[2024-01-25 20:22:50,631] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:50,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:50,632] [INFO] DQC Reference Directory: /var/lib/cwl/stga92b9176-ea00-490a-95c4-db836aa36dea/dqc_reference
[2024-01-25 20:22:51,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:51,785] [INFO] Task started: Prodigal
[2024-01-25 20:22:51,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg5be69558-2f9f-41b3-b33d-6e25c6fc6330/GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/cds.fna -a GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:04,245] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:04,246] [INFO] Task started: HMMsearch
[2024-01-25 20:23:04,246] [INFO] Running command: hmmsearch --tblout GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga92b9176-ea00-490a-95c4-db836aa36dea/dqc_reference/reference_markers.hmm GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:04,540] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:04,541] [INFO] Found 6/6 markers.
[2024-01-25 20:23:04,587] [INFO] Query marker FASTA was written to GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:23:04,587] [INFO] Task started: Blastn
[2024-01-25 20:23:04,588] [INFO] Running command: blastn -query GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga92b9176-ea00-490a-95c4-db836aa36dea/dqc_reference/reference_markers.fasta -out GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:05,311] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:05,315] [INFO] Selected 20 target genomes.
[2024-01-25 20:23:05,315] [INFO] Target genome list was writen to GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:23:05,342] [INFO] Task started: fastANI
[2024-01-25 20:23:05,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be69558-2f9f-41b3-b33d-6e25c6fc6330/GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna.gz --refList GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:20,450] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:20,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga92b9176-ea00-490a-95c4-db836aa36dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:20,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga92b9176-ea00-490a-95c4-db836aa36dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:20,463] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:20,464] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:20,464] [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
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	99.9995	1544	1546	95	conclusive
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	85.2934	1162	1546	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	79.3934	531	1546	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	78.0157	359	1546	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	77.8242	285	1546	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	77.5995	302	1546	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	77.5631	348	1546	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	77.4236	277	1546	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	77.301	290	1546	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	77.1798	349	1546	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	77.0561	248	1546	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.0219	177	1546	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.9225	144	1546	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.7569	124	1546	95	below_threshold
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	76.5273	158	1546	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.4461	149	1546	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.3801	122	1546	95	below_threshold
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	76.1602	119	1546	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	75.968	63	1546	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	75.8961	82	1546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:20,465] [INFO] DFAST Taxonomy check result was written to GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:23:20,466] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:20,466] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:20,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga92b9176-ea00-490a-95c4-db836aa36dea/dqc_reference/checkm_data
[2024-01-25 20:23:20,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:20,513] [INFO] Task started: CheckM
[2024-01-25 20:23:20,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/checkm_input GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:23:57,808] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:57,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:57,824] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:57,824] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:57,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:23:57,825] [INFO] Task started: Blastn
[2024-01-25 20:23:57,825] [INFO] Running command: blastn -query GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga92b9176-ea00-490a-95c4-db836aa36dea/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:58,741] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:58,744] [INFO] Selected 11 target genomes.
[2024-01-25 20:23:58,744] [INFO] Target genome list was writen to GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:58,756] [INFO] Task started: fastANI
[2024-01-25 20:23:58,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be69558-2f9f-41b3-b33d-6e25c6fc6330/GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna.gz --refList GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:08,436] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:08,443] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:08,443] [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_900102165.1	s__Cellulophaga baltica	99.9995	1544	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	conclusive
GCF_009797025.1	s__Cellulophaga sp009797025	86.5392	1182	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	85.3028	1161	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_019021925.1	s__Cellulophaga sp019021925	80.7102	666	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	79.3843	532	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861125.1	s__Cellulophaga baltica_A	79.0306	543	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799565.1	s__Cellulophaga sp000799565	78.3782	416	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119145.1	s__Cellulophaga fucicola	78.0162	359	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	77.8123	286	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744255.1	s__Maribacter_B sp016744255	77.2019	283	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855495.1	s__Euzebyella saccharophila	76.1602	119	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:08,446] [INFO] GTDB search result was written to GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:08,446] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:08,449] [INFO] DFAST_QC result json was written to GCF_900102165.1_IMG-taxon_2622736528_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:24:08,450] [INFO] DFAST_QC completed!
[2024-01-25 20:24:08,450] [INFO] Total running time: 0h1m18s