linux-64) -> 4.8.5 (defaults/linux-64)}
openssl {1.1.1g (defaults/linux-64) -> 1.1.1h (defaults/linux-64)}
tqdm {4.48.2 (defaults/noarch) -> 4.49.0 (defaults/noarch)}

2020-09-22 11:26:01 (rev 7)

2020-10-02 13:00:04 (rev 8)
+_libgcc_mutex-0.1 (defaults/linux-64)
+boost-1.74.0 (conda-forge/linux-64)
+boost-cpp-1.74.0 (conda-forge/linux-64)
+brotlipy-0.7.0 (defaults/linux-64)
+bzip2-1.0.8 (conda-forge/linux-64)
+ca-certificates-2020.6.20 (conda-forge/linux-64)
+cairo-1.16.0 (conda-forge/linux-64)
+certifi-2020.6.20 (conda-forge/linux-64)
+cffi-1.14.3 (defaults/linux-64)
+chardet-3.0.4 (defaults/linux-64)
+conda-4.8.5 (conda-forge/linux-64)
+conda-package-handling-1.6.1 (defaults/linux-64)
+cryptography-3.1 (defaults/linux-64)
+fontconfig-2.13.1 (conda-forge/linux-64)
+freetype-2.10.2 (conda-forge/linux-64)
+glib-2.65.0 (defaults/linux-64)
+icu-67.1 (conda-forge/linux-64)
+idna-2.10 (defaults/noarch)
+jpeg-9d (conda-forge/linux-64)
+lcms2-2.11 (conda-forge/linux-64)
+ld_impl_linux-64-2.33.1 (defaults/linux-64)
+libblas-3.8.0 (conda-forge/linux-64)
+libcblas-3.8.0 (conda-forge/linux-64)
+libedit-3.1.20191231 (defaults/linux-64)
+libffi-3.3 (defaults/linux-64)
+libgcc-ng-9.1.0 (defaults/linux-64)
+libgfortran-ng-7.5.0 (conda-forge/linux-64)
+libiconv-1.16 (conda-forge/linux-64)
+liblapack-3.8.0 (conda-forge/linux-64)
+libopenblas-0.3.10 (conda-forge/linux-64)
+libpng-1.6.37 (conda-forge/linux-64)
+libstdcxx-ng-9.1.0 (defaults/linux-64)
+libtiff-4.1.0 (conda-forge/linux-64)
+libuuid-2.32.1 (conda-forge/linux-64)
+libwebp-base-1.1.0 (conda-forge/linux-64)
+libxcb-1.13 (conda-forge/linux-64)
+libxml2-2.9.10 (conda-forge/linux-64)
+lz4-c-1.9.2 (conda-forge/linux-64)
+ncurses-6.2 (defaults/linux-64)
+numpy-1.19.1 (conda-forge/linux-64)
+olefile-0.46 (conda-forge/noarch)
+openssl-1.1.1h (conda-forge/linux-64)
+pandas-1.1.2 (conda-forge/linux-64)
+pcre-8.44 (conda-forge/linux-64)
+pillow-7.2.0 (conda-forge/linux-64)
+pip-20.2.2 (defaults/linux-64)
+pixman-0.38.0 (conda-forge/linux-64)
+pthread-stubs-0.4 (conda-forge/linux-64)
+pycairo-1.19.1 (conda-forge/linux-64)
+pycosat-0.6.3 (defaults/linux-64)
+pycparser-2.20 (defaults/noarch)
+pyopenssl-19.1.0 (defaults/noarch)
+pysocks-1.7.1 (defaults/linux-64)
+python-3.7.6 (defaults/linux-64)
+python-dateutil-2.8.1 (conda-forge/noarch)
+python_abi-3.7 (conda-forge/linux-64)
+pytz-2020.1 (conda-forge/noarch)
+rdkit-2020.03.6 (conda-forge/linux-64)
+readline-7.0 (defaults/linux-64)
+requests-2.24.0 (defaults/noarch)
+ruamel_yaml-0.15.87 (defaults/linux-64)
+setuptools-49.6.0 (defaults/linux-64)
+six-1.15.0 (defaults/noarch)
+sqlite-3.33.0 (defaults/linux-64)
+tk-8.6.10 (defaults/linux-64)
+tqdm-4.49.0 (defaults/noarch)
+urllib3-1.25.10 (defaults/noarch)
+wheel-0.35.1 (defaults/noarch)
+xorg-kbproto-1.0.7 (conda-forge/linux-64)
+xorg-libice-1.0.10 (conda-forge/linux-64)
+xorg-libsm-1.2.3 (conda-forge/linux-64)
+xorg-libx11-1.6.12 (conda-forge/linux-64)
+xorg-libxau-1.0.9 (conda-forge/linux-64)
+xorg-libxdmcp-1.1.3 (conda-forge/linux-64)
+xorg-libxext-1.3.4 (conda-forge/linux-64)
+xorg-libxrender-0.9.10 (conda-forge/linux-64)
+xorg-renderproto-0.11.1 (conda-forge/linux-64)
+xorg-xextproto-7.3.0 (conda-forge/linux-64)
+xorg-xproto-7.0.31 (conda-forge/linux-64)
+xz-5.2.5 (defaults/linux-64)
+yaml-0.2.5 (defaults/linux-64)
+zlib-1.2.11 (defaults/linux-64)
+zstd-1.4.5 (conda-forge/linux-64)

