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dms-vep / dms-vep-pipeline

Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
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RuleException in rule avg_muteffects #129

Closed Bernadetadad closed 1 year ago

Bernadetadad commented 1 year ago

I'm getting the following error at the bottom of snakemake run when running new pipeline:

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job stats:
job                              count    min threads    max threads
-----------------------------  -------  -------------  -------------
align_parse_PacBio_ccs               2              1              1
all                                  1              1              1
analyze_pacbio_ccs                   1              1              1
analyze_prob_escape                  1              1              1
analyze_variant_counts               1              1              1
avg_antibody_escape                  2              1              1
avg_muteffects                       1              1              1
build_codon_variants                 1              1              1
build_pacbio_consensus               1              1              1
check_adequate_variant_counts        1              1              1
compare_IC50s                        1              1              1
count_barcodes                      14              1              1
docs_index                           1              1              1
fit_polyclonal                       4              2              2
format_antibody_escape_plot          2              1              1
make_nblink                         12              1              1
prob_escape                          4              1              1
sphinx_build                         1              1              1
subindex                             2              1              1
variant_counts                      14              1              1
total                               67              1              2

Select jobs to execute...

[Wed Feb 15 06:12:57 2023]
rule align_parse_PacBio_ccs:
    input: /fh/fast/bloom_j/SR/ngs/pacbio/220623_Bernadeta/BA2_B-Cell4/m64272e_220627_155205.hifi_reads.fastq.gz, data/PacBio_amplicon.gb, data/PacBio_feature_parse_specs.yaml
    output: results/process_ccs/Lib-2_220629
    log: results/logs/align_parse_PacBio_ccs_Lib-2_220629.txt
    jobid: 7
    reason: Forced execution
    wildcards: pacbioRun=Lib-2_220629
    resources: tmpdir=/loc/scratch/10416739

[Wed Feb 15 06:12:57 2023]
rule align_parse_PacBio_ccs:
    input: /fh/fast/bloom_j/SR/ngs/pacbio/220623_Bernadeta/BA2_A-Cell3/m64272e_220626_160231.hifi_reads.fastq.gz, data/PacBio_amplicon.gb, data/PacBio_feature_parse_specs.yaml
    output: results/process_ccs/Lib-1_220629
    log: results/logs/align_parse_PacBio_ccs_Lib-1_220629.txt
    jobid: 6
    reason: Forced execution
    wildcards: pacbioRun=Lib-1_220629
    resources: tmpdir=/loc/scratch/10416739

[Wed Feb 15 06:12:57 2023]
rule avg_muteffects:
    input: results/func_scores/functional_selections.csv, dms-vep-pipeline/notebooks/avg_muteffects.ipynb
    output: results/muteffects_functional/muteffects_observed.csv, results/muteffects_functional/muteffects_latent.csv, results/muteffects_functional/muteffects_observed_heatmap_unformatted.html, results/muteffects_functional/muteffects_latent_heatmap_unformatted.html
    log: results/logs/avg_muteffects.txt
    jobid: 51
    reason: Updated input files: results/func_scores/functional_selections.csv
    resources: tmpdir=/loc/scratch/10416739

RuleException in rule avg_muteffects in file /fh/fast/bloom_j/computational_notebooks/bdadonai/2023/SARS-CoV-2_Omicron_BA.2_spike_DMS_COV2-2130/dms-vep-pipeline/func_scores.smk, line 179:
AttributeError: 'OutputFiles' object has no attribute 'nb', when formatting the following:
papermill {input.nb} {output.nb} &> {log}
Bernadetadad commented 1 year ago

never mind, was my mistake. closing