[2024-01-24 15:03:14,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:14,463] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:14,463] [INFO] DQC Reference Directory: /var/lib/cwl/stga0677429-ea57-4797-834d-15a8cad63755/dqc_reference
[2024-01-24 15:03:15,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:15,817] [INFO] Task started: Prodigal
[2024-01-24 15:03:15,817] [INFO] Running command: gunzip -c /var/lib/cwl/stg9540355a-42fe-4a37-a6af-b33d6a48bb36/GCF_019933175.1_ASM1993317v1_genomic.fna.gz | prodigal -d GCF_019933175.1_ASM1993317v1_genomic.fna/cds.fna -a GCF_019933175.1_ASM1993317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:26,381] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:26,381] [INFO] Task started: HMMsearch
[2024-01-24 15:03:26,381] [INFO] Running command: hmmsearch --tblout GCF_019933175.1_ASM1993317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0677429-ea57-4797-834d-15a8cad63755/dqc_reference/reference_markers.hmm GCF_019933175.1_ASM1993317v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:26,716] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:26,717] [INFO] Found 6/6 markers.
[2024-01-24 15:03:26,753] [INFO] Query marker FASTA was written to GCF_019933175.1_ASM1993317v1_genomic.fna/markers.fasta
[2024-01-24 15:03:26,753] [INFO] Task started: Blastn
[2024-01-24 15:03:26,753] [INFO] Running command: blastn -query GCF_019933175.1_ASM1993317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0677429-ea57-4797-834d-15a8cad63755/dqc_reference/reference_markers.fasta -out GCF_019933175.1_ASM1993317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:27,714] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:27,717] [INFO] Selected 9 target genomes.
[2024-01-24 15:03:27,718] [INFO] Target genome list was writen to GCF_019933175.1_ASM1993317v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:27,721] [INFO] Task started: fastANI
[2024-01-24 15:03:27,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg9540355a-42fe-4a37-a6af-b33d6a48bb36/GCF_019933175.1_ASM1993317v1_genomic.fna.gz --refList GCF_019933175.1_ASM1993317v1_genomic.fna/target_genomes.txt --output GCF_019933175.1_ASM1993317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:35,852] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:35,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0677429-ea57-4797-834d-15a8cad63755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:35,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0677429-ea57-4797-834d-15a8cad63755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:35,861] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:03:35,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:35,861] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Edwardsiella tarda	strain=FDAARGOS_1473	GCA_019933175.1	636	636	type	True	100.0	1264	1266	95	conclusive
Edwardsiella tarda	strain=ATCC 15947	GCA_003113495.2	636	636	type	True	99.9944	1259	1266	95	conclusive
Edwardsiella tarda	strain=ATCC 15947	GCA_000264805.1	636	636	type	True	99.8676	1093	1266	95	conclusive
Edwardsiella tarda	strain=NBRC 105688	GCA_000341505.1	636	636	type	True	99.1755	1112	1266	95	conclusive
Edwardsiella hoshinae	strain=NCTC12121	GCA_900447315.1	93378	93378	type	True	88.7844	1027	1266	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	78.8561	254	1266	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.8218	421	1266	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	78.6861	260	1266	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	78.1549	263	1266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:35,863] [INFO] DFAST Taxonomy check result was written to GCF_019933175.1_ASM1993317v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:35,864] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:35,864] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:35,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0677429-ea57-4797-834d-15a8cad63755/dqc_reference/checkm_data
[2024-01-24 15:03:35,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:35,907] [INFO] Task started: CheckM
[2024-01-24 15:03:35,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019933175.1_ASM1993317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019933175.1_ASM1993317v1_genomic.fna/checkm_input GCF_019933175.1_ASM1993317v1_genomic.fna/checkm_result
[2024-01-24 15:04:11,419] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:11,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:11,458] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:11,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:11,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019933175.1_ASM1993317v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:11,459] [INFO] Task started: Blastn
[2024-01-24 15:04:11,459] [INFO] Running command: blastn -query GCF_019933175.1_ASM1993317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0677429-ea57-4797-834d-15a8cad63755/dqc_reference/reference_markers_gtdb.fasta -out GCF_019933175.1_ASM1993317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:13,028] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:13,031] [INFO] Selected 5 target genomes.
[2024-01-24 15:04:13,031] [INFO] Target genome list was writen to GCF_019933175.1_ASM1993317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:13,035] [INFO] Task started: fastANI
[2024-01-24 15:04:13,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg9540355a-42fe-4a37-a6af-b33d6a48bb36/GCF_019933175.1_ASM1993317v1_genomic.fna.gz --refList GCF_019933175.1_ASM1993317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019933175.1_ASM1993317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:18,152] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:18,160] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:18,160] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000341505.1	s__Edwardsiella tarda	99.1572	1113	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.01	97.25	0.94	0.84	19	conclusive
GCF_000474215.1	s__Edwardsiella hoshinae	88.6118	1013	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.58	0.98	0.94	4	-
GCF_000264765.2	s__Edwardsiella anguillarum	84.3496	959	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.66	0.99	0.97	9	-
GCF_001896205.1	s__Edwardsiella piscicida	83.8705	924	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.37	99.20	0.95	0.93	23	-
GCF_000264785.1	s__Edwardsiella ictaluri	83.1752	847	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.74	99.41	0.96	0.93	11	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:18,167] [INFO] GTDB search result was written to GCF_019933175.1_ASM1993317v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:18,178] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:18,181] [INFO] DFAST_QC result json was written to GCF_019933175.1_ASM1993317v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:18,182] [INFO] DFAST_QC completed!
[2024-01-24 15:04:18,182] [INFO] Total running time: 0h1m4s