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bactopia_error.txt
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bactopia_error.txt
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N E X T F L O W ~ version 20.07.1
Launching `/home/tread/miniconda3/envs/bactopia/share/bactopia-1.4.x/main.nf` [sharp_becquerel] - revision: 81b320646a
bactopia - 1.4.5
Found 1 ARIBA datasets
/home/tread/tiramisu/Staphopia/datasets/ariba/vfdb_core.tar.gz
Found 5 minmer sketches/signatures
/home/tread/tiramisu/Staphopia/datasets/minmer/genbank-k21.json.gz
/home/tread/tiramisu/Staphopia/datasets/minmer/genbank-k31.json.gz
/home/tread/tiramisu/Staphopia/datasets/minmer/genbank-k51.json.gz
/home/tread/tiramisu/Staphopia/datasets/minmer/refseq-k21-s1000.msh
/home/tread/tiramisu/Staphopia/datasets/plasmid/plsdb.msh
Found 3 PLSDB (plasmid) BLAST files
tiramisu/Staphopia/datasets/plasmid/plsdb.fna.nin
tiramisu/Staphopia/datasets/plasmid/plsdb.fna.nhr
tiramisu/Staphopia/datasets/plasmid/plsdb.fna.nsq
Found Prokka proteins file
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/annotation/proteins.faa
Found Mash Sketch of RefSeq genomes
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/minmer/refseq-genomes.msh
Found 2 MLST datasets
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/mlst/default/default-ariba.tar.gz
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/mlst/default/default-blastdb.tar.gz
Found 1 reference genomes
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/reference-genomes/Staph_ASR.gba
Found 1 FASTAs to align reads against
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/mapping-sequences/sccmec_cassettes.fasta
Found 76 gene FASTAs to query with BLAST
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/genes/SaPImw2.fasta
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/genes/ISSau5.fasta
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/genes/IS1181.fasta
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/genes/phiPV83.fasta
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/genes/Tn5801.fasta
...More than 5, truncating...
Found 4 primer FASTAs to query with BLAST
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/primers/primers.fasta
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/primers/staphopia_short_seqs.fasta
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/primers/.DS_Store
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/primers/subtypes.fasta
Found 3 protein FASTAs to query with BLAST
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/proteins/VFDB_setA_pro-2020-04-13.fasta
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/proteins/proteins.fasta
/home/tread/tiramisu/Staphopia/datasets/species-specific/staphylococcus-aureus/optional/blast/proteins/PSMs_protein.fasta
If something looks wrong, now's your chance to back out (CTRL+C 3 times).
Sleeping for 5 seconds...
[- ] process > gather_fastqs -
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > gather_fastqs -
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[- ] process > update_antimicrobial_resistance -
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
executor > slurm (3)
[8a/17d398] process > gather_fastqs (2) [ 0%] 0 of 2
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [ 0%] 0 of 1
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
executor > slurm (3)
[8a/17d398] process > gather_fastqs (2) [ 33%] 1 of 3, failed: 1, retries: 1
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [ 0%] 0 of 1
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[8a/17d398] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (1)
executor > slurm (4)
[d6/be965a] process > gather_fastqs (2) [ 33%] 1 of 3, failed: 1, retries: 1
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [ 0%] 0 of 1
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[8a/17d398] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (1)
executor > slurm (5)
[59/25222e] process > gather_fastqs (2) [ 50%] 2 of 4, failed: 2, retries: 2
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [ 0%] 0 of 1
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[8a/17d398] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (1)
[d6/be965a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (2)
executor > slurm (6)
[a4/3efce1] process > gather_fastqs (2) [ 60%] 3 of 5, failed: 3, retries: 3
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [ 0%] 0 of 1
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[8a/17d398] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (1)
[d6/be965a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (2)
[59/25222e] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (3)
executor > slurm (7)
[c0/bfd09a] process > gather_fastqs (2) [ 67%] 4 of 6, failed: 4, retries: 4
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [ 0%] 0 of 1
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[8a/17d398] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (1)
[d6/be965a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (2)
[59/25222e] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (3)
[a4/3efce1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (4)
executor > slurm (8)
[b9/f81adc] process > gather_fastqs (2) [ 71%] 5 of 7, failed: 5, retries: 5
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[8a/17d398] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (1)
[d6/be965a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (2)
[59/25222e] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (3)
[a4/3efce1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (4)
[c0/bfd09a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (5)
executor > slurm (9)
[a0/cb9aec] process > gather_fastqs (2) [ 75%] 6 of 8, failed: 6, retries: 6
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[8a/17d398] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (1)
[d6/be965a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (2)
[59/25222e] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (3)
[a4/3efce1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (4)
[c0/bfd09a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (5)
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
executor > slurm (10)
[57/7fd556] process > gather_fastqs (2) [ 78%] 7 of 9, failed: 7, retries: 7
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[8a/17d398] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (1)
[d6/be965a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (2)
[59/25222e] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (3)
[a4/3efce1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (4)
[c0/bfd09a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (5)
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
executor > slurm (10)
[57/7fd556] process > gather_fastqs (2) [ 78%] 7 of 9, failed: 7, retries: 7
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[d6/be965a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (2)
[59/25222e] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (3)
[a4/3efce1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (4)
[c0/bfd09a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (5)
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
executor > slurm (11)
[8f/12cffa] process > gather_fastqs (2) [ 80%] 8 of 10, failed: 8, retries: 8
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[59/25222e] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (3)
[a4/3efce1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (4)
[c0/bfd09a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (5)
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
executor > slurm (11)
[8f/12cffa] process > gather_fastqs (2) [ 90%] 9 of 10, failed: 9, retries: 9
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[59/25222e] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (3)
[a4/3efce1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (4)
