snakemake --configfile=snakemake.yml --use-singularity --cores=all
INFO: Using cached SIF image
INFO: Converting SIF file to temporary sandbox...
INFO: Cleaning up image...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 80
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
----------------------------------------------- ------- ------------- -------------
ALL 1 1 1
collect 1 70 70
make_merge_config 1 1 1
mark_assembly_preliminary_gap_closed 1 1 1
mask_dust 1 1 1
mask_reads 1 1 1
mask_self 2 1 1
mask_tandem 2 1 1
mask_tandem_block 5 1 1
merge_insertions 1 1 1
preliminary_closed_gaps_bed2mask 1 1 1
preliminary_gap_closed2dam 1 1 1
preliminary_gap_closed_vs_reads_alignment 1 1 1
preliminary_gap_closed_vs_reads_alignment_block 1 70 70
preliminary_output 1 1 1
process 1 70 70
propagate_mask_back_to_reference 3 1 1
propagate_mask_back_to_reference_block 3 1 1
propagate_mask_batch 3 1 1
propagate_mask_to_reads_block 3 1 1
purged_output 1 1 1
reads2db 1 1 1
ref_vs_reads_alignment 1 1 1
ref_vs_reads_alignment_block 1 70 70
self_alignment 2 1 1
self_alignment_block 11 70 70
skip_gaps 1 1 1
split_preliminary_gap_closed_vs_reads_alignment 1 1 1
tandem_alignment_block 5 70 70
validate_regions 1 1 1
validate_regions_block 32 70 70
total 91 1 70
Select jobs to execute...
[Tue Sep 28 20:43:34 2021]
localcheckpoint reads2db:
input: pacbio_SRR6282347.fasta
output: /home/jon/Working_Files/dentist/pacbio_SRR6282347.db, /home/jon/Working_Files/dentist/.pacbio_SRR6282347.bps, /home/jon/Working_Files/dentist/.pacbio_SRR6282347.idx
jobid: 6
resources: tmpdir=/tmp
Downstream jobs will be updated after completion.
Activating singularity image /home/jon/Working_Files/dentist/.snakemake/singularity/1aa939115af17aa65dcd7164899b9ec7.simg
[Tue Sep 28 20:43:34 2021]
rule tandem_alignment_block:
input: dentist.json, <TBD>, /home/jon/Working_Files/dentist/.assembly.Ajap_genome
output: /home/jon/Working_Files/dentist/TAN.Ajap_genome.1.las
log: /home/jon/Working_Files/dentist/logs/tandem-alignment.Ajap_genome.1.log
jobid: 16
wildcards: dam=Ajap_genome, block=1
threads: 70
resources: tmpdir=/tmp
INFO: Converting SIF file to temporary sandbox...
File pacbio_SRR6282347.fasta, Line 1: Pacbio header line format error
INFO: Cleaning up image...
[Tue Sep 28 20:43:36 2021]
Error in rule reads2db:
jobid: 6
output: /home/jon/Working_Files/dentist/pacbio_SRR6282347.db, /home/jon/Working_Files/dentist/.pacbio_SRR6282347.bps, /home/jon/Working_Files/dentist/.pacbio_SRR6282347.idx
shell:
fasta2DB /home/jon/Working_Files/dentist/pacbio_SRR6282347.db pacbio_SRR6282347.fasta && DBsplit -x1000 -a -s200 /home/jon/Working_Files/dentist/pacbio_SRR6282347.db
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Activating singularity image /home/jon/Working_Files/dentist/.snakemake/singularity/1aa939115af17aa65dcd7164899b9ec7.simg
INFO: Converting SIF file to temporary sandbox...
INFO: Cleaning up image...
[Tue Sep 28 20:43:41 2021]
Error in rule tandem_alignment_block:
jobid: 16
output: /home/jon/Working_Files/dentist/TAN.Ajap_genome.1.las
log: /home/jon/Working_Files/dentist/logs/tandem-alignment.Ajap_genome.1.log (check log file(s) for error message)
shell:
{
cd /home/jon/Working_Files/dentist
datander '-T70' -s126 -l500 -e0.7 Ajap_genome.1
} &> /home/jon/Working_Files/dentist/logs/tandem-alignment.Ajap_genome.1.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/jon/Working_Files/dentist/.snakemake/log/2021-09-28T204325.753521.snakemake.log