[2024-01-24 13:55:19,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,217] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg30aa18d5-0a0e-4a26-9eb7-7571521dd51d/dqc_reference
[2024-01-24 13:55:20,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:20,643] [INFO] Task started: Prodigal
[2024-01-24 13:55:20,643] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc28108b-b039-42ab-9510-f0aa09b2d141/GCF_000620045.1_ASM62004v1_genomic.fna.gz | prodigal -d GCF_000620045.1_ASM62004v1_genomic.fna/cds.fna -a GCF_000620045.1_ASM62004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:31,331] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:31,331] [INFO] Task started: HMMsearch
[2024-01-24 13:55:31,331] [INFO] Running command: hmmsearch --tblout GCF_000620045.1_ASM62004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30aa18d5-0a0e-4a26-9eb7-7571521dd51d/dqc_reference/reference_markers.hmm GCF_000620045.1_ASM62004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:31,656] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:31,657] [INFO] Found 6/6 markers.
[2024-01-24 13:55:31,687] [INFO] Query marker FASTA was written to GCF_000620045.1_ASM62004v1_genomic.fna/markers.fasta
[2024-01-24 13:55:31,688] [INFO] Task started: Blastn
[2024-01-24 13:55:31,688] [INFO] Running command: blastn -query GCF_000620045.1_ASM62004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30aa18d5-0a0e-4a26-9eb7-7571521dd51d/dqc_reference/reference_markers.fasta -out GCF_000620045.1_ASM62004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:32,517] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:32,520] [INFO] Selected 22 target genomes.
[2024-01-24 13:55:32,520] [INFO] Target genome list was writen to GCF_000620045.1_ASM62004v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:32,534] [INFO] Task started: fastANI
[2024-01-24 13:55:32,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc28108b-b039-42ab-9510-f0aa09b2d141/GCF_000620045.1_ASM62004v1_genomic.fna.gz --refList GCF_000620045.1_ASM62004v1_genomic.fna/target_genomes.txt --output GCF_000620045.1_ASM62004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:51,241] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:51,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30aa18d5-0a0e-4a26-9eb7-7571521dd51d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:51,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30aa18d5-0a0e-4a26-9eb7-7571521dd51d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:51,260] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:51,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:51,260] [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 halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	100.0	1123	1128	95	conclusive
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	86.2011	833	1128	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	86.0376	816	1128	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	85.1328	805	1128	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	83.2849	749	1128	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	82.8841	747	1128	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	82.8591	728	1128	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	82.41	706	1128	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	82.1937	692	1128	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	81.7792	684	1128	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	81.6035	692	1128	95	below_threshold
Halomonas cerina	strain=CECT 7282	GCA_014192215.1	447424	447424	type	True	81.3223	643	1128	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	81.1454	623	1128	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	81.1293	643	1128	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	80.9134	609	1128	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	80.7834	619	1128	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	80.5583	562	1128	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	80.4297	597	1128	95	below_threshold
Chromohalobacter japonicus	strain=CECT 7219	GCA_023061175.1	223900	223900	type	True	78.1626	287	1128	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	76.1994	73	1128	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	75.8143	113	1128	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.5341	79	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:51,262] [INFO] DFAST Taxonomy check result was written to GCF_000620045.1_ASM62004v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:51,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:51,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:51,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30aa18d5-0a0e-4a26-9eb7-7571521dd51d/dqc_reference/checkm_data
[2024-01-24 13:55:51,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:51,305] [INFO] Task started: CheckM
[2024-01-24 13:55:51,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000620045.1_ASM62004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000620045.1_ASM62004v1_genomic.fna/checkm_input GCF_000620045.1_ASM62004v1_genomic.fna/checkm_result
[2024-01-24 13:56:24,669] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:24,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:24,690] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:24,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:24,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000620045.1_ASM62004v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:24,691] [INFO] Task started: Blastn
[2024-01-24 13:56:24,691] [INFO] Running command: blastn -query GCF_000620045.1_ASM62004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30aa18d5-0a0e-4a26-9eb7-7571521dd51d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000620045.1_ASM62004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:26,068] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:26,072] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:26,073] [INFO] Target genome list was writen to GCF_000620045.1_ASM62004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:26,103] [INFO] Task started: fastANI
[2024-01-24 13:56:26,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc28108b-b039-42ab-9510-f0aa09b2d141/GCF_000620045.1_ASM62004v1_genomic.fna.gz --refList GCF_000620045.1_ASM62004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000620045.1_ASM62004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:39,456] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:39,470] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:39,470] [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_000620045.1	s__Halomonas halodenitrificans	100.0	1123	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.15	97.15	0.89	0.89	2	conclusive
GCF_015595025.1	s__Halomonas sp015595025	86.9928	855	1128	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	86.201	833	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.73	97.73	0.87	0.87	2	-
GCF_009902005.1	s__Halomonas alimentaria	86.0376	816	1128	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	85.9521	728	1128	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	85.1295	806	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_003182195.1	s__Halomonas sp003182195	83.3606	666	1128	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	82.8758	748	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_009363755.1	s__Halomonas sp009363755	82.8175	731	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859505.1	s__Halomonas sp014859505	82.7477	631	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192215.1	s__Halomonas cerina	81.2974	645	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286975.1	s__Halomonas_B sp002286975	80.8909	612	1128	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_001971685.1	s__Halomonas_B sp001971685	80.8188	604	1128	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_017868935.1	s__Halomonas sp017868935	80.7689	620	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779595.1	s__Halomonas_B sp014779595	80.2692	565	1128	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_002374315.1	s__Halomonas nigrificans	78.2453	135	1128	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 13:56:39,472] [INFO] GTDB search result was written to GCF_000620045.1_ASM62004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:39,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:39,477] [INFO] DFAST_QC result json was written to GCF_000620045.1_ASM62004v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:39,477] [INFO] DFAST_QC completed!
[2024-01-24 13:56:39,477] [INFO] Total running time: 0h1m20s