[2024-01-24 15:18:18,820] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,822] [INFO] DQC Reference Directory: /var/lib/cwl/stg81f5e108-01f6-44f1-982f-34578c1c850c/dqc_reference
[2024-01-24 15:18:20,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,074] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,074] [INFO] Running command: gunzip -c /var/lib/cwl/stg562bdb8e-65f6-4786-b505-287335b5aa0e/GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/cds.fna -a GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:30,687] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:30,688] [INFO] Task started: HMMsearch
[2024-01-24 15:18:30,688] [INFO] Running command: hmmsearch --tblout GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81f5e108-01f6-44f1-982f-34578c1c850c/dqc_reference/reference_markers.hmm GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:30,983] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:30,984] [INFO] Found 6/6 markers.
[2024-01-24 15:18:31,028] [INFO] Query marker FASTA was written to GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:18:31,029] [INFO] Task started: Blastn
[2024-01-24 15:18:31,029] [INFO] Running command: blastn -query GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f5e108-01f6-44f1-982f-34578c1c850c/dqc_reference/reference_markers.fasta -out GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:31,760] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:31,763] [INFO] Selected 20 target genomes.
[2024-01-24 15:18:31,763] [INFO] Target genome list was writen to GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:18:31,773] [INFO] Task started: fastANI
[2024-01-24 15:18:31,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg562bdb8e-65f6-4786-b505-287335b5aa0e/GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna.gz --refList GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:47,501] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:47,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81f5e108-01f6-44f1-982f-34578c1c850c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:47,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81f5e108-01f6-44f1-982f-34578c1c850c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:47,522] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:47,522] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:47,522] [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
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	80.9538	580	1156	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	80.9226	574	1156	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	80.6271	647	1156	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	80.247	512	1156	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	78.7785	288	1156	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	78.7613	309	1156	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	78.7233	301	1156	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	78.5342	242	1156	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	78.5294	305	1156	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	77.9883	249	1156	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	77.8385	222	1156	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	77.7694	221	1156	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	77.5521	212	1156	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.3955	94	1156	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.3924	99	1156	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	76.2334	92	1156	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.0166	70	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:47,524] [INFO] DFAST Taxonomy check result was written to GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:18:47,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:47,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:47,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81f5e108-01f6-44f1-982f-34578c1c850c/dqc_reference/checkm_data
[2024-01-24 15:18:47,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:47,561] [INFO] Task started: CheckM
[2024-01-24 15:18:47,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/checkm_input GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:19:23,451] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:23,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:23,472] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:23,473] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:23,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:19:23,474] [INFO] Task started: Blastn
[2024-01-24 15:19:23,474] [INFO] Running command: blastn -query GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f5e108-01f6-44f1-982f-34578c1c850c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:24,546] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:24,550] [INFO] Selected 10 target genomes.
[2024-01-24 15:19:24,550] [INFO] Target genome list was writen to GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:24,561] [INFO] Task started: fastANI
[2024-01-24 15:19:24,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg562bdb8e-65f6-4786-b505-287335b5aa0e/GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna.gz --refList GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:32,443] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:32,462] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:19:32,462] [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_019061305.1	s__Marinobacterium sp019061305	81.511	600	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868415.1	s__Marinobacterium sp013868415	81.1686	575	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155945.1	s__Marinobacterium stanieri	80.9455	582	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
GCF_017776525.1	s__Marinobacterium alkalitolerans	80.9203	574	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014615.1	s__Marinobacterium halophilum	80.6377	645	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.87	98.87	0.91	0.91	2	-
GCF_900107855.1	s__Marinobacterium georgiense	80.2467	513	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.23	97.23	0.75	0.75	2	-
GCF_900108065.1	s__Marinobacterium lutimaris	78.7094	301	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641945.1	s__Marinobacterium zhoushanense	78.5691	300	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	78.0059	247	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378045.1	s__Marinobacterium_A rhizophilum	77.8487	223	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:32,476] [INFO] GTDB search result was written to GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:32,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:32,483] [INFO] DFAST_QC result json was written to GCF_900184155.1_IMG-taxon_2617270783_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:19:32,483] [INFO] DFAST_QC completed!
[2024-01-24 15:19:32,483] [INFO] Total running time: 0h1m14s