[2024-01-25 17:58:50,593] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:50,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:50,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg10f0f1bc-4980-401e-93c8-28fb1fe34ac8/dqc_reference
[2024-01-25 17:58:51,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:51,762] [INFO] Task started: Prodigal
[2024-01-25 17:58:51,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d22c7a5-1cc4-4709-b77e-318b327026f3/GCF_009664385.2_ASM966438v2_genomic.fna.gz | prodigal -d GCF_009664385.2_ASM966438v2_genomic.fna/cds.fna -a GCF_009664385.2_ASM966438v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:58:57,861] [INFO] Task succeeded: Prodigal
[2024-01-25 17:58:57,861] [INFO] Task started: HMMsearch
[2024-01-25 17:58:57,861] [INFO] Running command: hmmsearch --tblout GCF_009664385.2_ASM966438v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10f0f1bc-4980-401e-93c8-28fb1fe34ac8/dqc_reference/reference_markers.hmm GCF_009664385.2_ASM966438v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:58:58,051] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:58:58,052] [INFO] Found 6/6 markers.
[2024-01-25 17:58:58,077] [INFO] Query marker FASTA was written to GCF_009664385.2_ASM966438v2_genomic.fna/markers.fasta
[2024-01-25 17:58:58,077] [INFO] Task started: Blastn
[2024-01-25 17:58:58,077] [INFO] Running command: blastn -query GCF_009664385.2_ASM966438v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg10f0f1bc-4980-401e-93c8-28fb1fe34ac8/dqc_reference/reference_markers.fasta -out GCF_009664385.2_ASM966438v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:58:59,247] [INFO] Task succeeded: Blastn
[2024-01-25 17:58:59,250] [INFO] Selected 21 target genomes.
[2024-01-25 17:58:59,251] [INFO] Target genome list was writen to GCF_009664385.2_ASM966438v2_genomic.fna/target_genomes.txt
[2024-01-25 17:58:59,261] [INFO] Task started: fastANI
[2024-01-25 17:58:59,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d22c7a5-1cc4-4709-b77e-318b327026f3/GCF_009664385.2_ASM966438v2_genomic.fna.gz --refList GCF_009664385.2_ASM966438v2_genomic.fna/target_genomes.txt --output GCF_009664385.2_ASM966438v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:16,192] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:16,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10f0f1bc-4980-401e-93c8-28fb1fe34ac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:16,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10f0f1bc-4980-401e-93c8-28fb1fe34ac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:16,205] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:59:16,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:59:16,206] [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
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	100.0	806	811	95	conclusive
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	99.9957	811	811	95	conclusive
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	81.5361	469	811	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	81.5133	466	811	95	below_threshold
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	81.177	481	811	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	80.2635	425	811	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.5677	431	811	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	79.3091	349	811	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	79.2738	397	811	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	79.2679	442	811	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.1949	366	811	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.1946	403	811	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	79.074	346	811	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	79.0547	350	811	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	79.0522	347	811	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	79.0167	353	811	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	76.1245	266	811	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	75.972	234	811	95	below_threshold
Allorhizocola rhizosphaerae	strain=CPCC 204380	GCA_003426775.1	1872709	1872709	type	True	75.9552	152	811	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	75.8806	239	811	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	75.7624	232	811	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:16,207] [INFO] DFAST Taxonomy check result was written to GCF_009664385.2_ASM966438v2_genomic.fna/tc_result.tsv
[2024-01-25 17:59:16,207] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:16,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:16,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10f0f1bc-4980-401e-93c8-28fb1fe34ac8/dqc_reference/checkm_data
[2024-01-25 17:59:16,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:16,235] [INFO] Task started: CheckM
[2024-01-25 17:59:16,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009664385.2_ASM966438v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009664385.2_ASM966438v2_genomic.fna/checkm_input GCF_009664385.2_ASM966438v2_genomic.fna/checkm_result
[2024-01-25 17:59:39,754] [INFO] Task succeeded: CheckM
[2024-01-25 17:59:39,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:59:39,770] [INFO] ===== Completeness check finished =====
[2024-01-25 17:59:39,770] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:59:39,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009664385.2_ASM966438v2_genomic.fna/markers.fasta)
[2024-01-25 17:59:39,771] [INFO] Task started: Blastn
[2024-01-25 17:59:39,771] [INFO] Running command: blastn -query GCF_009664385.2_ASM966438v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg10f0f1bc-4980-401e-93c8-28fb1fe34ac8/dqc_reference/reference_markers_gtdb.fasta -out GCF_009664385.2_ASM966438v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:41,805] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:41,807] [INFO] Selected 16 target genomes.
[2024-01-25 17:59:41,808] [INFO] Target genome list was writen to GCF_009664385.2_ASM966438v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:59:41,825] [INFO] Task started: fastANI
[2024-01-25 17:59:41,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d22c7a5-1cc4-4709-b77e-318b327026f3/GCF_009664385.2_ASM966438v2_genomic.fna.gz --refList GCF_009664385.2_ASM966438v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009664385.2_ASM966438v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:59:53,069] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:53,079] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:59:53,079] [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_014200395.1	s__Chryseoglobus frigidaquae	99.9957	811	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_001464255.1	s__Chryseoglobus sp001464255	86.589	444	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280615.1	s__Chryseoglobus sp002280615	86.4708	363	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	83.8367	562	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425665.1	s__Yonghaparkia sp001425665	83.396	560	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	99.25	99.25	0.97	0.97	2	-
GCA_012530535.1	s__Yonghaparkia sp012530535	83.1467	541	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502445.1	s__Yonghaparkia sp005502445	83.1122	479	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137945.1	s__Yonghaparkia alkaliphila	82.5586	535	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823625.1	s__Chryseoglobus sp013823625	82.4268	560	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013414345.1	s__Marinisubtilis indicus	82.2982	531	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
GCA_013297625.1	s__Chryseoglobus sp013297625	82.2813	480	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777405.1	s__Chryseoglobus sp005777405	80.6124	404	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720635.1	s__Kitasatospora sp000720635	76.3387	249	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284295.1	s__Actinoplanes missouriensis	76.116	235	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426775.1	s__Allorhizocola rhizosphaerae	75.9655	151	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Allorhizocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:59:53,080] [INFO] GTDB search result was written to GCF_009664385.2_ASM966438v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:59:53,081] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:59:53,084] [INFO] DFAST_QC result json was written to GCF_009664385.2_ASM966438v2_genomic.fna/dqc_result.json
[2024-01-25 17:59:53,084] [INFO] DFAST_QC completed!
[2024-01-25 17:59:53,084] [INFO] Total running time: 0h1m2s