IPA error command

[wez078]

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$

[wez078]

Dears, I finally figured this out, now the IPA assembler worked for me Thanks wt

[tpshea2]

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 File "/cil/shed/apps/external/pbipa/etc/ipa.snakefile", line 57, in prenum

[armintoepfer]

Would be great if @wez078 shares his solution.

[wez078]

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

[tpshea2]

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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