flu-ngs snakemake error log

gistfile1.txt

babujee@iri-ubuntu-vm ~/0/bullsemen_irma (master) [1]> snakemake --snakefile workflow/irma.smk --cores all
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 120
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job                   count
------------------  -------
all                       1
by_segment_summary        2
combine_samples           2
concat_segment_aa         2
concat_segment_nt         2
concat_segments           2
find_irma_output          2
order_columns             6
total                    19

Select jobs to execute...

[Wed Feb 11 11:01:39 2026]
checkpoint find_irma_output:
    input: results/primary/irma-raw/147816-25_combined_extractions_longread
    output: results/primary/irma/147816-25_combined_extractions_longread
    log: .logs/irma-primary/147816-25_combined_extractions_longread.log
    jobid: 4
    reason: Updated input files: results/primary/irma-raw/147816-25_combined_extractions_longread
    wildcards: order=primary, sample=147816-25_combined_extractions, pair=longread
    resources: tmpdir=/tmp
DAG of jobs will be updated after completion.


[Wed Feb 11 11:01:39 2026]
checkpoint find_irma_output:
    input: results/secondary/irma-raw/147816-25_combined_extractions_longread
    output: results/secondary/irma/147816-25_combined_extractions_longread
    log: .logs/irma-secondary/147816-25_combined_extractions_longread.log
    jobid: 8
    reason: Updated input files: results/secondary/irma-raw/147816-25_combined_extractions_longread
    wildcards: order=secondary, sample=147816-25_combined_extractions, pair=longread
    resources: tmpdir=/tmp
DAG of jobs will be updated after completion.

[Wed Feb 11 11:01:39 2026]
Finished job 4.
1 of 19 steps (5%) done
Select jobs to execute...

[Wed Feb 11 11:01:39 2026]
rule make_gffgz:
    input: results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff
    output: results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff.gz
    log: .logs/write_gffgz/write_gffgz_147816-25_combined_extractions_longread_A_MP_primary.log
    jobid: 55
    reason: Missing output files: results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff.gz
    wildcards: order=primary, sample=147816-25_combined_extractions, pair=longread, segment=A_MP
    resources: tmpdir=/tmp


[Wed Feb 11 11:01:39 2026]
rule transcribe:
    input: results/primary/irma/147816-25_combined_extractions_longread/A_MP.fasta, results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff
    output: results/primary/seq/147816-25_combined_extractions_longread/separate/A_MP-nt.fasta
    log: .logs/gffread/gffread_147816-25_combined_extractions_longread_A_MP_primary.log
    jobid: 91
    reason: Missing output files: results/primary/seq/147816-25_combined_extractions_longread/separate/A_MP-nt.fasta
    wildcards: order=primary, sample=147816-25_combined_extractions, pair=longread, segment=A_MP
    resources: tmpdir=/tmp


[Wed Feb 11 11:01:39 2026]
rule transcribe:
    input: results/primary/irma/147816-25_combined_extractions_longread/A_PA.fasta, results/primary/irma/147816-25_combined_extractions_longread/A_PA.gff
    output: results/primary/seq/147816-25_combined_extractions_longread/separate/A_PA-nt.fasta
    log: .logs/gffread/gffread_147816-25_combined_extractions_longread_A_PA_primary.log
    jobid: 85
    reason: Missing output files: results/primary/seq/147816-25_combined_extractions_longread/separate/A_PA-nt.fasta
    wildcards: order=primary, sample=147816-25_combined_extractions, pair=longread, segment=A_PA
    resources: tmpdir=/tmp


[Wed Feb 11 11:01:39 2026]
rule write_gff:
    input: results/primary/irma/147816-25_combined_extractions_longread/A_NS.fasta
    output: results/primary/irma/147816-25_combined_extractions_longread/A_NS.gff
    log: .logs/write_gff/write_gff_147816-25_combined_extractions_longread_A_NS_primary.log
    jobid: 72
    reason: Missing output files: results/primary/irma/147816-25_combined_extractions_longread/A_NS.gff
    wildcards: order=primary, sample=147816-25_combined_extractions, pair=longread, segment=A_NS
    resources: tmpdir=/tmp

