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error while runing the example file. #256

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error while runing the example file.#256

Description

@mano2991
mano2991
opened on Apr 29, 2025

snakemake -j1

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.4 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last): File "/home/manoj/anaconda3/envs/abc-env/bin/snakemake", line 10, in
sys.exit(main())
File "/home/manoj/anaconda3/envs/abc-env/lib/python3.10/site-packages/snakemake/init.py", line 3141, in main
success = snakemake(
File "/home/manoj/anaconda3/envs/abc-env/lib/python3.10/site-packages/snakemake/init.py", line 671, in snakemake
workflow.include(
File "/home/manoj/anaconda3/envs/abc-env/lib/python3.10/site-packages/snakemake/workflow.py", line 1389, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/workflow/Snakefile", line 2, in
import pandas as pd
File "/home/manoj/.local/lib/python3.10/site-packages/pandas/init.py", line 26, in
from pandas.compat import (
File "/home/manoj/.local/lib/python3.10/site-packages/pandas/compat/init.py", line 27, in
from pandas.compat.pyarrow import (
File "/home/manoj/.local/lib/python3.10/site-packages/pandas/compat/pyarrow.py", line 8, in
import pyarrow as pa
File "/home/manoj/anaconda3/envs/abc-env/lib/python3.10/site-packages/pyarrow/init.py", line 65, in
import pyarrow.lib as _lib
AttributeError: _ARRAY_API not found

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.4 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last): File "/home/manoj/anaconda3/envs/abc-env/bin/snakemake", line 10, in
sys.exit(main())
File "/home/manoj/anaconda3/envs/abc-env/lib/python3.10/site-packages/snakemake/init.py", line 3141, in main
success = snakemake(
File "/home/manoj/anaconda3/envs/abc-env/lib/python3.10/site-packages/snakemake/init.py", line 671, in snakemake
workflow.include(
File "/home/manoj/anaconda3/envs/abc-env/lib/python3.10/site-packages/snakemake/workflow.py", line 1389, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/workflow/Snakefile", line 2, in
import pandas as pd
File "/home/manoj/.local/lib/python3.10/site-packages/pandas/init.py", line 49, in
from pandas.core.api import (
File "/home/manoj/.local/lib/python3.10/site-packages/pandas/core/api.py", line 9, in
from pandas.core.dtypes.dtypes import (
File "/home/manoj/.local/lib/python3.10/site-packages/pandas/core/dtypes/dtypes.py", line 24, in
from pandas._libs import (
File "/home/manoj/anaconda3/envs/abc-env/lib/python3.10/site-packages/pyarrow/init.py", line 65, in
import pyarrow.lib as _lib
AttributeError: _ARRAY_API not found
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job count

all 1
create_neighborhoods 1
create_predictions 1
filter_predictions 1
generate_qc_plot_and_summary 1
total 5

Select jobs to execute...

[Tue Apr 29 19:20:53 2025]
rule create_neighborhoods:
input: /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Peaks/macs2_peaks.narrowPeak.sorted.candidateRegions.bed, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/tmp/GRCh38_EBV.no_alt.chrom.sizes.tsv.bed
output: /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods/EnhancerList.txt, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods/GeneList.txt, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/processed_genes_file.bed
jobid: 2
reason: Missing output files: /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods/GeneList.txt, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods/EnhancerList.txt
wildcards: biosample=K562_chr22
resources: tmpdir=/tmp, mem_mb=32000, mem_mib=30518

Namespace(candidate_enhancer_regions='/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Peaks/macs2_peaks.narrowPeak.sorted.candidateRegions.bed', outdir='/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods', genes='/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/processed_genes_file.bed', genes_for_class_assignment=None, ubiquitously_expressed_genes='/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/reference/UbiquitouslyExpressedGenes.txt', gene_name_annotations='symbol', primary_gene_identifier='symbol', skip_gene_counts=False, H3K27ac='example_chr/chr22/ENCFF790GFL.chr22.sorted.se.bam', DHS='example_chr/chr22/ENCFF860XAE.chr22.sorted.se.bam', ATAC=None, default_accessibility_feature='DHS', expression_table='', qnorm='/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/reference/EnhancersQNormRef.K562.txt', tss_slop_for_class_assignment=500, skip_rpkm_quantile=False, use_secondary_counting_method=False, chrom_sizes='/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/reference/hg38/GRCh38_EBV.no_alt.chrom.sizes.tsv', chrom_sizes_bed='/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/tmp/GRCh38_EBV.no_alt.chrom.sizes.tsv.bed', enhancer_class_override=None, supplementary_features=None, cellType=None)
Traceback (most recent call last):
File "/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/workflow/scripts/run.neighborhoods.py", line 209, in
main(args)
File "/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/workflow/scripts/run.neighborhoods.py", line 204, in main
processCellType(args)
File "/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/workflow/scripts/run.neighborhoods.py", line 154, in processCellType
genes, genes_for_class_assignment = load_genes(
File "/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/workflow/scripts/neighborhoods.py", line 85, in load_genes
genes["Expression"] = np.NaN
File "/home/manoj/.local/lib/python3.10/site-packages/numpy/init.py", line 400, in getattr
raise AttributeError(
AttributeError: np.NaN was removed in the NumPy 2.0 release. Use np.nan instead.
[Tue Apr 29 19:20:55 2025]
Error in rule create_neighborhoods:
jobid: 2
input: /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Peaks/macs2_peaks.narrowPeak.sorted.candidateRegions.bed, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/tmp/GRCh38_EBV.no_alt.chrom.sizes.tsv.bed
output: /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods/EnhancerList.txt, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods/GeneList.txt, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/processed_genes_file.bed
conda-env: /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/.snakemake/conda/f7d452d6c9a651207203c859d17b792c_
shell:

            # get sorted & unique gene list
            # intersect first to remove alternate chromosomes
            bedtools intersect -u -a example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed -b /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/tmp/GRCh38_EBV.no_alt.chrom.sizes.tsv.bed |           bedtools sort -faidx /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/reference/hg38/GRCh38_EBV.no_alt.chrom.sizes.tsv -i stdin |                uniq > /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/processed_genes_file.bed

            python /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/workflow/scripts/run.neighborhoods.py                    --candidate_enhancer_regions /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Peaks/macs2_peaks.narrowPeak.sorted.candidateRegions.bed       --DHS example_chr/chr22/ENCFF860XAE.chr22.sorted.se.bam                  --ATAC                          --default_accessibility_feature DHS                    --chrom_sizes /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/reference/hg38/GRCh38_EBV.no_alt.chrom.sizes.tsv                   --chrom_sizes_bed /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/tmp/GRCh38_EBV.no_alt.chrom.sizes.tsv.bed                     --outdir /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods                       --genes /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/processed_genes_file.bed                     --ubiquitously_expressed_genes /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/reference/UbiquitouslyExpressedGenes.txt                         --H3K27ac example_chr/chr22/ENCFF790GFL.chr22.sorted.se.bam                    --qnorm /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/reference/EnhancersQNormRef.K562.txt 

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job create_neighborhoods since they might be corrupted:
/home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/Neighborhoods, /home/manoj/Downloads/Software/abc/ABC-Enhancer-Gene-Prediction/results/K562_chr22/processed_genes_file.bed
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-04-29T192052.408475.snakemake.log

the log file has been added for reference

2025-04-29T192052.408475.snakemake.log

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