Closed wez078 closed 9 months ago
Dears, I finally figured this out, now the IPA assembler worked for me Thanks wt
Hello- I know this issue was recently closed but I get the exact same error even after trying a number of modifications to the config.yaml file in the RUN directory. Any suggestions on what to try to get ipa to run? Thank you.
/path/to/pbipa/bin/python3 -m snakemake -j 6 -d RUN -p -s /path/to/pbipa/etc/ipa.snakefile --configfile RUN/config.yaml --reason
Invalid format specifier ' 02d ' for object of type 'int'
File "/cil/shed/apps/external/pbipa/etc/ipa.snakefile", line 59, in
Would be great if @wez078 shares his solution.
Hello looked like same issues as mines, I figured this it, by: change line 57 of snake file to specify the: return f'{RULE_COUNT:02d}-'" to the other format: return '{:02d}-'.format(RULE_COUNT)
and all worked well now for the IPA
cheers wt
Thank you very much for sharing. My job got further along with this edit to the snake file.
On Thu, Nov 30, 2023 at 11:38 AM Wentao Zhang @.***> wrote:
Hello looked like same issues as mines, I figured this it, by: change line 57 of snake file to specify the: return f'{RULE_COUNT:02d}-'" to the other format: return '{:02d}-'.format(RULE_COUNT)
and all worked well now for the IPA
cheers wt
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Dears, I am running the IPA assembler for my hifi reads under the Ubuntu Linux system and always got error as below
"ValueError in file /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/etc/ipa.snakefile, line 57: Invalid format specifier ' 02d ' for object of type 'int' File "/storage/proj/Pea_root_rot/Miniconda3/envs/ipa/etc/ipa.snakefile", line 59, in
File "/storage/proj/Pea_root_rot/Miniconda3/envs/ipa/etc/ipa.snakefile", line 57, in prenum
ERROR: Command '/storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/python3 -m snakemake --dryrun -j 2 -d RUN -p -s /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/etc/ipa.snakefile --configfile RUN/config.yaml --reason' returned non-zero exit status 1.
Exiting."
and also details running was below, I try reads in fasta and and fastq format, all reported same error, and my reads are hifi css read
Many thanks for your help on this cheers wentao
(ipa) wentao@rind1:/storage/proj/Pea_root_rot/pathogenome_assembly/ipa_test$ ipa local --nthreads 5 --njobs 2 --tmp-dir ./ --dry-run -i /storage/proj/Pea_root_rot/Pea_Pacbio_Pathogen/AE5.fasta.gz INFO: /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/ipa local --nthreads 5 --njobs 2 --tmp-dir ./ --dry-run -i /storage/proj/Pea_root_rot/Pea_Pacbio_Pathogen/AE5.fasta.gz INFO: ipa.py ipa (wrapper) version=1.8.0 ... Checking dependencies ... INFO: Dependencies /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/python3 /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/ipa2-task /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/falconc /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/minimap2 /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/nighthawk /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/pancake /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/pblayout /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/racon /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/samtools /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/ipa_purge_dups /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/ipa_purge_dups_split_fa snakemake version=7.32.4 ipa2-task 1.8.0 (commit 89f9124a7aa07d170db0eb490c12a5aeb36bcf64) Machine name: 'Linux' Copyright (C) 2004-2021 Pacific Biosciences of California, Inc. This program comes with ABSOLUTELY NO WARRANTY; it is intended for Research Use Only and not for use in diagnostic procedures.
falconc version=1.15.0+git., nim-version=1.2.0 minimap2 version=2.26-r1175 Nighthawk 1.0.0 (commit SL-release-10.2.0-11-g332ccaa) pancake 1.6.0 (commit SL-release-10.2.0-175-gb750c42) pblayout 1.4.0 (commit SL-release-10.2.0-64-gd59326a) racon version=1.5.0 samtools 1.18 Using htslib 1.18 ipa_purge_dups Version: 1.2.5
To run this yourself: /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/python3 -m snakemake --dryrun -j 2 -d RUN -p -s /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/etc/ipa.snakefile --configfile RUN/config.yaml --reason
Starting snakemake --dryrun ... CWD: /storage/proj/Pea_root_rot/pathogenome_assembly/ipa_test/RUN NPROC: 5 NPROC_SERIAL: 5 config: {'advanced_options': '', 'coverage': 0, 'genome_size': 0, 'm4filt_high_copy_sample_rate': 1.0, 'max_nchunks': 40, 'nproc': 5, 'phase_run': 1, 'polish_run': 1, 'purge_dups_calcuts': '', 'purge_dups_run': 1, 'reads_fn': 'RUN/input.fofn', 'tmp_dir': './'} ValueError in file /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/etc/ipa.snakefile, line 57: Invalid format specifier ' 02d ' for object of type 'int' File "/storage/proj/Pea_root_rot/Miniconda3/envs/ipa/etc/ipa.snakefile", line 59, in
File "/storage/proj/Pea_root_rot/Miniconda3/envs/ipa/etc/ipa.snakefile", line 57, in prenum
ERROR: Command '/storage/proj/Pea_root_rot/Miniconda3/envs/ipa/bin/python3 -m snakemake --dryrun -j 2 -d RUN -p -s /storage/proj/Pea_root_rot/Miniconda3/envs/ipa/etc/ipa.snakefile --configfile RUN/config.yaml --reason' returned non-zero exit status 1.
Exiting.
(ipa) wentao@rind1:/storage/proj/Pea_root_rot/pathogenome_assembly/ipa_test$