[c0/bfd09a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (5)
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
executor > slurm (12)
[7c/027859] process > gather_fastqs (2) [ 82%] 9 of 11, failed: 9, retries: 9
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[a4/3efce1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (4)
[c0/bfd09a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (5)
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
executor > slurm (12)
[7c/027859] process > gather_fastqs (2) [ 83%] 10 of 12, failed: 10, retries: 10
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[c0/bfd09a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (5)
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
executor > slurm (13)
[3f/b50864] process > gather_fastqs (2) [ 83%] 10 of 12, failed: 10, retries: 10
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[c0/bfd09a] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (5)
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
executor > slurm (13)
[3f/b50864] process > gather_fastqs (2) [ 85%] 11 of 13, failed: 11, retries: 11
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
executor > slurm (14)
[5d/8b4fdf] process > gather_fastqs (2) [ 85%] 11 of 13, failed: 11, retries: 11
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[b9/f81adc] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (6)
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
executor > slurm (15)
[63/14912c] process > gather_fastqs (2) [ 86%] 12 of 14, failed: 12, retries: 12
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[a0/cb9aec] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (7)
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
[5d/8b4fdf] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (12)
executor > slurm (15)
[63/14912c] process > gather_fastqs (2) [ 87%] 13 of 15, failed: 13, retries: 13
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
[5d/8b4fdf] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (12)
[63/14912c] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (13)
executor > slurm (16)
[e0/1569b1] process > gather_fastqs (2) [ 87%] 13 of 15, failed: 13, retries: 13
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
[5d/8b4fdf] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (12)
[63/14912c] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (13)
executor > slurm (17)
[6e/ba36b2] process > gather_fastqs (2) [ 88%] 14 of 16, failed: 14, retries: 14
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[57/7fd556] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (8)
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
[5d/8b4fdf] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (12)
[63/14912c] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (13)
[e0/1569b1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (14)
executor > slurm (18)
[87/a7d110] process > gather_fastqs (2) [ 88%] 15 of 17, failed: 15, retries: 15
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[8f/12cffa] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (9)
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
[5d/8b4fdf] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (12)
[63/14912c] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (13)
[e0/1569b1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (14)
[6e/ba36b2] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (15)
executor > slurm (18)
[87/a7d110] process > gather_fastqs (2) [ 88%] 15 of 17, failed: 15, retries: 15
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[7c/027859] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (10)
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
[5d/8b4fdf] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (12)
[63/14912c] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (13)
[e0/1569b1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (14)
[6e/ba36b2] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (15)
executor > slurm (19)
[a2/50d92b] process > gather_fastqs (2) [ 94%] 17 of 18, failed: 16, retries: 16
[- ] process > fastq_status -
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
[5d/8b4fdf] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (12)
[63/14912c] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (13)
[e0/1569b1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (14)
[6e/ba36b2] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (15)
[87/a7d110] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (16)
executor > slurm (20)
[a2/50d92b] process > gather_fastqs (2) [ 94%] 17 of 18, failed: 16, retries: 16
[b0/2de45f] process > fastq_status (1) [ 0%] 0 of 1
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[3f/b50864] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (11)
[5d/8b4fdf] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (12)
[63/14912c] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (13)
[e0/1569b1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (14)
[6e/ba36b2] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (15)
[87/a7d110] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (16)
executor > slurm (21)
[18/d12615] process > gather_fastqs (2) [ 95%] 18 of 19, failed: 17, retries: 17
[b0/2de45f] process > fastq_status (1) [ 0%] 0 of 1
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[5d/8b4fdf] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (12)
[63/14912c] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (13)
[e0/1569b1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (14)
[6e/ba36b2] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (15)
[87/a7d110] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (16)
[a2/50d92b] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (17)
executor > slurm (22)
[71/3ee710] process > gather_fastqs (2) [ 95%] 19 of 20, failed: 18, retries: 18
[b0/2de45f] process > fastq_status (1) [ 0%] 0 of 1
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[63/14912c] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (13)
[e0/1569b1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (14)
[6e/ba36b2] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (15)
[87/a7d110] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (16)
[a2/50d92b] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (17)
[18/d12615] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (18)
executor > slurm (23)
[1d/eeae19] process > gather_fastqs (2) [ 95%] 20 of 21, failed: 19, retries: 19
[b0/2de45f] process > fastq_status (1) [ 0%] 0 of 1
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -
[- ] process > qc_final_summary -
[- ] process > assemble_genome -
[- ] process > assembly_qc -
[- ] process > make_blastdb -
[- ] process > annotate_genome -
[- ] process > count_31mers -
[- ] process > sequence_type -
[- ] process > ariba_analysis -
[- ] process > minmer_sketch -
[- ] process > minmer_query -
[- ] process > call_variants -
[- ] process > download_references -
[- ] process > call_variants_auto -
[54/f040c4] process > update_antimicrobial_resistance (1) [100%] 1 of 1 ✔
[- ] process > antimicrobial_resistance -
[- ] process > plasmid_blast -
[- ] process > blast_genes -
[- ] process > blast_primers -
[- ] process > blast_proteins -
[- ] process > mapping_query -
[e0/1569b1] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (14)
[6e/ba36b2] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (15)
[87/a7d110] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (16)
[a2/50d92b] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (17)
[18/d12615] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (18)
[71/3ee710] NOTE: Process `gather_fastqs (2)` terminated with an error exit status (1) -- Execution is retried (19)
executor > slurm (23)
[1d/eeae19] process > gather_fastqs (2) [ 95%] 20 of 21, failed: 19, retries: 19
[b0/2de45f] process > fastq_status (1) [ 0%] 0 of 1
[- ] process > estimate_genome_size -
[- ] process > qc_reads -
[- ] process > qc_original_summary -