RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
Home Page: https://academic.oup.com/nargab/article/4/3/lqac070/6708509
License: GNU Affero General Public License v3.0
Hello,
I ran into some installation issues while following the README instructions: installing the conda environments fails due to conflicts.
After Running:
bash conda_virt_env.sh
This error appears:
Creating virtual environment and installing RiboTaxa... Thu Apr 13 14:17:28 CEST 2023 Collecting package metadata (repodata.json): done Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed
and then after a long time, a massive list of conflicts is listed.
Can you check if there is something wrong with the .yml files?
Thanks,
Flora
Hi,
Thank you for such great pipeline. I installed it, although while running it, there was a problem with the scikit-learn classifying step:
The scikit-learn version (0.23.1) used to generate this artifact does not match the current version of scikit-learn installed (0.24.1). Please retrain your classifier for your current deployment to prevent data-corruption errors.
I tried to downgrade the scikit-learn through mamba (conda is extremely slow), and I obtained this error:
package q2-diversity-2022.11.1-py38_0 requires scikit-learn 0.24.1.*, but none of the providers can be installed.
Do you have any idea about how to solve this inconvenient?
Hi, I am trying to use RiboTaxa but I'm encountering this error:
File "/data/ese-alexp/software/RiboTaxa//scripts/matam_db_preprocessing.py", line 10, in <module>
from binary_utils import Binary
ModuleNotFoundError: No module named 'binary_utils'
when trying to index the database:
bash -i /mypath/RiboTaxa/indexDB_RiboTaxa.sh /mypath/RiboTaxa/indexDB_arguments.conf
I followed the installation, and I have tried running indexDB_RiboTaxa.sh with:
conda activate RiboTaxa_py36, conda activate RiboTaxa_py27 and without activating conda, and always same issue.
Any idea about whats is going on?
Hi,
While running Ribotaxa:
bash -i /software/RiboTaxa/Pipeline_RiboTaxa_PE.sh /software/RiboTaxa/RiboTaxa_arguments.conf
I have encountered this error:
bowtie-build command:
bowtie-build -o 3 /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.00/iter.00.cons.fasta /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.00/bowtie.index.iter.00 > /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.00/bowtie.iter.00.log
bowtie command:
cat /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/emirge_tmp_reads_1.fastq | bowtie --phred33-quals -t -p 40 -n 3 -l 20 -e 300 --best --strata --all --sam --chunkmbs 128 --minins 300 --maxins 600 /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.00/bowtie.index.iter.00 -1 - -2 /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/emirge_tmp_reads_2.fastq | samtools view -S -h -u -b -F 0x0004 - > /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.00/bowtie.iter.00.PE.u.bam
Finished Bowtie for iteration 00 at Wed Nov 30 18:25:58 2022:
DONE with read mapping for iteration 0 at Wed Nov 30 18:25:58 2022 [0:00:10.112919]...
Finished iteration 0 at Wed Nov 30 18:25:58 2022...
Total time for iteration 0: 0:00:19.636305
Starting iteration 1 at Wed Nov 30 18:25:58 2022...
Reading bam file /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.00/bowtie.iter.00.PE.u.bam at Wed Nov 30 18:25:58 2022...
[E::idx_find_and_load] Could not retrieve index file for '/path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.00/bowtie.iter.00.PE.u.bam'
[E::idx_find_and_load] Could not retrieve index file for '/path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.00/bowtie.iter.00.PE.u.bam'
[E::idx_find_and_load] Could not retrieve index file for '/path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.00/bowtie.iter.00.PE.u.bam'
bowtie-build command:
bowtie-build -o 3 /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.01/iter.01.cons.fasta /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.01/bowtie.index.iter.01 > /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.01/bowtie.iter.01.log
bowtie command:
cat /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/emirge_tmp_reads_1.fastq | bowtie --phred33-quals -t -p 40 -n 3 -l 20 -e 300 --best --strata --all --sam --chunkmbs 128 --minins 300 --maxins 600 /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.01/bowtie.index.iter.01 -1 - -2 /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/emirge_tmp_reads_2.fastq | samtools view -S -h -u -b -F 0x0004 - > /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.01/bowtie.iter.01.PE.u.bam
Finished Bowtie for iteration 01 at Wed Nov 30 18:26:28 2022:
DONE with read mapping for iteration 1 at Wed Nov 30 18:26:28 2022 [0:00:10.717669]...
Finished iteration 1 at Wed Nov 30 18:26:28 2022...
Total time for iteration 1: 0:00:29.853800
Starting iteration 2 at Wed Nov 30 18:26:28 2022...
Reading bam file /path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.01/bowtie.iter.01.PE.u.bam at Wed Nov 30 18:26:28 2022...
[E::idx_find_and_load] Could not retrieve index file for '/path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.01/bowtie.iter.01.PE.u.bam'
[E::idx_find_and_load] Could not retrieve index file for '/path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.01/bowtie.iter.01.PE.u.bam'
[E::idx_find_and_load] Could not retrieve index file for '/path/SSU_sequences/output_emirge/Sample1_amplicon_16S18S_recons/iter.01/bowtie.iter.01.PE.u.bam'
...
Finished iteration 40 at Wed Nov 30 18:46:19 2022...
Total time for iteration 40: 0:00:30.781029
Converting last mapping file (bowtie.iter.40.PE.u.bam) to compressed bam at Wed Nov 30 18:46:19 2022...
DONE Converting last mapping file (bowtie.iter.40.PE.u.bam) to compressed bam at Wed Nov 30 18:46:24 2022.
Traceback (most recent call last):
File "/software/RiboTaxa/scripts/run_MetaRib_PE.py", line 423, in <module>
main()
File "/software/RiboTaxa/scripts/run_MetaRib_PE.py", line 374, in main
config.read(config_file)
File "/xxx/python/anaconda3/2021.11/envs/RiboTaxa_py27/lib/python2.7/ConfigParser.py", line 305, in read
self._read(fp, filename)
File "/xxx/python/anaconda3/2021.11/envs/RiboTaxa_py27/lib/python2.7/ConfigParser.py", line 512, in _read
raise MissingSectionHeaderError(fpname, lineno, line)
ConfigParser.MissingSectionHeaderError: File contains no section headers.
file: /software/RiboTaxa/RiboTaxa_arguments.conf, line: 3
'Other tool parameters have been optimized and can be left at default. \n'
These three directories have been produced:
quality_control
output_sortmerna
SSU_sequences
Any idea about what's wrong?
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