[2024-01-24 10:57:19,729] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:19,733] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:19,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg8737c267-666a-4d42-ae26-4ed4ff0c5321/dqc_reference
[2024-01-24 10:57:22,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:22,298] [INFO] Task started: Prodigal
[2024-01-24 10:57:22,298] [INFO] Running command: gunzip -c /var/lib/cwl/stg293277e0-a791-4bad-91f1-ba730a12bafc/GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/cds.fna -a GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:34,708] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:34,708] [INFO] Task started: HMMsearch
[2024-01-24 10:57:34,708] [INFO] Running command: hmmsearch --tblout GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8737c267-666a-4d42-ae26-4ed4ff0c5321/dqc_reference/reference_markers.hmm GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:34,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:34,977] [INFO] Found 6/6 markers.
[2024-01-24 10:57:35,017] [INFO] Query marker FASTA was written to GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:57:35,018] [INFO] Task started: Blastn
[2024-01-24 10:57:35,018] [INFO] Running command: blastn -query GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8737c267-666a-4d42-ae26-4ed4ff0c5321/dqc_reference/reference_markers.fasta -out GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:35,758] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:35,763] [INFO] Selected 21 target genomes.
[2024-01-24 10:57:35,763] [INFO] Target genome list was writen to GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:57:35,865] [INFO] Task started: fastANI
[2024-01-24 10:57:35,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg293277e0-a791-4bad-91f1-ba730a12bafc/GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna.gz --refList GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:50,228] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:50,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8737c267-666a-4d42-ae26-4ed4ff0c5321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:50,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8737c267-666a-4d42-ae26-4ed4ff0c5321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:50,249] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:50,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:50,249] [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
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	100.0	1337	1338	95	conclusive
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	80.3081	705	1338	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	79.7606	600	1338	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.7562	391	1338	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	77.1464	255	1338	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	77.1263	234	1338	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.0962	234	1338	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.0942	244	1338	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.0841	227	1338	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.0806	282	1338	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.9938	256	1338	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	76.9783	195	1338	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	76.9202	218	1338	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.8664	196	1338	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	76.8314	226	1338	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8275	265	1338	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	76.8258	195	1338	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	76.7937	225	1338	95	below_threshold
Paracoccus tibetensis	strain=CGMCC 1.8925	GCA_900102505.1	336292	336292	type	True	76.7866	171	1338	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.7085	236	1338	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	76.5027	196	1338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:50,250] [INFO] DFAST Taxonomy check result was written to GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:57:50,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:50,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:50,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8737c267-666a-4d42-ae26-4ed4ff0c5321/dqc_reference/checkm_data
[2024-01-24 10:57:50,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:50,296] [INFO] Task started: CheckM
[2024-01-24 10:57:50,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/checkm_input GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:58:28,887] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:28,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:28,910] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:28,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:28,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:58:28,911] [INFO] Task started: Blastn
[2024-01-24 10:58:28,911] [INFO] Running command: blastn -query GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8737c267-666a-4d42-ae26-4ed4ff0c5321/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:30,086] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:30,090] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:30,091] [INFO] Target genome list was writen to GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:30,121] [INFO] Task started: fastANI
[2024-01-24 10:58:30,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg293277e0-a791-4bad-91f1-ba730a12bafc/GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna.gz --refList GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:39,319] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:39,337] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:39,338] [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_900114485.1	s__Loktanella salsilacus	100.0	1337	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	conclusive
GCF_900128995.1	s__Loktanella atrilutea	80.3223	701	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110065.1	s__Loktanella fryxellensis	79.7561	601	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420005.1	s__Loktanella sp001420005	78.7971	493	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110705.1	s__Loktanella sp900110705	78.7787	492	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263905.1	s__Loktanella sp018263905	78.4956	506	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	77.7435	393	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	77.5758	284	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152785.1	s__Yoonia vestfoldensis_A	77.5727	344	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	77.1912	276	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	76.8974	166	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	76.846	202	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_003340555.1	s__Jannaschia formosa	76.5014	198	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:39,339] [INFO] GTDB search result was written to GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:39,340] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:39,344] [INFO] DFAST_QC result json was written to GCF_900114485.1_IMG-taxon_2622736595_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:58:39,344] [INFO] DFAST_QC completed!
[2024-01-24 10:58:39,344] [INFO] Total running time: 0h1m20s