[2024-01-24 11:05:03,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,931] [INFO] DQC Reference Directory: /var/lib/cwl/stga1c7d9ca-bbbf-4350-9f9f-720c14c8ae8d/dqc_reference
[2024-01-24 11:05:05,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,763] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg39d624b5-d113-4b32-8d72-19d4b77c2214/GCF_023653475.1_ASM2365347v1_genomic.fna.gz | prodigal -d GCF_023653475.1_ASM2365347v1_genomic.fna/cds.fna -a GCF_023653475.1_ASM2365347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:21,086] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:21,086] [INFO] Task started: HMMsearch
[2024-01-24 11:05:21,087] [INFO] Running command: hmmsearch --tblout GCF_023653475.1_ASM2365347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1c7d9ca-bbbf-4350-9f9f-720c14c8ae8d/dqc_reference/reference_markers.hmm GCF_023653475.1_ASM2365347v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:21,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:21,411] [INFO] Found 6/6 markers.
[2024-01-24 11:05:21,452] [INFO] Query marker FASTA was written to GCF_023653475.1_ASM2365347v1_genomic.fna/markers.fasta
[2024-01-24 11:05:21,453] [INFO] Task started: Blastn
[2024-01-24 11:05:21,453] [INFO] Running command: blastn -query GCF_023653475.1_ASM2365347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1c7d9ca-bbbf-4350-9f9f-720c14c8ae8d/dqc_reference/reference_markers.fasta -out GCF_023653475.1_ASM2365347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:22,218] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:22,221] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:22,221] [INFO] Target genome list was writen to GCF_023653475.1_ASM2365347v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:22,248] [INFO] Task started: fastANI
[2024-01-24 11:05:22,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d624b5-d113-4b32-8d72-19d4b77c2214/GCF_023653475.1_ASM2365347v1_genomic.fna.gz --refList GCF_023653475.1_ASM2365347v1_genomic.fna/target_genomes.txt --output GCF_023653475.1_ASM2365347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:35,999] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:35,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1c7d9ca-bbbf-4350-9f9f-720c14c8ae8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:36,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1c7d9ca-bbbf-4350-9f9f-720c14c8ae8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:36,008] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:36,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:36,008] [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
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	100.0	1801	1802	95	conclusive
Photobacterium galatheae	strain=S2753	GCA_000695255.1	1654360	1654360	type	True	99.9611	1467	1802	95	conclusive
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	81.5343	879	1802	95	below_threshold
Photobacterium arenosum	strain=CAU 1568	GCA_014841115.1	2774143	2774143	type	True	81.4958	878	1802	95	below_threshold
Photobacterium halotolerans	strain=DSM 18316	GCA_000425165.1	265726	265726	type	True	81.3667	893	1802	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	78.8916	421	1802	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	78.2504	192	1802	95	below_threshold
Vibrio albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	77.8059	140	1802	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	77.6738	143	1802	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	77.6523	140	1802	95	below_threshold
Vibrio fujianensis	strain=FJ201301	GCA_002749895.1	1974215	1974215	type	True	76.8913	84	1802	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:36,011] [INFO] DFAST Taxonomy check result was written to GCF_023653475.1_ASM2365347v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:36,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:36,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:36,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1c7d9ca-bbbf-4350-9f9f-720c14c8ae8d/dqc_reference/checkm_data
[2024-01-24 11:05:36,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:36,066] [INFO] Task started: CheckM
[2024-01-24 11:05:36,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023653475.1_ASM2365347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023653475.1_ASM2365347v1_genomic.fna/checkm_input GCF_023653475.1_ASM2365347v1_genomic.fna/checkm_result
[2024-01-24 11:06:25,397] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:25,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:25,416] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:25,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:25,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023653475.1_ASM2365347v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:25,417] [INFO] Task started: Blastn
[2024-01-24 11:06:25,417] [INFO] Running command: blastn -query GCF_023653475.1_ASM2365347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1c7d9ca-bbbf-4350-9f9f-720c14c8ae8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_023653475.1_ASM2365347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:26,501] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:26,504] [INFO] Selected 15 target genomes.
[2024-01-24 11:06:26,504] [INFO] Target genome list was writen to GCF_023653475.1_ASM2365347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:26,532] [INFO] Task started: fastANI
[2024-01-24 11:06:26,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d624b5-d113-4b32-8d72-19d4b77c2214/GCF_023653475.1_ASM2365347v1_genomic.fna.gz --refList GCF_023653475.1_ASM2365347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023653475.1_ASM2365347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:37,725] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:37,731] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:37,731] [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_000695255.1	s__Photobacterium galatheae	99.9611	1467	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018199995.1	s__Photobacterium sp018199995	82.1297	1015	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614885.1	s__Photobacterium sp003614885	81.5424	878	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841115.1	s__Photobacterium sp014841115	81.4988	878	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.86	98.86	0.94	0.94	2	-
GCF_000425165.1	s__Photobacterium halotolerans	81.3533	894	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.98	97.78	0.94	0.93	4	-
GCF_000972145.1	s__Photobacterium halotolerans_A	81.3298	887	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860525.1	s__Vibrio hepatarius_B	77.6202	84	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002196515.1	s__Vibrio gazogenes_A	77.154	100	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:37,732] [INFO] GTDB search result was written to GCF_023653475.1_ASM2365347v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:37,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:37,735] [INFO] DFAST_QC result json was written to GCF_023653475.1_ASM2365347v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:37,735] [INFO] DFAST_QC completed!
[2024-01-24 11:06:37,735] [INFO] Total running time: 0h1m34s