2021-02-18 11:35:16 (rev 9)
brotlipy {0.7.0 (defaults/linux-64) -> 0.7.0 (defaults/linux-64)}
bzip2 {1.0.8 (conda-forge/linux-64) -> 1.0.8 (defaults/linux-64)}
ca-certificates {2020.6.20 (conda-forge/linux-64) -> 2021.1.19 (defaults/linux-64)}
certifi {2020.6.20 (conda-forge/linux-64) -> 2020.12.5 (defaults/linux-64)}
cffi {1.14.3 (defaults/linux-64) -> 1.14.5 (defaults/linux-64)}
chardet {3.0.4 (defaults/linux-64) -> 4.0.0 (defaults/linux-64)}
conda {4.8.5 (conda-forge/linux-64) -> 4.9.2 (defaults/linux-64)}
conda-package-handling {1.6.1 (defaults/linux-64) -> 1.7.2 (defaults/linux-64)}
cryptography {3.1 (defaults/linux-64) -> 3.3.1 (defaults/linux-64)}
freetype {2.10.2 (conda-forge/linux-64) -> 2.10.4 (defaults/linux-64)}
glib {2.65.0 (defaults/linux-64) -> 2.67.4 (defaults/linux-64)}
idna {2.10 (defaults/noarch) -> 2.10 (defaults/noarch)}
jpeg {9d (conda-forge/linux-64) -> 9b (defaults/linux-64)}
lcms2 {2.11 (conda-forge/linux-64) -> 2.11 (defaults/linux-64)}
libpng {1.6.37 (conda-forge/linux-64) -> 1.6.37 (defaults/linux-64)}
libtiff {4.1.0 (conda-forge/linux-64) -> 4.1.0 (defaults/linux-64)}
libxcb {1.13 (conda-forge/linux-64) -> 1.14 (defaults/linux-64)}
lz4-c {1.9.2 (conda-forge/linux-64) -> 1.9.3 (defaults/linux-64)}
numpy {1.19.1 (conda-forge/linux-64) -> 1.19.2 (defaults/linux-64)}
olefile {0.46 (conda-forge/noarch) -> 0.46 (defaults/linux-64)}
openssl {1.1.1h (conda-forge/linux-64) -> 1.1.1i (defaults/linux-64)}
pandas {1.1.2 (conda-forge/linux-64) -> 1.2.1 (defaults/linux-64)}
pcre {8.44 (conda-forge/linux-64) -> 8.44 (defaults/linux-64)}
pillow {7.2.0 (conda-forge/linux-64) -> 8.1.0 (defaults/linux-64)}
pip {20.2.2 (defaults/linux-64) -> 20.3.3 (defaults/linux-64)}
pycairo {1.19.1 (conda-forge/linux-64) -> 1.19.1 (defaults/linux-64)}
pycosat {0.6.3 (defaults/linux-64) -> 0.6.3 (defaults/linux-64)}
pyopenssl {19.1.0 (defaults/noarch) -> 20.0.1 (defaults/noarch)}
python-dateutil {2.8.1 (conda-forge/noarch) -> 2.8.1 (defaults/noarch)}
pytz {2020.1 (conda-forge/noarch) -> 2021.1 (defaults/noarch)}
requests {2.24.0 (defaults/noarch) -> 2.25.1 (defaults/noarch)}
setuptools {49.6.0 (defaults/linux-64) -> 52.0.0 (defaults/linux-64)}
six {1.15.0 (defaults/noarch) -> 1.15.0 (defaults/linux-64)}
tqdm {4.49.0 (defaults/noarch) -> 4.56.0 (defaults/noarch)}
urllib3 {1.25.10 (defaults/noarch) -> 1.26.3 (defaults/noarch)}
wheel {0.35.1 (defaults/noarch) -> 0.36.2 (defaults/noarch)}
xorg-xproto {7.0.31 (conda-forge/linux-64) -> 7.0.31 (defaults/linux-64)}
zstd {1.4.5 (conda-forge/linux-64) -> 1.4.5 (defaults/linux-64)}
-libblas-3.8.0 (conda-forge/linux-64)
-libcblas-3.8.0 (conda-forge/linux-64)
-libgfortran-ng-7.5.0 (conda-forge/linux-64)
-liblapack-3.8.0 (conda-forge/linux-64)
-libopenblas-0.3.10 (conda-forge/linux-64)
-libwebp-base-1.1.0 (conda-forge/linux-64)
-pthread-stubs-0.4 (conda-forge/linux-64)
-xorg-libxau-1.0.9 (conda-forge/linux-64)
-xorg-libxdmcp-1.1.3 (conda-forge/linux-64)
+blas-1.0 (defaults/linux-64)
+intel-openmp-2020.2 (defaults/linux-64)
+mkl-2020.2 (defaults/linux-64)
+mkl-service-2.3.0 (defaults/linux-64)
+mkl_fft-1.2.0 (defaults/linux-64)
+mkl_random-1.1.1 (defaults/linux-64)
+numpy-base-1.19.2 (defaults/linux-64)