[Wed Feb 11 11:01:39 2026]
Error in rule transcribe:
    jobid: 91
    input: results/primary/irma/147816-25_combined_extractions_longread/A_MP.fasta, results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff
    output: results/primary/seq/147816-25_combined_extractions_longread/separate/A_MP-nt.fasta
    log: .logs/gffread/gffread_147816-25_combined_extractions_longread_A_MP_primary.log (check log file(s) for error details)
    conda-env: /home/babujee/001_miseq/bullsemen_irma/.snakemake/conda/ffa2b63b07ad61c31b50015b1db6b846_
    shell:
        gffread -w results/primary/seq/147816-25_combined_extractions_longread/separate/A_MP-nt.fasta -g results/primary/irma/147816-25_combined_extractions_longread/A_MP.fasta results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff > .logs/gffread/gffread_147816-25_combined_extractions_longread_A_MP_primary.log 2>&1
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Feb 11 11:01:39 2026]
[Wed Feb 11 11:01:39 2026]
Error in rule transcribe:
    jobid: 85
    input: results/primary/irma/147816-25_combined_extractions_longread/A_PA.fasta, results/primary/irma/147816-25_combined_extractions_longread/A_PA.gff
    output: results/primary/seq/147816-25_combined_extractions_longread/separate/A_PA-nt.fasta
    log: .logs/gffread/gffread_147816-25_combined_extractions_longread_A_PA_primary.log (check log file(s) for error details)
    conda-env: /home/babujee/001_miseq/bullsemen_irma/.snakemake/conda/ffa2b63b07ad61c31b50015b1db6b846_
    shell:
        gffread -w results/primary/seq/147816-25_combined_extractions_longread/separate/A_PA-nt.fasta -g results/primary/irma/147816-25_combined_extractions_longread/A_PA.fasta results/primary/irma/147816-25_combined_extractions_longread/A_PA.gff > .logs/gffread/gffread_147816-25_combined_extractions_longread_A_PA_primary.log 2>&1
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Finished job 8.
2 of 34 steps (6%) done
[Wed Feb 11 11:01:39 2026]
Error in rule make_gffgz:
    jobid: 55
    input: results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff
    output: results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff.gz
    log: .logs/write_gffgz/write_gffgz_147816-25_combined_extractions_longread_A_MP_primary.log (check log file(s) for error details)
    conda-env: /home/babujee/001_miseq/bullsemen_irma/.snakemake/conda/eac345144ddbfa21064a115782d94748_
    shell:

        bgzip -c results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff > results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff.gz 2> .logs/write_gffgz/write_gffgz_147816-25_combined_extractions_longread_A_MP_primary.log
        tabix -p gff results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff.gz 2> .logs/write_gffgz/write_gffgz_147816-25_combined_extractions_longread_A_MP_primary.log

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

Removing output files of failed job transcribe since they might be corrupted:
results/primary/seq/147816-25_combined_extractions_longread/separate/A_MP-nt.fasta
Removing output files of failed job transcribe since they might be corrupted:
results/primary/seq/147816-25_combined_extractions_longread/separate/A_PA-nt.fasta
Removing output files of failed job make_gffgz since they might be corrupted:
results/primary/irma/147816-25_combined_extractions_longread/A_MP.gff.gz
[Wed Feb 11 11:01:39 2026]
Error in rule write_gff:
    jobid: 72
    input: results/primary/irma/147816-25_combined_extractions_longread/A_NS.fasta
    output: results/primary/irma/147816-25_combined_extractions_longread/A_NS.gff
    log: .logs/write_gff/write_gff_147816-25_combined_extractions_longread_A_NS_primary.log (check log file(s) for error details)
    shell:

        workflow/scripts/write-gff.py             --fasta-in results/primary/irma/147816-25_combined_extractions_longread/A_NS.fasta             --segment A_NS             --transcript_id A_NS             --errors warn 2> .logs/write_gff/write_gff_147816-25_combined_extractions_longread_A_NS_primary.log > results/primary/irma/147816-25_combined_extractions_longread/A_NS.gff

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

Removing output files of failed job write_gff since they might be corrupted:
results/primary/irma/147816-25_combined_extractions_longread/A_NS.gff
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2026-02-11T110139.450967.snakemake.log