[2024-01-24 13:28:15,889] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:15,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:15,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d987adf-b71b-454b-96b0-2de0d05ecd56/dqc_reference
[2024-01-24 13:28:17,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:17,136] [INFO] Task started: Prodigal
[2024-01-24 13:28:17,136] [INFO] Running command: gunzip -c /var/lib/cwl/stg10415fa3-d2a5-4c26-8ac3-82334b13b04c/GCF_003113495.2_ASM311349v2_genomic.fna.gz | prodigal -d GCF_003113495.2_ASM311349v2_genomic.fna/cds.fna -a GCF_003113495.2_ASM311349v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:28,177] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:28,177] [INFO] Task started: HMMsearch
[2024-01-24 13:28:28,177] [INFO] Running command: hmmsearch --tblout GCF_003113495.2_ASM311349v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d987adf-b71b-454b-96b0-2de0d05ecd56/dqc_reference/reference_markers.hmm GCF_003113495.2_ASM311349v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:28,485] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:28,486] [INFO] Found 6/6 markers.
[2024-01-24 13:28:28,520] [INFO] Query marker FASTA was written to GCF_003113495.2_ASM311349v2_genomic.fna/markers.fasta
[2024-01-24 13:28:28,520] [INFO] Task started: Blastn
[2024-01-24 13:28:28,520] [INFO] Running command: blastn -query GCF_003113495.2_ASM311349v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d987adf-b71b-454b-96b0-2de0d05ecd56/dqc_reference/reference_markers.fasta -out GCF_003113495.2_ASM311349v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:29,521] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:29,524] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:29,525] [INFO] Target genome list was writen to GCF_003113495.2_ASM311349v2_genomic.fna/target_genomes.txt
[2024-01-24 13:28:29,530] [INFO] Task started: fastANI
[2024-01-24 13:28:29,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg10415fa3-d2a5-4c26-8ac3-82334b13b04c/GCF_003113495.2_ASM311349v2_genomic.fna.gz --refList GCF_003113495.2_ASM311349v2_genomic.fna/target_genomes.txt --output GCF_003113495.2_ASM311349v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:38,034] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:38,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d987adf-b71b-454b-96b0-2de0d05ecd56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:38,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d987adf-b71b-454b-96b0-2de0d05ecd56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:38,046] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:28:38,046] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:38,047] [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=ATCC 15947	GCA_003113495.2	636	636	type	True	100.0	1265	1265	95	conclusive
Edwardsiella tarda	strain=FDAARGOS_1473	GCA_019933175.1	636	636	type	True	99.9941	1261	1265	95	conclusive
Edwardsiella tarda	strain=ATCC 15947	GCA_000264805.1	636	636	type	True	99.8413	1094	1265	95	conclusive
Edwardsiella tarda	strain=NBRC 105688	GCA_000341505.1	636	636	type	True	99.1697	1114	1265	95	conclusive
Edwardsiella hoshinae	strain=NCTC12121	GCA_900447315.1	93378	93378	type	True	88.8168	1024	1265	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.8264	429	1265	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	78.7658	260	1265	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	78.481	260	1265	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	78.1528	258	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:38,048] [INFO] DFAST Taxonomy check result was written to GCF_003113495.2_ASM311349v2_genomic.fna/tc_result.tsv
[2024-01-24 13:28:38,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:38,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:38,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d987adf-b71b-454b-96b0-2de0d05ecd56/dqc_reference/checkm_data
[2024-01-24 13:28:38,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:38,091] [INFO] Task started: CheckM
[2024-01-24 13:28:38,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003113495.2_ASM311349v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003113495.2_ASM311349v2_genomic.fna/checkm_input GCF_003113495.2_ASM311349v2_genomic.fna/checkm_result
[2024-01-24 13:29:13,569] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:13,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:13,592] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:13,592] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:13,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003113495.2_ASM311349v2_genomic.fna/markers.fasta)
[2024-01-24 13:29:13,593] [INFO] Task started: Blastn
[2024-01-24 13:29:13,593] [INFO] Running command: blastn -query GCF_003113495.2_ASM311349v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d987adf-b71b-454b-96b0-2de0d05ecd56/dqc_reference/reference_markers_gtdb.fasta -out GCF_003113495.2_ASM311349v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:15,051] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:15,054] [INFO] Selected 5 target genomes.
[2024-01-24 13:29:15,054] [INFO] Target genome list was writen to GCF_003113495.2_ASM311349v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:15,062] [INFO] Task started: fastANI
[2024-01-24 13:29:15,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg10415fa3-d2a5-4c26-8ac3-82334b13b04c/GCF_003113495.2_ASM311349v2_genomic.fna.gz --refList GCF_003113495.2_ASM311349v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003113495.2_ASM311349v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:19,769] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:19,776] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:19,776] [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	99.1898	1113	1265	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	88.6476	1002	1265	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	84.3671	954	1265	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	83.8574	932	1265	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	83.1854	851	1265	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 13:29:19,778] [INFO] GTDB search result was written to GCF_003113495.2_ASM311349v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:19,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:19,782] [INFO] DFAST_QC result json was written to GCF_003113495.2_ASM311349v2_genomic.fna/dqc_result.json
[2024-01-24 13:29:19,782] [INFO] DFAST_QC completed!
[2024-01-24 13:29:19,782] [INFO] Total running time: 0h1m4s