bakta
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oschwengers
'SQL error!', IndexError('tuple index out of range')
So, here I am with this error which I do not know how to solve. I recently installed Bakta (using conda, but had to use nanoporetech channel to install few dependencies as the others ones were not suppported on this CPU) on one of the new machine in the lab which is based on aarch64-CPU. However, running just the trial run generated this error.
bakta ../1313.fasta -p try -o ./jay/ --db ../db/ --force --verbose --debug
Bakta v1.8.1
Options and arguments:
input: /home/jay/1313.fasta
db: /home/jay/db, version 5.1, full
output: /home/jay/jay/jay
force: True
tmp directory: /tmp/tmpcmre_8ml
prefix: try
threads: 8
debug: True
translation table: 11
Bakta runs in DEBUG mode! Temporary data will not be destroyed at: /tmp/tmpcmre_8ml
parse genome sequences...
imported: 52
filtered & revised: 52
contigs: 52
start annotation...
predict tRNAs...
found: 46
predict tmRNAs...
found: 1
predict rRNAs...
found: 6
predict ncRNAs...
found: 44
predict ncRNA regions...
found: 21
predict CRISPR arrays...
found: 0
predict & annotate CDSs...
predicted: 2097
discarded spurious: 0
revised translational exceptions: 0
--- Logging error ---
Traceback (most recent call last):
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/site-packages/bakta/ups.py", line 43, in lookup
if(rec is not None and rec[DB_UPS_COL_LENGTH] == len(feature['aa'])):
~~~^^^^^^^^^^^^^^^^^^^
IndexError: tuple index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/logging/__init__.py", line 1160, in emit
msg = self.format(record)
^^^^^^^^^^^^^^^^^^^
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/logging/__init__.py", line 999, in format
return fmt.format(record)
^^^^^^^^^^^^^^^^^^
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/logging/__init__.py", line 703, in format
record.message = record.getMessage()
^^^^^^^^^^^^^^^^^^^
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/logging/__init__.py", line 392, in getMessage
msg = msg % self.args
~~~~^~~~~~~~~~~
TypeError: not all arguments converted during string formatting
Call stack:
File "/home/jay/miniconda3/envs/bakta/bin/bakta", line 10, in <module>
sys.exit(main())
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/site-packages/bakta/main.py", line 247, in main
cdss_ups, cdss_not_found = ups.lookup(cdss)
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/site-packages/bakta/ups.py", line 57, in lookup
log.exception('Could not read UPSs from db!', ex)
Message: 'Could not read UPSs from db!'
Arguments: (IndexError('tuple index out of range'),)
Traceback (most recent call last):
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/site-packages/bakta/ups.py", line 43, in lookup
if(rec is not None and rec[DB_UPS_COL_LENGTH] == len(feature['aa'])):
~~~^^^^^^^^^^^^^^^^^^^
IndexError: tuple index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jay/miniconda3/envs/bakta/bin/bakta", line 10, in <module>
sys.exit(main())
^^^^^^
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/site-packages/bakta/main.py", line 247, in main
cdss_ups, cdss_not_found = ups.lookup(cdss)
^^^^^^^^^^^^^^^^
File "/home/jay/miniconda3/envs/bakta/lib/python3.12/site-packages/bakta/ups.py", line 58, in lookup
raise Exception("SQL error!", ex)
Exception: ('SQL error!', IndexError('tuple index out of range'))
