[2024-01-24 14:12:04,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:04,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:04,272] [INFO] DQC Reference Directory: /var/lib/cwl/stgc690f29e-95ff-421c-bc0d-8fecf8f9dffc/dqc_reference
[2024-01-24 14:12:05,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:05,637] [INFO] Task started: Prodigal
[2024-01-24 14:12:05,637] [INFO] Running command: gunzip -c /var/lib/cwl/stgedabd9c1-fc9c-40a3-b0fc-34374c06b5d4/GCF_008632335.1_ASM863233v1_genomic.fna.gz | prodigal -d GCF_008632335.1_ASM863233v1_genomic.fna/cds.fna -a GCF_008632335.1_ASM863233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:18,793] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:18,794] [INFO] Task started: HMMsearch
[2024-01-24 14:12:18,794] [INFO] Running command: hmmsearch --tblout GCF_008632335.1_ASM863233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc690f29e-95ff-421c-bc0d-8fecf8f9dffc/dqc_reference/reference_markers.hmm GCF_008632335.1_ASM863233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:19,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:19,163] [INFO] Found 6/6 markers.
[2024-01-24 14:12:19,206] [INFO] Query marker FASTA was written to GCF_008632335.1_ASM863233v1_genomic.fna/markers.fasta
[2024-01-24 14:12:19,207] [INFO] Task started: Blastn
[2024-01-24 14:12:19,207] [INFO] Running command: blastn -query GCF_008632335.1_ASM863233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc690f29e-95ff-421c-bc0d-8fecf8f9dffc/dqc_reference/reference_markers.fasta -out GCF_008632335.1_ASM863233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:20,264] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:20,267] [INFO] Selected 23 target genomes.
[2024-01-24 14:12:20,268] [INFO] Target genome list was writen to GCF_008632335.1_ASM863233v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:20,278] [INFO] Task started: fastANI
[2024-01-24 14:12:20,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgedabd9c1-fc9c-40a3-b0fc-34374c06b5d4/GCF_008632335.1_ASM863233v1_genomic.fna.gz --refList GCF_008632335.1_ASM863233v1_genomic.fna/target_genomes.txt --output GCF_008632335.1_ASM863233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:38,145] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:38,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc690f29e-95ff-421c-bc0d-8fecf8f9dffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:38,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc690f29e-95ff-421c-bc0d-8fecf8f9dffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:38,164] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:38,164] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:38,164] [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
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	100.0	1388	1393	95	conclusive
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	79.6839	614	1393	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	78.9818	428	1393	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	78.9403	452	1393	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	78.937	436	1393	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	78.8478	437	1393	95	below_threshold
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	78.7851	427	1393	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	78.6763	367	1393	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	78.6541	365	1393	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	78.5899	379	1393	95	below_threshold
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	78.3217	449	1393	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	78.0294	391	1393	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	77.9255	302	1393	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.8835	315	1393	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.8726	272	1393	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	76.8611	180	1393	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.7053	231	1393	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.1261	144	1393	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	76.0483	72	1393	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	75.6174	65	1393	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	75.5977	68	1393	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	75.422	67	1393	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	75.2367	65	1393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:38,166] [INFO] DFAST Taxonomy check result was written to GCF_008632335.1_ASM863233v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:38,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:38,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:38,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc690f29e-95ff-421c-bc0d-8fecf8f9dffc/dqc_reference/checkm_data
[2024-01-24 14:12:38,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:38,220] [INFO] Task started: CheckM
[2024-01-24 14:12:38,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008632335.1_ASM863233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008632335.1_ASM863233v1_genomic.fna/checkm_input GCF_008632335.1_ASM863233v1_genomic.fna/checkm_result
[2024-01-24 14:13:20,743] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:20,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:20,762] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:20,763] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:20,763] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008632335.1_ASM863233v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:20,763] [INFO] Task started: Blastn
[2024-01-24 14:13:20,764] [INFO] Running command: blastn -query GCF_008632335.1_ASM863233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc690f29e-95ff-421c-bc0d-8fecf8f9dffc/dqc_reference/reference_markers_gtdb.fasta -out GCF_008632335.1_ASM863233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:22,571] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:22,575] [INFO] Selected 19 target genomes.
[2024-01-24 14:13:22,575] [INFO] Target genome list was writen to GCF_008632335.1_ASM863233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:22,594] [INFO] Task started: fastANI
[2024-01-24 14:13:22,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgedabd9c1-fc9c-40a3-b0fc-34374c06b5d4/GCF_008632335.1_ASM863233v1_genomic.fna.gz --refList GCF_008632335.1_ASM863233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008632335.1_ASM863233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:38,108] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:38,125] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:38,126] [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_008632335.1	s__Thiohalocapsa marina	100.0	1388	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016583825.1	s__Thiohalocapsa halophila	79.687	615	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	95.31	95.31	0.87	0.87	2	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	79.4289	611	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584085.1	s__Halochromatium glycolicum	78.9301	453	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	78.9162	438	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_016653295.1	s__Halochromatium salexigens	78.7852	427	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	78.7221	368	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	78.638	367	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_013385175.1	s__Allochromatium humboldtianum	78.6139	378	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908845.1	s__Halochromatium sp009908845	78.4778	375	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	78.3701	295	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938795.1	s__Marichromatium sp016938795	78.036	237	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693535.1	s__Halochromatium sp007693535	78.0237	432	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820565.1	s__Thiorhodococcus minor	78.0186	393	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	77.8283	320	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016745215.1	s__Thiohalocapsa sp003525925	76.9831	305	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	99.92	99.92	0.99	0.98	3	-
GCA_016710335.1	s__JADJXQ01 sp016710335	76.1039	64	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__JADJXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	75.2648	71	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:38,128] [INFO] GTDB search result was written to GCF_008632335.1_ASM863233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:38,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:38,136] [INFO] DFAST_QC result json was written to GCF_008632335.1_ASM863233v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:38,136] [INFO] DFAST_QC completed!
[2024-01-24 14:13:38,136] [INFO] Total running time: 0h1m34s