[Thu Jun 25 10:34:56 2026]
localrule fdr_table:
input: temp/h3/shuffle/v0.1-shuffled-pileup.bed.gz, results/h3/additional-outputs-v0.1/coverage/h3-v0.1-minimum-coverage.txt, results/h3/additional-outputs-v0.1/coverage/h3-v0.1-maximum-coverage.txt
output: results/h3/additional-outputs-v0.1/fire-peaks/h3-v0.1-fire-score-to-fdr.tbl
jobid: 11
reason: Missing output files: results/h3/additional-outputs-v0.1/fire-peaks/h3-v0.1-fire-score-to-fdr.tbl; Input files updated by another job: temp/h3/shuffle/v0.1-shuffled-pileup.bed.gz, results/h3/additional-outputs-v0.1/coverage/h3-v0.1-maximum-coverage.txt, results/h3/additional-outputs-v0.1/coverage/h3-v0.1-minimum-coverage.txt
wildcards: sm=h3, v=v0.1
resources: tmpdir=/DATA3/users/suyanan/research/fiberseq/analysis/20260507_1_peanut/output/run_FIRE/tmp, mem_mb=94208, mem_mib=89844
Activating conda environment: .snakemake/conda/fc1fdba7ebe99668a597ba84c09bfdc0_
[INFO][Time elapsed (ms) 501]: Header of the pileup file:
['#chrom', 'start', 'end', 'coverage', 'fire_coverage', 'score', 'coverage_shuffled', 'fire_coverage_shuffled', 'score_shuffled']
[INFO][Time elapsed (ms) 501]: Schema overrides for the pileup file:
{'column_1': String, 'column_6': Float64, 'column_9': Float64}
[INFO][Time elapsed (ms) 1318]: Done reading pileup file:
shape: (4_040_967, 9)
┌────────┬───────────┬───────────┬──────────┬───┬───────────┬────────────┬────────────┬────────────┐
│ #chrom ┆ start ┆ end ┆ coverage ┆ … ┆ score ┆ coverage_s ┆ fire_cover ┆ score_shuf │
│ --- ┆ --- ┆ --- ┆ --- ┆ ┆ --- ┆ huffled ┆ age_shuffl ┆ fled │
│ str ┆ i64 ┆ i64 ┆ i64 ┆ ┆ f64 ┆ --- ┆ ed ┆ --- │
│ ┆ ┆ ┆ ┆ ┆ ┆ i64 ┆ --- ┆ f64 │
│ ┆ ┆ ┆ ┆ ┆ ┆ ┆ i64 ┆ │
╞════════╪═══════════╪═══════════╪══════════╪═══╪═══════════╪════════════╪════════════╪════════════╡
│ chr1 ┆ 83868 ┆ 83893 ┆ 2 ┆ … ┆ -1.0 ┆ 0 ┆ 0 ┆ -1.0 │
│ chr1 ┆ 83893 ┆ 84285 ┆ 2 ┆ … ┆ 33.628685 ┆ 0 ┆ 0 ┆ -1.0 │
│ chr1 ┆ 84285 ┆ 84315 ┆ 3 ┆ … ┆ 22.419123 ┆ 0 ┆ 0 ┆ -1.0 │
│ chr1 ┆ 84315 ┆ 84422 ┆ 3 ┆ … ┆ -1.0 ┆ 0 ┆ 0 ┆ -1.0 │
│ chr1 ┆ 84422 ┆ 84454 ┆ 3 ┆ … ┆ -1.0 ┆ 1 ┆ 0 ┆ -1.0 │
│ … ┆ … ┆ … ┆ … ┆ … ┆ … ┆ … ┆ … ┆ … │
│ chr1 ┆ 112416304 ┆ 112416322 ┆ 1 ┆ … ┆ -1.0 ┆ 3 ┆ 1 ┆ 21.789316 │
│ chr1 ┆ 112416322 ┆ 112416344 ┆ 1 ┆ … ┆ -1.0 ┆ 2 ┆ 1 ┆ 32.683975 │
│ chr1 ┆ 112416344 ┆ 112416654 ┆ 1 ┆ … ┆ -1.0 ┆ 2 ┆ 0 ┆ -1.0 │
│ chr1 ┆ 112416654 ┆ 112416675 ┆ 0 ┆ … ┆ -1.0 ┆ 2 ┆ 0 ┆ -1.0 │
│ chr1 ┆ 112416675 ┆ 112416884 ┆ 0 ┆ … ┆ -1.0 ┆ 1 ┆ 0 ┆ -1.0 │
└────────┴───────────┴───────────┴──────────┴───┴───────────┴────────────┴────────────┴────────────┘
/home/suyanan/.cache/snakemake/snakemake/source-cache/runtime-cache/tmpxk9ji2hw/file/home/suyanan/software/anaconda3/envs/snakemake/FIRE-main/workflow/rules/../scripts/fdr-table.py:170: DeprecationWarning: `DataFrame.melt` is deprecated; use `DataFrame.unpivot` instead, with `index` instead of `id_vars` and `on` instead of `value_vars`
pileup.melt(
[INFO][Time elapsed (ms) 2104]: Number of Mbp in each category:
shape: (2, 2)
┌─────────┬────────────┐
│ is_real ┆ Mbp │
│ --- ┆ --- │
│ bool ┆ f64 │
╞═════════╪════════════╡
│ false ┆ 111.002786 │
│ true ┆ 111.002786 │
└─────────┴────────────┘
[INFO][Time elapsed (ms) 2104]: Done aggregating pileup file:
shape: (227_670, 3)
┌───────────┬─────────┬──────────┐
│ score ┆ is_real ┆ bp │
│ --- ┆ --- ┆ --- │
│ f64 ┆ bool ┆ i64 │
╞═══════════╪═════════╪══════════╡
│ 58.856922 ┆ true ┆ 81 │
│ 56.8301 ┆ true ┆ 101 │
│ 54.49021 ┆ true ┆ 16 │
│ 54.233547 ┆ false ┆ 101 │
│ 53.639194 ┆ false ┆ 141 │
│ … ┆ … ┆ … │
│ 1.4461327 ┆ true ┆ 269 │
│ 1.4139963 ┆ false ┆ 78 │
│ 1.4139963 ┆ true ┆ 40 │
│ -1.0 ┆ false ┆ 11864608 │
│ -1.0 ┆ true ┆ 21596502 │
└───────────┴─────────┴──────────┘
[INFO][Time elapsed (ms) 2446]: FDR results
threshold FDR shuffled_bp real_bp
2329 -1.00 1.000000 1.0 1.0
2328 7.81 0.999879 38407185.0 38411852.0
2327 7.82 0.999997 38338210.0 38338319.0
2326 7.83 0.999168 38288191.0 38320059.0
2325 7.84 0.999017 38229169.0 38266791.0
... ... ... ... ...
