[2024-01-24 13:49:55,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,769] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,770] [INFO] DQC Reference Directory: /var/lib/cwl/stgde9b9910-02a6-4a05-bc5e-d01a7579c758/dqc_reference
[2024-01-24 13:49:57,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:57,224] [INFO] Task started: Prodigal
[2024-01-24 13:49:57,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg75bf9a49-13e4-4240-9f51-dc95665c5ef1/GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/cds.fna -a GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:10,967] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:10,968] [INFO] Task started: HMMsearch
[2024-01-24 13:50:10,968] [INFO] Running command: hmmsearch --tblout GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde9b9910-02a6-4a05-bc5e-d01a7579c758/dqc_reference/reference_markers.hmm GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:11,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:11,267] [INFO] Found 6/6 markers.
[2024-01-24 13:50:11,315] [INFO] Query marker FASTA was written to GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:50:11,315] [INFO] Task started: Blastn
[2024-01-24 13:50:11,315] [INFO] Running command: blastn -query GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgde9b9910-02a6-4a05-bc5e-d01a7579c758/dqc_reference/reference_markers.fasta -out GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:12,325] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:12,328] [INFO] Selected 21 target genomes.
[2024-01-24 13:50:12,328] [INFO] Target genome list was writen to GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:50:12,331] [INFO] Task started: fastANI
[2024-01-24 13:50:12,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg75bf9a49-13e4-4240-9f51-dc95665c5ef1/GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna.gz --refList GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:33,392] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:33,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde9b9910-02a6-4a05-bc5e-d01a7579c758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:33,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde9b9910-02a6-4a05-bc5e-d01a7579c758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:33,411] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:33,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:33,412] [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 pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	100.0	1445	1448	95	conclusive
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	88.8771	1221	1448	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	82.3307	827	1448	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	82.3159	803	1448	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	82.2676	820	1448	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	82.2589	756	1448	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	82.0608	713	1448	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	82.0538	640	1448	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	82.0089	770	1448	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	81.9809	802	1448	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	81.8776	697	1448	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	81.8245	709	1448	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	81.6431	706	1448	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	81.4634	735	1448	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	81.4588	709	1448	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	81.3853	686	1448	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.372	792	1448	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	81.0062	722	1448	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	80.9595	728	1448	95	below_threshold
Halomonas cerina	strain=CECT 7282	GCA_014192215.1	447424	447424	type	True	80.8757	633	1448	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	80.6953	656	1448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:33,414] [INFO] DFAST Taxonomy check result was written to GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:50:33,414] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:33,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:33,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde9b9910-02a6-4a05-bc5e-d01a7579c758/dqc_reference/checkm_data
[2024-01-24 13:50:33,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:33,457] [INFO] Task started: CheckM
[2024-01-24 13:50:33,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/checkm_input GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:51:12,988] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:12,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,010] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:13,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:13,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:51:13,012] [INFO] Task started: Blastn
[2024-01-24 13:51:13,012] [INFO] Running command: blastn -query GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgde9b9910-02a6-4a05-bc5e-d01a7579c758/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:14,708] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:14,712] [INFO] Selected 7 target genomes.
[2024-01-24 13:51:14,712] [INFO] Target genome list was writen to GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:14,730] [INFO] Task started: fastANI
[2024-01-24 13:51:14,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg75bf9a49-13e4-4240-9f51-dc95665c5ef1/GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna.gz --refList GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:23,192] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:23,202] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:23,202] [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_900102875.1	s__Halomonas_B pantelleriensis	100.0	1445	1448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001971685.1	s__Halomonas_B sp001971685	88.9083	1115	1448	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_002286975.1	s__Halomonas_B sp002286975	88.8712	1221	1448	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	88.3715	1154	1448	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	87.61	1227	1448	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_000265245.1	s__Halomonas smyrnensis	81.9996	645	1448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_014840935.1	s__Halomonas_E sp014840935	81.5189	633	1448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:23,204] [INFO] GTDB search result was written to GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:23,204] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:23,208] [INFO] DFAST_QC result json was written to GCF_900102875.1_IMG-taxon_2654587879_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:51:23,208] [INFO] DFAST_QC completed!
[2024-01-24 13:51:23,208] [INFO] Total running time: 0h1m27s