[2024-01-24 12:13:42,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:42,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:42,808] [INFO] DQC Reference Directory: /var/lib/cwl/stged55e3b8-a809-4f23-bbab-5c3886572063/dqc_reference
[2024-01-24 12:13:44,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:44,221] [INFO] Task started: Prodigal
[2024-01-24 12:13:44,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg284d6126-c243-4a52-aa50-b602425b4960/GCF_030704205.1_ASM3070420v1_genomic.fna.gz | prodigal -d GCF_030704205.1_ASM3070420v1_genomic.fna/cds.fna -a GCF_030704205.1_ASM3070420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:54,982] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:54,982] [INFO] Task started: HMMsearch
[2024-01-24 12:13:54,982] [INFO] Running command: hmmsearch --tblout GCF_030704205.1_ASM3070420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged55e3b8-a809-4f23-bbab-5c3886572063/dqc_reference/reference_markers.hmm GCF_030704205.1_ASM3070420v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:55,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:55,350] [INFO] Found 6/6 markers.
[2024-01-24 12:13:55,388] [INFO] Query marker FASTA was written to GCF_030704205.1_ASM3070420v1_genomic.fna/markers.fasta
[2024-01-24 12:13:55,389] [INFO] Task started: Blastn
[2024-01-24 12:13:55,389] [INFO] Running command: blastn -query GCF_030704205.1_ASM3070420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged55e3b8-a809-4f23-bbab-5c3886572063/dqc_reference/reference_markers.fasta -out GCF_030704205.1_ASM3070420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:56,323] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:56,327] [INFO] Selected 20 target genomes.
[2024-01-24 12:13:56,328] [INFO] Target genome list was writen to GCF_030704205.1_ASM3070420v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:56,335] [INFO] Task started: fastANI
[2024-01-24 12:13:56,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg284d6126-c243-4a52-aa50-b602425b4960/GCF_030704205.1_ASM3070420v1_genomic.fna.gz --refList GCF_030704205.1_ASM3070420v1_genomic.fna/target_genomes.txt --output GCF_030704205.1_ASM3070420v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:14,968] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:14,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged55e3b8-a809-4f23-bbab-5c3886572063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:14,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged55e3b8-a809-4f23-bbab-5c3886572063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:14,986] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:14,987] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:14,987] [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 campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	88.9561	906	1203	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	87.1467	825	1203	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	86.015	797	1203	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	85.5563	809	1203	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	85.5269	835	1203	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	85.5148	780	1203	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	85.3887	840	1203	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	84.0686	704	1203	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	84.0345	784	1203	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	83.8197	764	1203	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	83.4173	742	1203	95	below_threshold
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	83.2606	737	1203	95	below_threshold
Halomonas cerina	strain=CECT 7282	GCA_014192215.1	447424	447424	type	True	83.1221	754	1203	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	83.0677	739	1203	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	82.7896	771	1203	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	82.4049	709	1203	95	below_threshold
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	76.6086	126	1203	95	below_threshold
Pseudomonas syringae pv. coryli	strain=NCPPB 4273	GCA_000972175.1	317659	317659	pathovar	True	76.5235	142	1203	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	76.5166	226	1203	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	75.6276	62	1203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:14,989] [INFO] DFAST Taxonomy check result was written to GCF_030704205.1_ASM3070420v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:14,989] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:14,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:14,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged55e3b8-a809-4f23-bbab-5c3886572063/dqc_reference/checkm_data
[2024-01-24 12:14:14,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:15,034] [INFO] Task started: CheckM
[2024-01-24 12:14:15,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030704205.1_ASM3070420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030704205.1_ASM3070420v1_genomic.fna/checkm_input GCF_030704205.1_ASM3070420v1_genomic.fna/checkm_result
[2024-01-24 12:14:53,205] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:53,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:53,231] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:53,231] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:53,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030704205.1_ASM3070420v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:53,232] [INFO] Task started: Blastn
[2024-01-24 12:14:53,232] [INFO] Running command: blastn -query GCF_030704205.1_ASM3070420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged55e3b8-a809-4f23-bbab-5c3886572063/dqc_reference/reference_markers_gtdb.fasta -out GCF_030704205.1_ASM3070420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:54,842] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:54,847] [INFO] Selected 16 target genomes.
[2024-01-24 12:14:54,848] [INFO] Target genome list was writen to GCF_030704205.1_ASM3070420v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:54,860] [INFO] Task started: fastANI
[2024-01-24 12:14:54,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg284d6126-c243-4a52-aa50-b602425b4960/GCF_030704205.1_ASM3070420v1_genomic.fna.gz --refList GCF_030704205.1_ASM3070420v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030704205.1_ASM3070420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:09,218] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:09,240] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:09,241] [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_003182195.1	s__Halomonas sp003182195	95.4958	877	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	conclusive
GCA_014859505.1	s__Halomonas sp014859505	90.5355	776	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552795.1	s__Halomonas sp003552795	89.2807	623	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	88.9388	907	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553625.1	s__Halomonas sp003553625	87.7771	689	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.58	0.84	0.80	4	-
GCF_900104135.1	s__Halomonas shengliensis	87.1594	823	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCA_018401555.1	s__Halomonas sp018401555	86.078	741	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009902005.1	s__Halomonas alimentaria	85.9969	798	1203	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	85.566	808	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003202205.1	s__Halomonas sp003202205	85.3368	806	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361885.1	s__Halomonas ventosae_C	83.5426	675	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620045.1	s__Halomonas halodenitrificans	83.2431	740	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.15	97.15	0.89	0.89	2	-
GCF_014192215.1	s__Halomonas cerina	83.111	755	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100195.1	s__Halomonas gudaonensis	82.8691	738	1203	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	82.3564	703	1203	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	79.6956	155	1203	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 12:15:09,243] [INFO] GTDB search result was written to GCF_030704205.1_ASM3070420v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:09,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:09,252] [INFO] DFAST_QC result json was written to GCF_030704205.1_ASM3070420v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:09,252] [INFO] DFAST_QC completed!
[2024-01-24 12:15:09,252] [INFO] Total running time: 0h1m26s