[2024-01-25 17:46:50,569] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:50,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:50,570] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6822d6a-3115-402d-8be2-c352471a8b83/dqc_reference
[2024-01-25 17:46:51,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:51,750] [INFO] Task started: Prodigal
[2024-01-25 17:46:51,751] [INFO] Running command: gunzip -c /var/lib/cwl/stgfff6c079-3402-433a-9dbe-8952d1450e9e/GCF_014192215.1_ASM1419221v1_genomic.fna.gz | prodigal -d GCF_014192215.1_ASM1419221v1_genomic.fna/cds.fna -a GCF_014192215.1_ASM1419221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:02,671] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:02,672] [INFO] Task started: HMMsearch
[2024-01-25 17:47:02,672] [INFO] Running command: hmmsearch --tblout GCF_014192215.1_ASM1419221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6822d6a-3115-402d-8be2-c352471a8b83/dqc_reference/reference_markers.hmm GCF_014192215.1_ASM1419221v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:02,897] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:02,898] [INFO] Found 6/6 markers.
[2024-01-25 17:47:02,934] [INFO] Query marker FASTA was written to GCF_014192215.1_ASM1419221v1_genomic.fna/markers.fasta
[2024-01-25 17:47:02,934] [INFO] Task started: Blastn
[2024-01-25 17:47:02,934] [INFO] Running command: blastn -query GCF_014192215.1_ASM1419221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6822d6a-3115-402d-8be2-c352471a8b83/dqc_reference/reference_markers.fasta -out GCF_014192215.1_ASM1419221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:03,756] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:03,759] [INFO] Selected 21 target genomes.
[2024-01-25 17:47:03,759] [INFO] Target genome list was writen to GCF_014192215.1_ASM1419221v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:03,778] [INFO] Task started: fastANI
[2024-01-25 17:47:03,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgfff6c079-3402-433a-9dbe-8952d1450e9e/GCF_014192215.1_ASM1419221v1_genomic.fna.gz --refList GCF_014192215.1_ASM1419221v1_genomic.fna/target_genomes.txt --output GCF_014192215.1_ASM1419221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:23,994] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:23,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6822d6a-3115-402d-8be2-c352471a8b83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:23,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6822d6a-3115-402d-8be2-c352471a8b83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:24,008] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:47:24,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:24,008] [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
Halomonas cerina	strain=CECT 7282	GCA_014192215.1	447424	447424	type	True	100.0	1360	1365	95	conclusive
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	84.9779	895	1365	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	84.7827	864	1365	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	84.5269	894	1365	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	84.5182	865	1365	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	84.2822	810	1365	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	84.1988	873	1365	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	83.7205	790	1365	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	83.5857	756	1365	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	83.5089	763	1365	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	83.1981	723	1365	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	83.1328	803	1365	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	83.1298	803	1365	95	below_threshold
Halomonas daqiaonensis	strain=CGMCC 1.9150	GCA_900109725.1	650850	650850	type	True	82.8445	799	1365	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	82.6771	812	1365	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	81.9801	783	1365	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	81.6346	691	1365	95	below_threshold
Halomonas gudaonensis	strain=CGMCC 1.6133	GCA_900100195.1	376427	376427	type	True	81.5899	718	1365	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	81.3533	667	1365	95	below_threshold
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	81.2535	657	1365	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.1606	717	1365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:24,009] [INFO] DFAST Taxonomy check result was written to GCF_014192215.1_ASM1419221v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:24,010] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:24,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:24,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6822d6a-3115-402d-8be2-c352471a8b83/dqc_reference/checkm_data
[2024-01-25 17:47:24,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:24,053] [INFO] Task started: CheckM
[2024-01-25 17:47:24,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192215.1_ASM1419221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192215.1_ASM1419221v1_genomic.fna/checkm_input GCF_014192215.1_ASM1419221v1_genomic.fna/checkm_result
[2024-01-25 17:47:56,972] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:56,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:56,990] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:56,990] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:56,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192215.1_ASM1419221v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:56,991] [INFO] Task started: Blastn
[2024-01-25 17:47:56,991] [INFO] Running command: blastn -query GCF_014192215.1_ASM1419221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6822d6a-3115-402d-8be2-c352471a8b83/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192215.1_ASM1419221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:58,519] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:58,521] [INFO] Selected 17 target genomes.
[2024-01-25 17:47:58,522] [INFO] Target genome list was writen to GCF_014192215.1_ASM1419221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:58,543] [INFO] Task started: fastANI
[2024-01-25 17:47:58,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgfff6c079-3402-433a-9dbe-8952d1450e9e/GCF_014192215.1_ASM1419221v1_genomic.fna.gz --refList GCF_014192215.1_ASM1419221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192215.1_ASM1419221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:14,268] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:14,279] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:14,279] [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_014192215.1	s__Halomonas cerina	100.0	1360	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014192275.1	s__Halomonas stenophila	84.9824	895	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	84.7827	864	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_003966155.1	s__Halomonas nitroreducens	84.5277	894	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	84.507	866	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	84.459	870	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	84.2943	821	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886615.1	s__Halomonas aestuarii	84.2781	811	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005780185.1	s__Halomonas urmiana	84.1974	874	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	83.6037	754	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_007989465.1	s__Halomonas halophila	83.5329	761	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_003182195.1	s__Halomonas sp003182195	83.0826	714	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCF_004361885.1	s__Halomonas ventosae_C	82.8838	661	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109725.1	s__Halomonas daqiaonensis	82.8758	796	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552795.1	s__Halomonas sp003552795	82.76	526	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286975.1	s__Halomonas_B sp002286975	81.3817	664	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779595.1	s__Halomonas_B sp014779595	80.7745	628	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:14,281] [INFO] GTDB search result was written to GCF_014192215.1_ASM1419221v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:14,282] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:14,285] [INFO] DFAST_QC result json was written to GCF_014192215.1_ASM1419221v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:14,285] [INFO] DFAST_QC completed!
[2024-01-25 17:48:14,286] [INFO] Total running time: 0h1m24s