[2024-01-25 19:48:05,523] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:05,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:05,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b3e2f0a-c5ef-4878-9c9d-45d747031281/dqc_reference
[2024-01-25 19:48:06,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:06,622] [INFO] Task started: Prodigal
[2024-01-25 19:48:06,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg379f64af-efee-4925-88e8-4c72a1c78677/GCF_000382245.1_ASM38224v1_genomic.fna.gz | prodigal -d GCF_000382245.1_ASM38224v1_genomic.fna/cds.fna -a GCF_000382245.1_ASM38224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:15,854] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:15,854] [INFO] Task started: HMMsearch
[2024-01-25 19:48:15,854] [INFO] Running command: hmmsearch --tblout GCF_000382245.1_ASM38224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b3e2f0a-c5ef-4878-9c9d-45d747031281/dqc_reference/reference_markers.hmm GCF_000382245.1_ASM38224v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:16,064] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:16,065] [INFO] Found 6/6 markers.
[2024-01-25 19:48:16,100] [INFO] Query marker FASTA was written to GCF_000382245.1_ASM38224v1_genomic.fna/markers.fasta
[2024-01-25 19:48:16,101] [INFO] Task started: Blastn
[2024-01-25 19:48:16,101] [INFO] Running command: blastn -query GCF_000382245.1_ASM38224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3e2f0a-c5ef-4878-9c9d-45d747031281/dqc_reference/reference_markers.fasta -out GCF_000382245.1_ASM38224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:16,852] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:16,855] [INFO] Selected 18 target genomes.
[2024-01-25 19:48:16,855] [INFO] Target genome list was writen to GCF_000382245.1_ASM38224v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:16,901] [INFO] Task started: fastANI
[2024-01-25 19:48:16,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg379f64af-efee-4925-88e8-4c72a1c78677/GCF_000382245.1_ASM38224v1_genomic.fna.gz --refList GCF_000382245.1_ASM38224v1_genomic.fna/target_genomes.txt --output GCF_000382245.1_ASM38224v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:31,276] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:31,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b3e2f0a-c5ef-4878-9c9d-45d747031281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:31,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b3e2f0a-c5ef-4878-9c9d-45d747031281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:31,287] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:48:31,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:31,288] [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
Kushneria aurantia	strain=DSM 21353	GCA_000382245.1	504092	504092	type	True	100.0	1207	1214	95	conclusive
Kushneria avicenniae	strain=DSM 23439	GCA_900112585.1	402385	402385	type	True	79.3867	536	1214	95	below_threshold
Kushneria indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	79.3035	553	1214	95	below_threshold
Kushneria sinocarnis	strain=DSM 23229	GCA_003633775.1	595502	595502	type	True	79.1746	441	1214	95	below_threshold
Kushneria pakistanensis	strain=KCTC 42082	GCA_014652795.1	1508770	1508770	type	True	78.9473	475	1214	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	78.9153	362	1214	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	78.8481	353	1214	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	78.6746	345	1214	95	below_threshold
Kushneria konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	78.65	472	1214	95	below_threshold
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	78.6157	483	1214	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.5653	354	1214	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	78.4832	361	1214	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.476	314	1214	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	78.4366	375	1214	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.2785	312	1214	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.2303	329	1214	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.1584	337	1214	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	78.0211	303	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:31,290] [INFO] DFAST Taxonomy check result was written to GCF_000382245.1_ASM38224v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:31,292] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:31,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:31,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b3e2f0a-c5ef-4878-9c9d-45d747031281/dqc_reference/checkm_data
[2024-01-25 19:48:31,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:31,336] [INFO] Task started: CheckM
[2024-01-25 19:48:31,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000382245.1_ASM38224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000382245.1_ASM38224v1_genomic.fna/checkm_input GCF_000382245.1_ASM38224v1_genomic.fna/checkm_result
[2024-01-25 19:49:00,705] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:00,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:00,726] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:00,726] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:00,727] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000382245.1_ASM38224v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:00,727] [INFO] Task started: Blastn
[2024-01-25 19:49:00,727] [INFO] Running command: blastn -query GCF_000382245.1_ASM38224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3e2f0a-c5ef-4878-9c9d-45d747031281/dqc_reference/reference_markers_gtdb.fasta -out GCF_000382245.1_ASM38224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:01,948] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:01,951] [INFO] Selected 17 target genomes.
[2024-01-25 19:49:01,951] [INFO] Target genome list was writen to GCF_000382245.1_ASM38224v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:01,966] [INFO] Task started: fastANI
[2024-01-25 19:49:01,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg379f64af-efee-4925-88e8-4c72a1c78677/GCF_000382245.1_ASM38224v1_genomic.fna.gz --refList GCF_000382245.1_ASM38224v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000382245.1_ASM38224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:15,043] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:15,054] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:15,054] [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_000382245.1	s__Kushneria aurantia	100.0	1207	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112585.1	s__Kushneria avicenniae	79.3855	536	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385845.1	s__Kushneria indalinina	79.3034	553	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633775.1	s__Kushneria sinocarnis	79.1746	441	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652795.1	s__Kushneria pakistanensis	78.9417	475	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	78.9123	363	1214	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	78.8943	451	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
GCF_009363755.1	s__Halomonas sp009363755	78.889	358	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254665.1	s__Halomonas lactosivorans	78.8412	354	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004551485.1	s__Halomonas azerbaijanica	78.7829	362	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005780185.1	s__Halomonas urmiana	78.6621	346	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155145.1	s__Kushneria konosiri	78.6506	472	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312995.1	s__Kushneria phyllosphaerae	78.619	482	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157205.1	s__Kushneria marisflavi	78.5396	484	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011742915.1	s__Halomonas desiderata	78.4411	354	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.30	98.24	0.88	0.88	3	-
GCF_000246875.1	s__Halomonas sp000246875	78.1786	325	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621205.1	s__Halotalea alkalilenta	77.6672	317	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halotalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:15,068] [INFO] GTDB search result was written to GCF_000382245.1_ASM38224v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:15,068] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:15,072] [INFO] DFAST_QC result json was written to GCF_000382245.1_ASM38224v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:15,072] [INFO] DFAST_QC completed!
[2024-01-25 19:49:15,072] [INFO] Total running time: 0h1m10s