Apart from this, since the installation has been a bit different for me (Atleast I think it was, but I am not sure if this is trivial thing only), just putting the list of tools installed in the environment:
(bakta) jay@jetmimd-desktop:~/jay$ conda list
# packages in environment at /home/jay/miniconda3/envs/bakta:
#
# Name Version Build Channel
_openmp_mutex 4.5 2_gnu conda-forge
about-time 4.2.1 pyhd8ed1ab_0 conda-forge
alive-progress 3.0.1 pyhd8ed1ab_0 conda-forge
aragorn 1.2.41 h920789f_1 nanoporetech
archspec 0.2.3 pyhd8ed1ab_0 conda-forge
bakta 1.8.1 pyhdfd78af_0 bioconda
biopython 1.83 py312hdd3e373_0 conda-forge
blast 2.13.0 1 nanoporetech
brotli-python 1.1.0 py312h2aa54b4_1 conda-forge
bzip2 1.0.8 h31becfc_5 conda-forge
c-ares 1.27.0 h31becfc_0 conda-forge
ca-certificates 2024.2.2 hcefe29a_0 conda-forge
certifi 2024.2.2 py312hd43f75c_0
cffi 1.16.0 py312hf3c74c0_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
circos 0.69.9 hdfd78af_0 bioconda
curl 8.5.0 h4e8248e_0 conda-forge
diamond 2.1.8 hbfd4b83_0 nanoporetech
expat 2.5.0 hd600fc2_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 ha9a116f_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 hf0a5ef3_2 conda-forge
giflib 5.2.1 hb4cce97_3 conda-forge
grapheme 0.6.0 pyhd8ed1ab_0 conda-forge
hmmer 3.4 hbfd4b83_0 nanoporetech
icu 73.2 h787c7f5_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
infernal 1.1.4+neon h920789f_1 nanoporetech
isa-l 2.31.0 h31becfc_1 conda-forge
keyutils 1.6.1 h4e544f5_0 conda-forge
krb5 1.21.2 hc419048_0 conda-forge
ld_impl_linux-aarch64 2.40 h2d8c526_0 conda-forge
lerc 4.0.0 h4de3ea5_0 conda-forge
libblas 3.9.0 21_linuxaarch64_openblas conda-forge
libcblas 3.9.0 21_linuxaarch64_openblas conda-forge
libcurl 8.5.0 h4e8248e_0 conda-forge
libdeflate 1.19 h31becfc_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h31becfc_2 conda-forge
libexpat 2.5.0 hd600fc2_1 conda-forge
libffi 3.4.2 h3557bc0_5 conda-forge
libgcc-ng 13.2.0 hf8544c7_5 conda-forge
libgd 2.3.3 hcd22fd5_9 conda-forge
libgfortran-ng 13.2.0 he9431aa_5 conda-forge
libgfortran5 13.2.0 h582850c_5 conda-forge
libgomp 13.2.0 hf8544c7_5 conda-forge
libiconv 1.17 h31becfc_2 conda-forge
libjpeg-turbo 3.0.0 h31becfc_1 conda-forge
liblapack 3.9.0 21_linuxaarch64_openblas conda-forge
libnghttp2 1.58.0 hb0e430d_1 conda-forge
libnsl 2.0.1 h31becfc_0 conda-forge
libopenblas 0.3.26 pthreads_h5a5ec62_0 conda-forge
libpng 1.6.43 h194ca79_0 conda-forge
libsqlite 3.45.1 h194ca79_0 conda-forge
libssh2 1.11.0 h492db2e_0 conda-forge
libstdcxx-ng 13.2.0 h9a76618_5 conda-forge
libtiff 4.6.0 h1708d11_2 conda-forge
libuuid 2.38.1 hb4cce97_0 conda-forge
libwebp 1.3.2 heb2ea1b_1 conda-forge
libwebp-base 1.3.2 h31becfc_0 conda-forge
libxcrypt 4.4.36 h31becfc_1 conda-forge
libxml2 2.12.5 h3091e33_0 conda-forge
libzlib 1.2.13 h31becfc_5 conda-forge
ncbi-amrfinderplus 3.11.20 h3f4af3b_0 nanoporetech
ncurses 6.4 h0425590_2 conda-forge
numpy 1.26.4 py312h470d778_0 conda-forge
openssl 3.2.1 h31becfc_0 conda-forge
pbzip2 1.1.13 ha36d286_2 conda-forge
perl 5.32.1 7_h31becfc_perl5 conda-forge
perl-b-cow 0.007 pl5321h920789f_0 nanoporetech
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-clone 0.46 pl5321h920789f_0 nanoporetech
perl-config-general 2.65 pl5321hdfd78af_0 bioconda
perl-digest-perl-md5 1.9 pl5321hdfd78af_2 bioconda
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-font-ttf 1.06 pl5321hdfd78af_1 bioconda
