[2024-01-24 13:49:28,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:28,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:28,940] [INFO] DQC Reference Directory: /var/lib/cwl/stgf585bdbd-ffd1-4ddd-8141-d05538559ff0/dqc_reference
[2024-01-24 13:49:30,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:30,230] [INFO] Task started: Prodigal
[2024-01-24 13:49:30,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e55d6e8-38d7-4ec9-bab6-b9d2984b98c6/GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/cds.fna -a GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,663] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,663] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,663] [INFO] Running command: hmmsearch --tblout GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf585bdbd-ffd1-4ddd-8141-d05538559ff0/dqc_reference/reference_markers.hmm GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:42,971] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:42,973] [INFO] Found 6/6 markers.
[2024-01-24 13:49:43,018] [INFO] Query marker FASTA was written to GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:43,018] [INFO] Task started: Blastn
[2024-01-24 13:49:43,019] [INFO] Running command: blastn -query GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf585bdbd-ffd1-4ddd-8141-d05538559ff0/dqc_reference/reference_markers.fasta -out GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:44,011] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:44,014] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:44,015] [INFO] Target genome list was writen to GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:44,018] [INFO] Task started: fastANI
[2024-01-24 13:49:44,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e55d6e8-38d7-4ec9-bab6-b9d2984b98c6/GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna.gz --refList GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:00,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf585bdbd-ffd1-4ddd-8141-d05538559ff0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:00,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf585bdbd-ffd1-4ddd-8141-d05538559ff0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:00,142] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:00,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:00,143] [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 korlensis	strain=CGMCC 1.6981	GCA_900116705.1	463301	463301	type	True	100.0	1328	1331	95	conclusive
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	82.5986	813	1331	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	82.2272	736	1331	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	82.0458	788	1331	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	81.9759	782	1331	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	81.9101	704	1331	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	81.8901	737	1331	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	81.8806	683	1331	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	81.8689	748	1331	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	81.7342	718	1331	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	81.4565	736	1331	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	81.2908	696	1331	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.9619	730	1331	95	below_threshold
Halomonas gudaonensis	strain=CGMCC 1.6133	GCA_900100195.1	376427	376427	type	True	80.535	654	1331	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	80.5197	690	1331	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	80.5044	669	1331	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	80.2307	602	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,149] [INFO] DFAST Taxonomy check result was written to GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:50:00,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:00,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:00,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf585bdbd-ffd1-4ddd-8141-d05538559ff0/dqc_reference/checkm_data
[2024-01-24 13:50:00,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:00,219] [INFO] Task started: CheckM
[2024-01-24 13:50:00,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/checkm_input GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:41,171] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:41,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:41,189] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:41,190] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:41,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:41,191] [INFO] Task started: Blastn
[2024-01-24 13:50:41,191] [INFO] Running command: blastn -query GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf585bdbd-ffd1-4ddd-8141-d05538559ff0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:43,036] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:43,040] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:43,041] [INFO] Target genome list was writen to GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:43,048] [INFO] Task started: fastANI
[2024-01-24 13:50:43,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e55d6e8-38d7-4ec9-bab6-b9d2984b98c6/GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna.gz --refList GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:53,288] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:53,304] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:53,304] [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_900116705.1	s__Halomonas korlensis	100.0	1327	1331	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_018448785.1	s__Halomonas sp018448785	88.2777	1006	1331	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	82.5918	814	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_003056305.1	s__Halomonas denitrificans	82.2163	737	1331	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	82.2162	785	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	81.9879	781	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001886615.1	s__Halomonas aestuarii	81.8952	706	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116405.1	s__Halomonas saccharevitans	81.8908	682	1331	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	81.8248	693	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104135.1	s__Halomonas shengliensis	81.7711	714	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCA_003552795.1	s__Halomonas sp003552795	80.9799	484	1331	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 13:50:53,306] [INFO] GTDB search result was written to GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:53,306] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:53,310] [INFO] DFAST_QC result json was written to GCF_900116705.1_IMG-taxon_2617270784_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:50:53,310] [INFO] DFAST_QC completed!
[2024-01-24 13:50:53,310] [INFO] Total running time: 0h1m24s