[2024-01-24 12:30:52,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,695] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0045cd4-9ad9-42e9-8093-919fd4ca6e67/dqc_reference
[2024-01-24 12:30:53,978] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,979] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg7512c1a9-6c54-4569-adcb-7c1d7d6d8bb3/GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/cds.fna -a GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:03,461] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:03,461] [INFO] Task started: HMMsearch
[2024-01-24 12:31:03,461] [INFO] Running command: hmmsearch --tblout GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0045cd4-9ad9-42e9-8093-919fd4ca6e67/dqc_reference/reference_markers.hmm GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:03,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:03,752] [INFO] Found 6/6 markers.
[2024-01-24 12:31:03,783] [INFO] Query marker FASTA was written to GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:03,783] [INFO] Task started: Blastn
[2024-01-24 12:31:03,783] [INFO] Running command: blastn -query GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0045cd4-9ad9-42e9-8093-919fd4ca6e67/dqc_reference/reference_markers.fasta -out GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:04,623] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:04,626] [INFO] Selected 19 target genomes.
[2024-01-24 12:31:04,626] [INFO] Target genome list was writen to GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:04,634] [INFO] Task started: fastANI
[2024-01-24 12:31:04,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg7512c1a9-6c54-4569-adcb-7c1d7d6d8bb3/GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna.gz --refList GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:19,721] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:19,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0045cd4-9ad9-42e9-8093-919fd4ca6e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:19,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0045cd4-9ad9-42e9-8093-919fd4ca6e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:19,737] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:19,737] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:19,738] [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 subglaciescola	strain=ACAM 12	GCA_900142895.1	29571	29571	type	True	100.0	1033	1036	95	conclusive
Halomonas jeotgali	strain=Hwa	GCA_000334215.1	553386	553386	type	True	82.1504	647	1036	95	below_threshold
Halomonas massiliensis	strain=Marseille-P2426	GCA_900155385.1	1816686	1816686	type	True	79.0709	395	1036	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	79.0007	387	1036	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	78.9685	444	1036	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	78.9575	386	1036	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	78.7771	405	1036	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.6873	392	1036	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	78.6533	395	1036	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	78.5911	395	1036	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	78.5902	342	1036	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	78.5898	306	1036	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.5442	353	1036	95	below_threshold
Halomonas litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	78.4917	347	1036	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.4129	322	1036	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	78.3776	311	1036	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.3626	358	1036	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.2316	341	1036	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	78.089	257	1036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:19,739] [INFO] DFAST Taxonomy check result was written to GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:31:19,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:19,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:19,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0045cd4-9ad9-42e9-8093-919fd4ca6e67/dqc_reference/checkm_data
[2024-01-24 12:31:19,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:19,773] [INFO] Task started: CheckM
[2024-01-24 12:31:19,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/checkm_input GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:31:51,705] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:51,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:51,727] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:51,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:51,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:31:51,729] [INFO] Task started: Blastn
[2024-01-24 12:31:51,729] [INFO] Running command: blastn -query GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0045cd4-9ad9-42e9-8093-919fd4ca6e67/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:53,183] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:53,188] [INFO] Selected 21 target genomes.
[2024-01-24 12:31:53,189] [INFO] Target genome list was writen to GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:53,203] [INFO] Task started: fastANI
[2024-01-24 12:31:53,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg7512c1a9-6c54-4569-adcb-7c1d7d6d8bb3/GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna.gz --refList GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:09,178] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:09,200] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:09,201] [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_900142895.1	s__Halomonas subglaciescola	100.0	1034	1036	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_000334215.1	s__Halomonas jeotgali	82.1523	648	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686925.1	s__Halomonas sp000686925	79.3023	402	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001971685.1	s__Halomonas_B sp001971685	79.2356	388	1036	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_010977575.1	s__Halomonas_B socia	79.1011	375	1036	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_900155385.1	s__Halomonas massiliensis	79.0617	395	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.38	98.38	0.88	0.88	2	-
GCF_000265245.1	s__Halomonas smyrnensis	78.9867	387	1036	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	78.9402	388	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_009846525.1	s__Halomonas sp002696125	78.9398	341	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_014840935.1	s__Halomonas_E sp014840935	78.9329	337	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005780185.1	s__Halomonas urmiana	78.9016	408	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000275725.1	s__Halomonas stevensii	78.8523	385	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_900104135.1	s__Halomonas shengliensis	78.7836	404	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_014651775.1	s__Halomonas hamiltonii	78.7558	372	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_014193375.1	s__Halomonas campaniensis	78.7022	390	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731955.1	s__Halomonas_C zincidurans	78.6089	308	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003045775.1	s__Halomonas litopenaei	78.5068	345	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.31	97.80	0.93	0.89	11	-
GCF_011742165.1	s__Halomonas bachuensis	78.349	314	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206575.1	s__Salinicola endophyticus	78.1024	256	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
GCF_014897985.1	s__Halomonas sp014897985	77.9704	278	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.34	98.34	0.90	0.90	2	-
GCF_001651035.1	s__Halomonas sp001651035	77.9678	278	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.79	97.57	0.91	0.81	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:09,203] [INFO] GTDB search result was written to GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:09,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:09,209] [INFO] DFAST_QC result json was written to GCF_900142895.1_IMG-taxon_2698536942_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:32:09,209] [INFO] DFAST_QC completed!
[2024-01-24 12:32:09,209] [INFO] Total running time: 0h1m17s