[2024-01-24 10:57:38,987] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,989] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg46c2254f-ac34-40b2-9e53-48d7ad53972d/dqc_reference
[2024-01-24 10:57:40,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,279] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,279] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf64a1ca-6ca1-49f6-a905-541b458d8c24/GCF_008124525.1_ASM812452v1_genomic.fna.gz | prodigal -d GCF_008124525.1_ASM812452v1_genomic.fna/cds.fna -a GCF_008124525.1_ASM812452v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:48,914] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:48,915] [INFO] Task started: HMMsearch
[2024-01-24 10:57:48,915] [INFO] Running command: hmmsearch --tblout GCF_008124525.1_ASM812452v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46c2254f-ac34-40b2-9e53-48d7ad53972d/dqc_reference/reference_markers.hmm GCF_008124525.1_ASM812452v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:49,227] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:49,228] [INFO] Found 6/6 markers.
[2024-01-24 10:57:49,257] [INFO] Query marker FASTA was written to GCF_008124525.1_ASM812452v1_genomic.fna/markers.fasta
[2024-01-24 10:57:49,258] [INFO] Task started: Blastn
[2024-01-24 10:57:49,258] [INFO] Running command: blastn -query GCF_008124525.1_ASM812452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c2254f-ac34-40b2-9e53-48d7ad53972d/dqc_reference/reference_markers.fasta -out GCF_008124525.1_ASM812452v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:50,433] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:50,436] [INFO] Selected 23 target genomes.
[2024-01-24 10:57:50,436] [INFO] Target genome list was writen to GCF_008124525.1_ASM812452v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:50,445] [INFO] Task started: fastANI
[2024-01-24 10:57:50,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf64a1ca-6ca1-49f6-a905-541b458d8c24/GCF_008124525.1_ASM812452v1_genomic.fna.gz --refList GCF_008124525.1_ASM812452v1_genomic.fna/target_genomes.txt --output GCF_008124525.1_ASM812452v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:09,849] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:09,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46c2254f-ac34-40b2-9e53-48d7ad53972d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:09,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46c2254f-ac34-40b2-9e53-48d7ad53972d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:09,867] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:09,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:09,868] [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
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	100.0	1076	1076	95	conclusive
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	79.0972	424	1076	95	below_threshold
Meinhardsimonia xiamenensis	strain=CGMCC 1.10789	GCA_900102905.1	990712	990712	type	True	79.019	425	1076	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	79.0067	665	1076	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	78.8776	608	1076	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.7486	555	1076	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.7386	452	1076	95	below_threshold
Thermohalobaculum xanthum	strain=M0105	GCA_016623495.1	2753746	2753746	type	True	78.6402	467	1076	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	78.5022	503	1076	95	below_threshold
Albidovulum inexpectatum	strain=DSM 12048	GCA_002927635.1	196587	196587	type	True	78.4203	329	1076	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	77.9815	451	1076	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	77.9552	396	1076	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	77.9284	400	1076	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	77.8058	424	1076	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	77.7717	341	1076	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.7196	410	1076	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.688	408	1076	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5606	335	1076	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.5403	307	1076	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.4741	434	1076	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.2828	410	1076	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.5381	276	1076	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.418	277	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:09,870] [INFO] DFAST Taxonomy check result was written to GCF_008124525.1_ASM812452v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:09,871] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:09,871] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:09,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46c2254f-ac34-40b2-9e53-48d7ad53972d/dqc_reference/checkm_data
[2024-01-24 10:58:09,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:09,908] [INFO] Task started: CheckM
[2024-01-24 10:58:09,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008124525.1_ASM812452v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008124525.1_ASM812452v1_genomic.fna/checkm_input GCF_008124525.1_ASM812452v1_genomic.fna/checkm_result
[2024-01-24 10:58:56,233] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:56,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:56,251] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:56,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:56,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008124525.1_ASM812452v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:56,253] [INFO] Task started: Blastn
[2024-01-24 10:58:56,253] [INFO] Running command: blastn -query GCF_008124525.1_ASM812452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c2254f-ac34-40b2-9e53-48d7ad53972d/dqc_reference/reference_markers_gtdb.fasta -out GCF_008124525.1_ASM812452v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:58,556] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:58,561] [INFO] Selected 22 target genomes.
[2024-01-24 10:58:58,561] [INFO] Target genome list was writen to GCF_008124525.1_ASM812452v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:58,592] [INFO] Task started: fastANI
[2024-01-24 10:58:58,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf64a1ca-6ca1-49f6-a905-541b458d8c24/GCF_008124525.1_ASM812452v1_genomic.fna.gz --refList GCF_008124525.1_ASM812452v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008124525.1_ASM812452v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:17,496] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:17,517] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:17,518] [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_008124525.1	s__Oceanicella actignis	100.0	1076	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	conclusive
GCF_900113695.1	s__Albimonas pacifica	78.9753	669	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106695.1	s__Albimonas donghaensis	78.9014	605	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.7562	483	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	78.7387	557	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013093415.1	s__Halovulum dunhuangense	78.7292	453	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	78.5938	543	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	78.4911	323	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887635.2	s__Paroceanicella profunda	78.4855	504	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002927635.1	s__Albidovulum inexpectatum	78.4572	326	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	78.3975	429	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	78.1434	440	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.8793	398	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003053725.1	s__Rhodovulum kholense	77.7773	434	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.7202	409	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003241785.1	s__Amaricoccus sp003241785	77.6987	459	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258405.1	s__Amaricoccus sp003258405	77.6471	341	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995835.1	s__Amaricoccus sp017995835	77.6429	356	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131685.1	s__Rhodobaculum sp007131685	77.5424	296	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.44	99.41	0.86	0.86	3	-
GCF_006385685.1	s__Amaricoccus solimangrovi	77.4766	435	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.4174	536	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.3682	206	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:17,519] [INFO] GTDB search result was written to GCF_008124525.1_ASM812452v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:17,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:17,524] [INFO] DFAST_QC result json was written to GCF_008124525.1_ASM812452v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:17,525] [INFO] DFAST_QC completed!
[2024-01-24 10:59:17,525] [INFO] Total running time: 0h1m39s