Error in rule basecall_final
SergioMG97 opened this issue · comments
Sergio Muñoz Gonzalez commented
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.