bhattlab / lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Error in rule basecall_final

SergioMG97 opened this issue · comments

Hi I'm trying to use your workflow Lathe and it raises this error following tutorial:

snakemake --use-singularity --cores 32 --singularity-args '--bind $LUSTRE/metagenomics/ ' -s ./Snakefile --configfile ./tutorial/config_nobasecalling.yaml --restart-times 0 --keep-going --latency-wait 30
Building DAG of jobs...
Using shell: /mnt/netapp1/Optcesga_FT2_RHEL7/2020/gentoo/22072020/bin/bash
Provided cores: 32
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        3       align_bam
        1       all
        1       assemble_final
        2       assemble_flye
        3       bam_idx
        1       basecall_final
        4       faidx
        1       final
        1       merge
        3       misassemblies_correct
        3       misassemblies_detect
        1       nanoplot
        1       pilon_aggregate_vcf
        1       pilon_consensus
        1       pilon_ranges
        1       polish_final
        28
Checking for updates or modifications to workflow
No updates or modifications found
Select jobs to execute...

[Tue Apr 12 13:47:58 2022]
rule basecall_final:
    output: atcc_tutorial/0.basecall/atcc_tutorial.fq
    jobid: 11
    wildcards: sample=atcc_tutorial

find: ‘atcc_tutorial/0.basecall/raw_calls/*/*.fastq’: No such file or directory
[Tue Apr 12 13:47:58 2022]
Error in rule basecall_final:
    jobid: 11
    output: atcc_tutorial/0.basecall/atcc_tutorial.fq
    shell:
        find atcc_tutorial/0.basecall/raw_calls/*/*.fastq | xargs cat > atcc_tutorial/0.basecall/atcc_tutorial.fq
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job basecall_final since they might be corrupted:
atcc_tutorial/0.basecall/atcc_tutorial.fq
Job failed, going on with independent jobs.
Exiting because a job execution failed. Look above for error message
Complete log: /mnt/netapp1/Store_CSIC/home/csic/nmy/vgc/metagenomics/lathe/.snakemake/log/2022-04-12T134757.510755.snakemake.log

Do you figure out why it could be, have you seen it before? Thank so much.