[2024-01-24 15:14:52,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:52,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:52,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b1366ef-3e0d-4503-b364-bdbb30c39732/dqc_reference
[2024-01-24 15:14:53,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:53,620] [INFO] Task started: Prodigal
[2024-01-24 15:14:53,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg1fbfac56-24d6-408f-86fc-b23432d8e242/GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/cds.fna -a GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:06,971] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:06,971] [INFO] Task started: HMMsearch
[2024-01-24 15:15:06,972] [INFO] Running command: hmmsearch --tblout GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b1366ef-3e0d-4503-b364-bdbb30c39732/dqc_reference/reference_markers.hmm GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:07,238] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:07,241] [INFO] Found 6/6 markers.
[2024-01-24 15:15:07,287] [INFO] Query marker FASTA was written to GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:15:07,288] [INFO] Task started: Blastn
[2024-01-24 15:15:07,288] [INFO] Running command: blastn -query GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b1366ef-3e0d-4503-b364-bdbb30c39732/dqc_reference/reference_markers.fasta -out GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:08,186] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:08,189] [INFO] Selected 18 target genomes.
[2024-01-24 15:15:08,190] [INFO] Target genome list was writen to GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:15:08,197] [INFO] Task started: fastANI
[2024-01-24 15:15:08,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fbfac56-24d6-408f-86fc-b23432d8e242/GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna.gz --refList GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:22,854] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:22,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b1366ef-3e0d-4503-b364-bdbb30c39732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:22,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b1366ef-3e0d-4503-b364-bdbb30c39732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:22,870] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:15:22,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:22,871] [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 xianhensis	strain=CGMCC 1.6848	GCA_900113605.1	442341	442341	type	True	100.0	1429	1432	95	conclusive
Halomonas lutea	strain=DSM 23508	GCA_000378505.1	453962	453962	type	True	83.5356	1002	1432	95	below_threshold
Halomonas lutea	strain=KCTC 12847	GCA_014651575.1	453962	453962	type	True	83.5166	1010	1432	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	80.7498	629	1432	95	below_threshold
Halomonas ilicicola	strain=DSM 19980	GCA_900128925.1	480814	480814	type	True	80.3916	611	1432	95	below_threshold
Halomonas muralis	strain=DSM 14789	GCA_900102945.1	119000	119000	type	True	79.9788	640	1432	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	79.9446	499	1432	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.8903	567	1432	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	79.8752	534	1432	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	79.8732	531	1432	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	79.663	523	1432	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	79.6574	508	1432	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	79.5502	507	1432	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	79.5398	491	1432	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.48	528	1432	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	79.2853	493	1432	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	79.219	491	1432	95	below_threshold
Salinicola rhizosphaerae	strain=KCTC 32998	GCA_014652715.1	1443141	1443141	type	True	78.3217	357	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:22,873] [INFO] DFAST Taxonomy check result was written to GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:15:22,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:22,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:22,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b1366ef-3e0d-4503-b364-bdbb30c39732/dqc_reference/checkm_data
[2024-01-24 15:15:22,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:22,917] [INFO] Task started: CheckM
[2024-01-24 15:15:22,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/checkm_input GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:16:04,036] [INFO] Task succeeded: CheckM
[2024-01-24 15:16:04,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:16:04,058] [INFO] ===== Completeness check finished =====
[2024-01-24 15:16:04,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:16:04,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:16:04,059] [INFO] Task started: Blastn
[2024-01-24 15:16:04,059] [INFO] Running command: blastn -query GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b1366ef-3e0d-4503-b364-bdbb30c39732/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:16:05,448] [INFO] Task succeeded: Blastn
[2024-01-24 15:16:05,452] [INFO] Selected 20 target genomes.
[2024-01-24 15:16:05,453] [INFO] Target genome list was writen to GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:16:05,469] [INFO] Task started: fastANI
[2024-01-24 15:16:05,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fbfac56-24d6-408f-86fc-b23432d8e242/GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna.gz --refList GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:16:20,757] [INFO] Task succeeded: fastANI
[2024-01-24 15:16:20,778] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:16:20,778] [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_900113605.1	s__Halomonas_C xianhensis	100.0	1429	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	96.25	96.25	0.87	0.87	2	conclusive
GCF_000378505.1	s__Halomonas_C lutea	83.5315	1000	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010993675.1	s__Halomonas_C sp010993675	80.8796	627	1432	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_000731955.1	s__Halomonas_C zincidurans	80.7176	634	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001577635.1	s__Halomonas_C sp001577635	80.7069	643	1432	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_004117855.1	s__Halomonas_C coralii	80.4847	683	1432	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_900128925.1	s__Halomonas_C ilicicola	80.3916	611	1432	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_900102945.1	s__Halomonas_C muralis	79.9871	639	1432	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_009363755.1	s__Halomonas sp009363755	79.9285	507	1432	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	79.845	537	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989465.1	s__Halomonas halophila	79.8428	534	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_900104135.1	s__Halomonas shengliensis	79.6727	507	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_015645095.1	s__Halomonas_F sp015645095	79.3609	517	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989625.1	s__Halomonas_F pacifica	79.2334	490	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	98.81	98.81	0.96	0.96	2	-
GCF_004361885.1	s__Halomonas ventosae_C	79.115	430	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129225.1	s__Halomonas sp007129225	78.6343	318	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298015.1	s__Salinicola sp008298015	78.4473	417	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000272025.2	s__AKCV01 sp000272025	75.4632	73	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AKCV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:16:20,780] [INFO] GTDB search result was written to GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:16:20,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:16:20,788] [INFO] DFAST_QC result json was written to GCF_900113605.1_IMG-taxon_2617270878_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:16:20,788] [INFO] DFAST_QC completed!
[2024-01-24 15:16:20,788] [INFO] Total running time: 0h1m28s