perl-gd 2.76 pl5321hbfd4b83_2 nanoporetech
perl-io-string 1.08 pl5321hdfd78af_4 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h920789f_2 nanoporetech
perl-math-bezier 0.01 pl5321hdfd78af_2 bioconda
perl-math-round 0.07 pl5321hdfd78af_2 bioconda
perl-math-vecstat 0.08 pl5321hdfd78af_2 bioconda
perl-module-implementation 0.09 pl5321hdfd78af_3 bioconda
perl-module-runtime 0.016 pl5321hdfd78af_2 bioconda
perl-number-format 1.76 pl5321hd8ed1ab_0 conda-forge
perl-params-validate 1.31 pl5321h920789f_2 nanoporetech
perl-pathtools 3.75 pl5321h920789f_0 nanoporetech
perl-readonly 2.05 pl5321hdfd78af_1 bioconda
perl-regexp-common 2017060201 pl5321hd8ed1ab_0 conda-forge
perl-scalar-list-utils 1.63 pl5321h920789f_0 nanoporetech
perl-set-intspan 1.19 pl5321hdfd78af_2 bioconda
perl-statistics-basic 1.6611 pl5321hdfd78af_3 bioconda
perl-svg 2.87 pl5321hd8ed1ab_0 conda-forge
perl-text-format 0.62 pl5321hdfd78af_0 bioconda
perl-time-hires 1.9764 pl5321h920789f_4 nanoporetech
perl-try-tiny 0.31 pl5321hdfd78af_1 bioconda
perl-xml-parser 2.44_01 pl5321he03bdfe_1003 conda-forge
pigz 2.8 h194ca79_0 conda-forge
piler-cr 1.06 h3f4af3b_4 nanoporetech
pip 24.0 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyrodigal 2.3.0 py312h920789f_0 nanoporetech
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.12.2 h43d1f9e_0_cpython conda-forge
python-isal 1.6.0 py312h9ef2f89_0 conda-forge
python_abi 3.12 4_cp312 conda-forge
pyyaml 6.0.1 py312hdd3e373_1 conda-forge
readline 8.2 h8fc344f_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
setuptools 69.1.1 pyhd8ed1ab_0 conda-forge
sqlite 3.41.2 h998d150_0
tk 8.6.13 h194ca79_0 conda-forge
trnascan-se 2.0.12 pl5321h920789f_0 nanoporetech
tzdata 2024a h0c530f3_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xopen 1.9.0 py312h8025657_0 conda-forge
xz 5.2.6 h9cdd2b7_0 conda-forge
yaml 0.2.5 hf897c2e_2 conda-forge
zlib 1.2.13 h31becfc_5 conda-forge
zstandard 0.22.0 py312hb120188_0 conda-forge
zstd 1.5.5 h4c53e97_0 conda-forge
Lastly, here is the log file as well. try.log
Apologies if this is very trivial thing!
Thanking you in advance.
Hi and thanks a lot for this very detailed description. This is very interesting and the first time I see this type of error occurring. Unfortunately, as I do not have access to an aarch64 system, I can only speculate about what's the cause for this. Hence, I apologize that (currently) I cannot debug this. Have you tried Bakta on another machine?
I leave this open, just in case others face this sort of error, as well.
Hi, yes I usually use bakta on my laptop, there it works nicely. Currently I am thinking of creating the environment(on my laptop) with same tools from the same channel as they are there in the above mentioned aarch64 device and see if there also it generates the same error. Let's see! Do you suspect anything/tool for which I should try changing/changing version there first?
I'd keep an eye on sqlite and python itself. And could you maybe try to use a non-3.12 Python version, so 3.9, 3.10 or 3.11?
Hey, sorry for the wait, but no updates yet. Been pretty tied up with other stuff lately, so haven't had much time to dive into this. Once things calm down, I'll have a chance to try out some variations. Will definitely keep posting here!
Thanks for the update, and no pressure intended at all. Just a gentle keep alive ping to sort out stalled issues ;-)