2021-02-18 11:54:43 (rev 10)
openssl {1.1.1i (defaults/linux-64) -> 1.1.1j (defaults/linux-64)}

2021-02-26 11:21:32 (rev 11)
mkl_fft {1.2.0 (defaults/linux-64) -> 1.2.1 (defaults/linux-64)}
pandas {1.2.1 (defaults/linux-64) -> 1.2.2 (defaults/linux-64)}
pip {20.3.3 (defaults/linux-64) -> 21.0.1 (defaults/linux-64)}
pycairo {1.19.1 (defaults/linux-64) -> 1.19.1 (defaults/linux-64)}

2021-09-02 11:03:41 (rev 12)
ca-certificates {2021.1.19 (defaults/linux-64) -> 2021.7.5 (defaults/linux-64)}
certifi {2020.12.5 (defaults/linux-64) -> 2021.5.30 (defaults/linux-64)}
cffi {1.14.5 (defaults/linux-64) -> 1.14.6 (defaults/linux-64)}
conda {4.9.2 (defaults/linux-64) -> 4.10.3 (defaults/linux-64)}
conda-package-handling {1.7.2 (defaults/linux-64) -> 1.7.3 (defaults/linux-64)}
cryptography {3.3.1 (defaults/linux-64) -> 3.4.7 (defaults/linux-64)}
glib {2.67.4 (defaults/linux-64) -> 2.69.1 (defaults/linux-64)}
idna {2.10 (defaults/noarch) -> 3.2 (defaults/noarch)}
intel-openmp {2020.2 (defaults/linux-64) -> 2021.3.0 (defaults/linux-64)}
lcms2 {2.11 (defaults/linux-64) -> 2.12 (defaults/linux-64)}
ld_impl_linux-64 {2.33.1 (defaults/linux-64) -> 2.35.1 (defaults/linux-64)}
libedit {3.1.20191231 (defaults/linux-64) -> 3.1.20210714 (defaults/linux-64)}
libgcc-ng {9.1.0 (defaults/linux-64) -> 9.3.0 (defaults/linux-64)}
libstdcxx-ng {9.1.0 (defaults/linux-64) -> 9.3.0 (defaults/linux-64)}
libtiff {4.1.0 (defaults/linux-64) -> 4.2.0 (defaults/linux-64)}
lz4-c {1.9.3 (defaults/linux-64) -> 1.9.3 (defaults/linux-64)}
mkl {2020.2 (defaults/linux-64) -> 2021.3.0 (defaults/linux-64)}
mkl-service {2.3.0 (defaults/linux-64) -> 2.4.0 (defaults/linux-64)}
mkl_fft {1.2.1 (defaults/linux-64) -> 1.3.0 (defaults/linux-64)}
mkl_random {1.1.1 (defaults/linux-64) -> 1.2.2 (defaults/linux-64)}
numpy {1.19.2 (defaults/linux-64) -> 1.20.3 (defaults/linux-64)}
numpy-base {1.19.2 (defaults/linux-64) -> 1.20.3 (defaults/linux-64)}
