[2024-01-24 12:14:33,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg54107657-d0a8-4559-8e1c-22dfcf8e97f3/dqc_reference
[2024-01-24 12:14:35,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,189] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg910faa0e-484f-45bb-bb69-7f1e1d10b62b/GCF_004339545.1_ASM433954v1_genomic.fna.gz | prodigal -d GCF_004339545.1_ASM433954v1_genomic.fna/cds.fna -a GCF_004339545.1_ASM433954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:44,486] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:44,487] [INFO] Task started: HMMsearch
[2024-01-24 12:14:44,487] [INFO] Running command: hmmsearch --tblout GCF_004339545.1_ASM433954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54107657-d0a8-4559-8e1c-22dfcf8e97f3/dqc_reference/reference_markers.hmm GCF_004339545.1_ASM433954v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:44,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:44,794] [INFO] Found 6/6 markers.
[2024-01-24 12:14:44,828] [INFO] Query marker FASTA was written to GCF_004339545.1_ASM433954v1_genomic.fna/markers.fasta
[2024-01-24 12:14:44,829] [INFO] Task started: Blastn
[2024-01-24 12:14:44,829] [INFO] Running command: blastn -query GCF_004339545.1_ASM433954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54107657-d0a8-4559-8e1c-22dfcf8e97f3/dqc_reference/reference_markers.fasta -out GCF_004339545.1_ASM433954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:45,576] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:45,580] [INFO] Selected 28 target genomes.
[2024-01-24 12:14:45,581] [INFO] Target genome list was writen to GCF_004339545.1_ASM433954v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:45,592] [INFO] Task started: fastANI
[2024-01-24 12:14:45,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg910faa0e-484f-45bb-bb69-7f1e1d10b62b/GCF_004339545.1_ASM433954v1_genomic.fna.gz --refList GCF_004339545.1_ASM433954v1_genomic.fna/target_genomes.txt --output GCF_004339545.1_ASM433954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:07,669] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:07,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54107657-d0a8-4559-8e1c-22dfcf8e97f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:07,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54107657-d0a8-4559-8e1c-22dfcf8e97f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:07,682] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:07,683] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:07,683] [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
Celerinatantimonas diazotrophica	strain=DSM 18577	GCA_004339545.1	412034	412034	type	True	100.0	1313	1313	95	conclusive
Agarivorans litoreus	strain=NBRC 110444	GCA_019649015.1	1510455	1510455	type	True	77.132	60	1313	95	below_threshold
Agarivorans gilvus	strain=WH0801	GCA_001420915.1	680279	680279	type	True	77.0092	67	1313	95	below_threshold
Agarivorans gilvus	strain=CGMCC 1.10131	GCA_014636215.1	680279	680279	type	True	76.7101	64	1313	95	below_threshold
Alginatibacterium sediminis	strain=ALS 81	GCA_003610775.1	2164068	2164068	type	True	76.5511	52	1313	95	below_threshold
Vibrio anguillarum	strain=NCTC12159	GCA_900452855.1	55601	55601	type	True	76.0448	56	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:07,684] [INFO] DFAST Taxonomy check result was written to GCF_004339545.1_ASM433954v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:07,685] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:07,685] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:07,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54107657-d0a8-4559-8e1c-22dfcf8e97f3/dqc_reference/checkm_data
[2024-01-24 12:15:07,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:07,731] [INFO] Task started: CheckM
[2024-01-24 12:15:07,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339545.1_ASM433954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339545.1_ASM433954v1_genomic.fna/checkm_input GCF_004339545.1_ASM433954v1_genomic.fna/checkm_result
[2024-01-24 12:15:41,622] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:41,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,651] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:41,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:41,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339545.1_ASM433954v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:41,653] [INFO] Task started: Blastn
[2024-01-24 12:15:41,653] [INFO] Running command: blastn -query GCF_004339545.1_ASM433954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54107657-d0a8-4559-8e1c-22dfcf8e97f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339545.1_ASM433954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:42,770] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:42,776] [INFO] Selected 29 target genomes.
[2024-01-24 12:15:42,776] [INFO] Target genome list was writen to GCF_004339545.1_ASM433954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:42,796] [INFO] Task started: fastANI
[2024-01-24 12:15:42,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg910faa0e-484f-45bb-bb69-7f1e1d10b62b/GCF_004339545.1_ASM433954v1_genomic.fna.gz --refList GCF_004339545.1_ASM433954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339545.1_ASM433954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:05,438] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:05,448] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:05,449] [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_004339545.1	s__Celerinatantimonas diazotrophica	100.0	1313	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Celerinatantimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900537085.1	s__Agarivorans sp900537085	77.325	56	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420915.1	s__Agarivorans gilvus	77.0092	67	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	99.99	99.99	1.00	1.00	2	-
GCF_005405585.1	s__Agarivorans sp005405585	76.9595	62	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610775.1	s__Alginatibacterium sediminis	76.583	51	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Alginatibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:05,451] [INFO] GTDB search result was written to GCF_004339545.1_ASM433954v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:05,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:05,456] [INFO] DFAST_QC result json was written to GCF_004339545.1_ASM433954v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:05,457] [INFO] DFAST_QC completed!
[2024-01-24 12:16:05,457] [INFO] Total running time: 0h1m32s