[2024-01-24 12:29:52,670] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:52,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:52,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg41ae8d00-c876-4de4-aa14-c7f47950e75f/dqc_reference
[2024-01-24 12:29:53,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:53,873] [INFO] Task started: Prodigal
[2024-01-24 12:29:53,874] [INFO] Running command: gunzip -c /var/lib/cwl/stge28e1039-df14-4989-903b-7d1e725b2900/GCF_015265475.1_ASM1526547v1_genomic.fna.gz | prodigal -d GCF_015265475.1_ASM1526547v1_genomic.fna/cds.fna -a GCF_015265475.1_ASM1526547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:58,478] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:58,478] [INFO] Task started: HMMsearch
[2024-01-24 12:29:58,479] [INFO] Running command: hmmsearch --tblout GCF_015265475.1_ASM1526547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41ae8d00-c876-4de4-aa14-c7f47950e75f/dqc_reference/reference_markers.hmm GCF_015265475.1_ASM1526547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:58,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:58,707] [INFO] Found 6/6 markers.
[2024-01-24 12:29:58,733] [INFO] Query marker FASTA was written to GCF_015265475.1_ASM1526547v1_genomic.fna/markers.fasta
[2024-01-24 12:29:58,733] [INFO] Task started: Blastn
[2024-01-24 12:29:58,733] [INFO] Running command: blastn -query GCF_015265475.1_ASM1526547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41ae8d00-c876-4de4-aa14-c7f47950e75f/dqc_reference/reference_markers.fasta -out GCF_015265475.1_ASM1526547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:59,328] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:59,331] [INFO] Selected 11 target genomes.
[2024-01-24 12:29:59,331] [INFO] Target genome list was writen to GCF_015265475.1_ASM1526547v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:59,341] [INFO] Task started: fastANI
[2024-01-24 12:29:59,341] [INFO] Running command: fastANI --query /var/lib/cwl/stge28e1039-df14-4989-903b-7d1e725b2900/GCF_015265475.1_ASM1526547v1_genomic.fna.gz --refList GCF_015265475.1_ASM1526547v1_genomic.fna/target_genomes.txt --output GCF_015265475.1_ASM1526547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:04,355] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:04,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41ae8d00-c876-4de4-aa14-c7f47950e75f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:04,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41ae8d00-c876-4de4-aa14-c7f47950e75f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:04,365] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:04,366] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:04,366] [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
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	100.0	827	829	95	conclusive
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	88.9396	664	829	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	79.5457	330	829	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	79.3737	331	829	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	78.7969	235	829	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	78.5931	240	829	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.9617	193	829	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	77.8715	188	829	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	77.3614	151	829	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	76.968	66	829	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:04,368] [INFO] DFAST Taxonomy check result was written to GCF_015265475.1_ASM1526547v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:04,369] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:04,369] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:04,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41ae8d00-c876-4de4-aa14-c7f47950e75f/dqc_reference/checkm_data
[2024-01-24 12:30:04,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:04,406] [INFO] Task started: CheckM
[2024-01-24 12:30:04,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015265475.1_ASM1526547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015265475.1_ASM1526547v1_genomic.fna/checkm_input GCF_015265475.1_ASM1526547v1_genomic.fna/checkm_result
[2024-01-24 12:30:25,460] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:25,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:25,476] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:25,476] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:25,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015265475.1_ASM1526547v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:25,477] [INFO] Task started: Blastn
[2024-01-24 12:30:25,477] [INFO] Running command: blastn -query GCF_015265475.1_ASM1526547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41ae8d00-c876-4de4-aa14-c7f47950e75f/dqc_reference/reference_markers_gtdb.fasta -out GCF_015265475.1_ASM1526547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:26,259] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:26,262] [INFO] Selected 17 target genomes.
[2024-01-24 12:30:26,262] [INFO] Target genome list was writen to GCF_015265475.1_ASM1526547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:26,275] [INFO] Task started: fastANI
[2024-01-24 12:30:26,275] [INFO] Running command: fastANI --query /var/lib/cwl/stge28e1039-df14-4989-903b-7d1e725b2900/GCF_015265475.1_ASM1526547v1_genomic.fna.gz --refList GCF_015265475.1_ASM1526547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015265475.1_ASM1526547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:33,542] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:33,562] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:33,563] [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_015265475.1	s__Sulfurimonas marisnigri	100.0	828	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015265455.1	s__Sulfurimonas baltica	88.9242	665	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242915.1	s__Sulfurimonas gotlandica	79.5987	328	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002732645.1	s__Sulfurimonas sp002732645	79.0701	184	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744025.1	s__Sulfurimonas sp016744025	78.6404	288	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903705.1	s__Sulfurimonas sp903903705	78.5429	129	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009883775.1	s__Sulfurimonas sp002452895	78.5005	239	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.89	98.30	0.92	0.92	4	-
GCA_002781365.1	s__Sulfurimonas sp002781365	78.3494	220	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.89	0.98	0.96	19	-
GCA_001829675.1	s__Sulfurimonas sp001829675	78.3466	248	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.77	99.75	0.96	0.96	4	-
GCA_001873135.1	s__Sulfurimonas sp001873135	78.3367	194	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829785.1	s__Sulfurimonas sp001829785	78.287	249	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.93	99.89	1.00	1.00	4	-
GCA_002733155.1	s__Sulfurimonas sp002733155	78.2522	205	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829715.1	s__Sulfurimonas sp001829715	78.2501	212	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	-
GCA_001829625.1	s__Sulfurimonas sp001829625	78.0029	126	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.76	99.76	0.87	0.87	2	-
GCA_011391635.1	s__Sulfurimonas sp011391635	77.8801	175	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005217605.1	s__Sulfurimonas crateris	77.8715	188	829	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:33,564] [INFO] GTDB search result was written to GCF_015265475.1_ASM1526547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:33,565] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:33,569] [INFO] DFAST_QC result json was written to GCF_015265475.1_ASM1526547v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:33,569] [INFO] DFAST_QC completed!
[2024-01-24 12:30:33,569] [INFO] Total running time: 0h0m41s