openssl {1.1.1j (defaults/linux-64) -> 1.1.1k (defaults/linux-64)}
pandas {1.2.2 (defaults/linux-64) -> 1.3.2 (defaults/linux-64)}
pcre {8.44 (defaults/linux-64) -> 8.45 (defaults/linux-64)}
pillow {8.1.0 (defaults/linux-64) -> 8.3.1 (defaults/linux-64)}
python-dateutil {2.8.1 (defaults/noarch) -> 2.8.2 (defaults/noarch)}
requests {2.25.1 (defaults/noarch) -> 2.26.0 (defaults/noarch)}
ruamel_yaml {0.15.87 (defaults/linux-64) -> 0.15.100 (defaults/linux-64)}
six {1.15.0 (defaults/linux-64) -> 1.16.0 (defaults/noarch)}
tqdm {4.56.0 (defaults/noarch) -> 4.62.1 (defaults/noarch)}
urllib3 {1.26.3 (defaults/noarch) -> 1.26.6 (defaults/noarch)}
wheel {0.36.2 (defaults/noarch) -> 0.37.0 (defaults/noarch)}
zstd {1.4.5 (defaults/linux-64) -> 1.4.9 (defaults/linux-64)}
-chardet-4.0.0 (defaults/linux-64)
+_openmp_mutex-4.5 (defaults/linux-64)
+bottleneck-1.3.2 (defaults/linux-64)
+charset-normalizer-2.0.4 (defaults/noarch)
+libgomp-9.3.0 (defaults/linux-64)
+libwebp-base-1.2.0 (defaults/linux-64)
+numexpr-2.7.3 (defaults/linux-64)
+openjpeg-2.4.0 (defaults/linux-64)

Server information

• CPU: grep -m 1 "^model name" /proc/cpuinfo && grep -c "^processor" /proc/cpuinfo
  model name : Intel(R) Xeon(R) CPU E5-2683 v4 @ 2.10GHz
  64
• RAM: grep "^MemTotal" /proc/meminfo
  MemTotal: 263849352 kB
• OS: cat /etc/os-release
  NAME="CentOS Linux"
  VERSION="7 (Core)"
  ID="centos"
  ID_LIKE="rhel fedora"
  VERSION_ID="7"
  PRETTY_NAME="CentOS Linux 7 (Core)"
  ANSI_COLOR="0;31"
  CPE_NAME="cpe:/o:centos:centos:7"
  HOME_URL="https://www.centos.org/"
  BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

Debugging information

• gtdbtk.log has been included (drag and drop the file to upload).
  gtdbtk.log
• Genomes have been included (if possible, and there are few).

[kevinmyers]

I realized I was using a Node on our server cluster with too little RAM. I have gotten it to work fine when I increase the available RAM. Closing now.