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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.
The text was updated successfully, but these errors were encountered:
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Hi I'm trying to use your workflow Lathe and it raises this error following tutorial:
Do you figure out why it could be, have you seen it before? Thank so much.
The text was updated successfully, but these errors were encountered: