[2024-01-24 12:47:22,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,144] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb74ea3a-3562-44db-831b-6c5c6887cd67/dqc_reference
[2024-01-24 12:47:23,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,417] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,417] [INFO] Running command: gunzip -c /var/lib/cwl/stga14f0e40-a21f-4985-9f24-e7f695f78478/GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/cds.fna -a GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:39,246] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:39,246] [INFO] Task started: HMMsearch
[2024-01-24 12:47:39,246] [INFO] Running command: hmmsearch --tblout GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb74ea3a-3562-44db-831b-6c5c6887cd67/dqc_reference/reference_markers.hmm GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:39,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:39,532] [INFO] Found 6/6 markers.
[2024-01-24 12:47:39,574] [INFO] Query marker FASTA was written to GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:47:39,575] [INFO] Task started: Blastn
[2024-01-24 12:47:39,575] [INFO] Running command: blastn -query GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb74ea3a-3562-44db-831b-6c5c6887cd67/dqc_reference/reference_markers.fasta -out GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:40,266] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:40,269] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:40,270] [INFO] Target genome list was writen to GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:47:40,276] [INFO] Task started: fastANI
[2024-01-24 12:47:40,277] [INFO] Running command: fastANI --query /var/lib/cwl/stga14f0e40-a21f-4985-9f24-e7f695f78478/GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna.gz --refList GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:51,856] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:51,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb74ea3a-3562-44db-831b-6c5c6887cd67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:51,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb74ea3a-3562-44db-831b-6c5c6887cd67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:51,868] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:51,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:51,868] [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
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	100.0	1490	1492	95	conclusive
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	84.461	1030	1492	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	83.3599	960	1492	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	83.0978	958	1492	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	83.0636	996	1492	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	82.0163	940	1492	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	81.6221	908	1492	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	79.0867	521	1492	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	77.344	133	1492	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	77.0036	179	1492	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.4069	73	1492	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.8557	67	1492	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	75.7903	50	1492	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:51,871] [INFO] DFAST Taxonomy check result was written to GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:47:51,871] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:51,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:51,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb74ea3a-3562-44db-831b-6c5c6887cd67/dqc_reference/checkm_data
[2024-01-24 12:47:51,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:51,921] [INFO] Task started: CheckM
[2024-01-24 12:47:51,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/checkm_input GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:48:40,752] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:40,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:40,773] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:40,774] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:40,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:48:40,775] [INFO] Task started: Blastn
[2024-01-24 12:48:40,775] [INFO] Running command: blastn -query GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb74ea3a-3562-44db-831b-6c5c6887cd67/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:41,697] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:41,702] [INFO] Selected 10 target genomes.
[2024-01-24 12:48:41,702] [INFO] Target genome list was writen to GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:41,710] [INFO] Task started: fastANI
[2024-01-24 12:48:41,710] [INFO] Running command: fastANI --query /var/lib/cwl/stga14f0e40-a21f-4985-9f24-e7f695f78478/GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna.gz --refList GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:51,648] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:51,662] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:51,662] [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_900155985.1	s__Maribacter ulvicola	100.0	1490	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000744105.1	s__Maribacter forsetii	84.4708	1029	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	83.3618	960	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	83.0888	959	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	83.07	995	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	82.0087	941	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_900112245.1	s__Maribacter stanieri	81.6301	907	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCA_011050675.1	s__Maribacter sp011050675	81.5862	881	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900188415.1	s__Maribacter sedimenticola	79.0874	520	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	77.3184	135	1492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:51,664] [INFO] GTDB search result was written to GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:51,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:51,668] [INFO] DFAST_QC result json was written to GCF_900155985.1_IMG-taxon_2681813549_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:48:51,668] [INFO] DFAST_QC completed!
[2024-01-24 12:48:51,668] [INFO] Total running time: 0h1m30s