[2024-01-24 13:40:30,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,310] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,310] [INFO] DQC Reference Directory: /var/lib/cwl/stga5cb43ed-ea05-4203-9d77-a33adcc5a2f7/dqc_reference
[2024-01-24 13:40:31,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,697] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,698] [INFO] Running command: gunzip -c /var/lib/cwl/stgb74ae3b8-759d-4e54-9adc-0ee735e91b67/GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/cds.fna -a GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:42,776] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:42,777] [INFO] Task started: HMMsearch
[2024-01-24 13:40:42,777] [INFO] Running command: hmmsearch --tblout GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5cb43ed-ea05-4203-9d77-a33adcc5a2f7/dqc_reference/reference_markers.hmm GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:43,071] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:43,072] [INFO] Found 6/6 markers.
[2024-01-24 13:40:43,106] [INFO] Query marker FASTA was written to GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:43,106] [INFO] Task started: Blastn
[2024-01-24 13:40:43,106] [INFO] Running command: blastn -query GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga5cb43ed-ea05-4203-9d77-a33adcc5a2f7/dqc_reference/reference_markers.fasta -out GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:44,236] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:44,240] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:44,241] [INFO] Target genome list was writen to GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:44,246] [INFO] Task started: fastANI
[2024-01-24 13:40:44,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgb74ae3b8-759d-4e54-9adc-0ee735e91b67/GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna.gz --refList GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:00,273] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:00,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5cb43ed-ea05-4203-9d77-a33adcc5a2f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:00,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5cb43ed-ea05-4203-9d77-a33adcc5a2f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:00,288] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:00,288] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:00,288] [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 shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	100.0	1167	1167	95	conclusive
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	89.4752	905	1167	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	87.4357	875	1167	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	86.6776	893	1167	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	86.1614	868	1167	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	85.3594	834	1167	95	below_threshold
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	85.2364	844	1167	95	below_threshold
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	85.2238	794	1167	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	85.1512	800	1167	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	85.1397	833	1167	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	84.6833	780	1167	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	84.4824	804	1167	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	84.0531	817	1167	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	83.9937	817	1167	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	83.9384	808	1167	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	82.8664	753	1167	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	82.3557	741	1167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:00,290] [INFO] DFAST Taxonomy check result was written to GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:00,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:00,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:00,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5cb43ed-ea05-4203-9d77-a33adcc5a2f7/dqc_reference/checkm_data
[2024-01-24 13:41:00,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:00,333] [INFO] Task started: CheckM
[2024-01-24 13:41:00,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/checkm_input GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:41:36,231] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:36,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:36,250] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:36,251] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:36,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:41:36,252] [INFO] Task started: Blastn
[2024-01-24 13:41:36,252] [INFO] Running command: blastn -query GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga5cb43ed-ea05-4203-9d77-a33adcc5a2f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:38,473] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:38,476] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:38,476] [INFO] Target genome list was writen to GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:38,487] [INFO] Task started: fastANI
[2024-01-24 13:41:38,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgb74ae3b8-759d-4e54-9adc-0ee735e91b67/GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna.gz --refList GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:52,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:52,138] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:52,138] [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_900104135.1	s__Halomonas shengliensis	100.0	1167	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	conclusive
GCF_009902005.1	s__Halomonas alimentaria	89.4829	905	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401555.1	s__Halomonas sp018401555	89.1669	817	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	87.4122	876	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	87.2704	795	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCF_004363555.1	s__Halomonas ventosae	86.6377	895	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCA_014859505.1	s__Halomonas sp014859505	86.2141	721	1167	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	86.1262	871	1167	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	86.1259	873	1167	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	85.8649	592	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202205.1	s__Halomonas sp003202205	85.2326	823	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901955.1	s__Halomonas icarae	85.2235	845	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.73	97.73	0.87	0.87	2	-
GCF_002879645.1	s__Halomonas heilongjiangensis	85.1402	803	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003966155.1	s__Halomonas nitroreducens	84.007	821	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:52,140] [INFO] GTDB search result was written to GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:52,141] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:52,145] [INFO] DFAST_QC result json was written to GCF_900104135.1_IMG-taxon_2617270760_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:41:52,145] [INFO] DFAST_QC completed!
[2024-01-24 13:41:52,145] [INFO] Total running time: 0h1m22s