4 42.47 0.162946 365.0 2240.0
3 44.53 0.244142 323.0 1323.0
2 45.93 0.321893 272.0 845.0
1 46.51 0.296569 242.0 816.0
0 54.23 0.510101 101.0 198.0
[2330 rows x 4 columns]
Traceback (most recent call last):
File "/home/suyanan/.cache/snakemake/snakemake/source-cache/runtime-cache/tmpxk9ji2hw/file/home/suyanan/software/anaconda3/envs/snakemake/FIRE-main/workflow/rules/../scripts/fdr-table.py", line 338, in <module>
defopt.run(main, show_types=True, version="0.0.1")
File "/DATA3/users/suyanan/research/fiberseq/analysis/20260507_1_peanut/output/run_FIRE/.snakemake/conda/fc1fdba7ebe99668a597ba84c09bfdc0_/lib/python3.12/site-packages/defopt.py", line 308, in run
return bind(
^^^^^
File "/home/suyanan/.cache/snakemake/snakemake/source-cache/runtime-cache/tmpxk9ji2hw/file/home/suyanan/software/anaconda3/envs/snakemake/FIRE-main/workflow/rules/../scripts/fdr-table.py", line 331, in main
fdr_table = make_fdr_table(
^^^^^^^^^^^^^^^
File "/home/suyanan/.cache/snakemake/snakemake/source-cache/runtime-cache/tmpxk9ji2hw/file/home/suyanan/software/anaconda3/envs/snakemake/FIRE-main/workflow/rules/../scripts/fdr-table.py", line 197, in make_fdr_table
raise ValueError(
ValueError: No FIRE score threshold has an FDR < 0.05. Check the input Fiber-seq data with the QC pipeline and make sure you are using WGS Fiber-seq data.
[Thu Jun 25 10:35:00 2026]
Error in rule fdr_table:
jobid: 11
input: temp/h3/shuffle/v0.1-shuffled-pileup.bed.gz, results/h3/additional-outputs-v0.1/coverage/h3-v0.1-minimum-coverage.txt, results/h3/additional-outputs-v0.1/coverage/h3-v0.1-maximum-coverage.txt
output: results/h3/additional-outputs-v0.1/fire-peaks/h3-v0.1-fire-score-to-fdr.tbl
conda-env: /DATA3/users/suyanan/research/fiberseq/analysis/20260507_1_peanut/output/run_FIRE/.snakemake/conda/fc1fdba7ebe99668a597ba84c09bfdc0_
shell:
MIN=$(cat results/h3/additional-outputs-v0.1/coverage/h3-v0.1-minimum-coverage.txt)
MAX=$(cat results/h3/additional-outputs-v0.1/coverage/h3-v0.1-maximum-coverage.txt)
python /home/suyanan/.cache/snakemake/snakemake/source-cache/runtime-cache/tmpxk9ji2hw/file/home/suyanan/software/anaconda3/envs/snakemake/FIRE-main/workflow/rules/../scripts/fdr-table.py -v 1 temp/h3/shuffle/v0.1-shuffled-pileup.bed.gz results/h3/additional-outputs-v0.1/fire-peaks/h3-v0.1-fire-score-to-fdr.tbl --max-cov $MAX --min-cov $MIN
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job fdr_table since they might be corrupted:
results/h3/additional-outputs-v0.1/fire-peaks/h3-v0.1-fire-score-to-fdr.tbl
[Thu Jun 25 10:38:38 2026]
Finished job 33.
19 of 39 steps (49%) done
Removing temporary output temp/h3/decorate/v0.1-chr1.dec.bed.gz.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2026-06-25T102041.210767.snakemake.log
WorkflowError:
At least one job did not complete successfully.
Look forward to your reply, thanks.
I run FIRE got this error:
make_fdr_table step, this Error
No FIRE score threshold has an FDR < 0.05. Check the input Fiber-seq data with the QC pipeline and make sure you are using WGS Fiber-seq data.How can I debug this from
QC pipeline, my peanut sample is m6A mark rate 4.29% with depth 32.23.Look forward to your reply, thanks.