[2024-01-24 12:45:09,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:09,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:09,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7034693-eb29-401f-8d55-1eb96346e01a/dqc_reference
[2024-01-24 12:45:13,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,083] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg18a8b01c-e9fd-4119-b0cb-5976497ee3bc/GCF_014841115.1_ASM1484111v1_genomic.fna.gz | prodigal -d GCF_014841115.1_ASM1484111v1_genomic.fna/cds.fna -a GCF_014841115.1_ASM1484111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:26,092] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:26,092] [INFO] Task started: HMMsearch
[2024-01-24 12:45:26,092] [INFO] Running command: hmmsearch --tblout GCF_014841115.1_ASM1484111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7034693-eb29-401f-8d55-1eb96346e01a/dqc_reference/reference_markers.hmm GCF_014841115.1_ASM1484111v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:26,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:26,399] [INFO] Found 6/6 markers.
[2024-01-24 12:45:26,441] [INFO] Query marker FASTA was written to GCF_014841115.1_ASM1484111v1_genomic.fna/markers.fasta
[2024-01-24 12:45:26,442] [INFO] Task started: Blastn
[2024-01-24 12:45:26,442] [INFO] Running command: blastn -query GCF_014841115.1_ASM1484111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7034693-eb29-401f-8d55-1eb96346e01a/dqc_reference/reference_markers.fasta -out GCF_014841115.1_ASM1484111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:27,321] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:27,376] [INFO] Selected 10 target genomes.
[2024-01-24 12:45:27,377] [INFO] Target genome list was writen to GCF_014841115.1_ASM1484111v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:27,382] [INFO] Task started: fastANI
[2024-01-24 12:45:27,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg18a8b01c-e9fd-4119-b0cb-5976497ee3bc/GCF_014841115.1_ASM1484111v1_genomic.fna.gz --refList GCF_014841115.1_ASM1484111v1_genomic.fna/target_genomes.txt --output GCF_014841115.1_ASM1484111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:37,610] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:37,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7034693-eb29-401f-8d55-1eb96346e01a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:37,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7034693-eb29-401f-8d55-1eb96346e01a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:37,658] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:37,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:37,659] [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 arenosum	strain=CAU 1568	GCA_014841115.1	2774143	2774143	type	True	100.0	1570	1572	95	conclusive
Photobacterium halotolerans	strain=DSM 18316	GCA_000425165.1	265726	265726	type	True	93.59	1343	1572	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	91.1905	1368	1572	95	below_threshold
Photobacterium galatheae	strain=S2753	GCA_000695255.1	1654360	1654360	type	True	81.7182	717	1572	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	81.5055	894	1572	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	78.7484	421	1572	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	78.1479	189	1572	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	77.9941	73	1572	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	77.8243	163	1572	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	76.5378	96	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:37,660] [INFO] DFAST Taxonomy check result was written to GCF_014841115.1_ASM1484111v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:37,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:37,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:37,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7034693-eb29-401f-8d55-1eb96346e01a/dqc_reference/checkm_data
[2024-01-24 12:45:37,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:37,713] [INFO] Task started: CheckM
[2024-01-24 12:45:37,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014841115.1_ASM1484111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014841115.1_ASM1484111v1_genomic.fna/checkm_input GCF_014841115.1_ASM1484111v1_genomic.fna/checkm_result
[2024-01-24 12:46:20,929] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:20,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:20,957] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:20,958] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:20,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014841115.1_ASM1484111v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:20,959] [INFO] Task started: Blastn
[2024-01-24 12:46:20,959] [INFO] Running command: blastn -query GCF_014841115.1_ASM1484111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7034693-eb29-401f-8d55-1eb96346e01a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014841115.1_ASM1484111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:22,274] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:22,277] [INFO] Selected 6 target genomes.
[2024-01-24 12:46:22,278] [INFO] Target genome list was writen to GCF_014841115.1_ASM1484111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:22,284] [INFO] Task started: fastANI
[2024-01-24 12:46:22,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg18a8b01c-e9fd-4119-b0cb-5976497ee3bc/GCF_014841115.1_ASM1484111v1_genomic.fna.gz --refList GCF_014841115.1_ASM1484111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014841115.1_ASM1484111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:29,789] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:29,800] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:29,800] [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_014841115.1	s__Photobacterium sp014841115	100.0	1570	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.86	98.86	0.94	0.94	2	conclusive
GCF_000425165.1	s__Photobacterium halotolerans	93.59	1343	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.98	97.78	0.94	0.93	4	-
GCF_003614885.1	s__Photobacterium sp003614885	91.1905	1368	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972145.1	s__Photobacterium halotolerans_A	89.8406	1334	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695255.1	s__Photobacterium galatheae	81.7088	718	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018199995.1	s__Photobacterium sp018199995	81.7077	892	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:29,802] [INFO] GTDB search result was written to GCF_014841115.1_ASM1484111v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:29,802] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:29,806] [INFO] DFAST_QC result json was written to GCF_014841115.1_ASM1484111v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:29,806] [INFO] DFAST_QC completed!
[2024-01-24 12:46:29,806] [INFO] Total running time: 0h1m20s