[2024-01-24 11:26:28,063] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,065] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,065] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d89deb3-05df-4a54-b347-7c22959e348c/dqc_reference
[2024-01-24 11:26:29,459] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,460] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,460] [INFO] Running command: gunzip -c /var/lib/cwl/stg704476c6-9ed0-405c-a610-e5f573ed2c2a/GCF_030268045.1_ASM3026804v1_genomic.fna.gz | prodigal -d GCF_030268045.1_ASM3026804v1_genomic.fna/cds.fna -a GCF_030268045.1_ASM3026804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:38,958] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:38,959] [INFO] Task started: HMMsearch
[2024-01-24 11:26:38,959] [INFO] Running command: hmmsearch --tblout GCF_030268045.1_ASM3026804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d89deb3-05df-4a54-b347-7c22959e348c/dqc_reference/reference_markers.hmm GCF_030268045.1_ASM3026804v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:39,241] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:39,243] [INFO] Found 6/6 markers.
[2024-01-24 11:26:39,273] [INFO] Query marker FASTA was written to GCF_030268045.1_ASM3026804v1_genomic.fna/markers.fasta
[2024-01-24 11:26:39,274] [INFO] Task started: Blastn
[2024-01-24 11:26:39,274] [INFO] Running command: blastn -query GCF_030268045.1_ASM3026804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d89deb3-05df-4a54-b347-7c22959e348c/dqc_reference/reference_markers.fasta -out GCF_030268045.1_ASM3026804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:40,046] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:40,049] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:40,049] [INFO] Target genome list was writen to GCF_030268045.1_ASM3026804v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:40,060] [INFO] Task started: fastANI
[2024-01-24 11:26:40,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg704476c6-9ed0-405c-a610-e5f573ed2c2a/GCF_030268045.1_ASM3026804v1_genomic.fna.gz --refList GCF_030268045.1_ASM3026804v1_genomic.fna/target_genomes.txt --output GCF_030268045.1_ASM3026804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:57,024] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:57,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d89deb3-05df-4a54-b347-7c22959e348c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:57,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d89deb3-05df-4a54-b347-7c22959e348c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:57,038] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:57,038] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:57,038] [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
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	88.756	868	1051	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.6065	300	1051	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.0866	89	1051	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	75.7504	70	1051	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.6281	130	1051	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	75.6024	140	1051	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	75.5418	168	1051	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	75.5321	54	1051	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	75.4611	166	1051	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	75.4157	51	1051	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	75.3853	52	1051	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	75.3182	54	1051	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.1977	82	1051	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.0633	91	1051	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	74.8589	111	1051	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	74.8552	81	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:57,040] [INFO] DFAST Taxonomy check result was written to GCF_030268045.1_ASM3026804v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:57,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:57,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:57,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d89deb3-05df-4a54-b347-7c22959e348c/dqc_reference/checkm_data
[2024-01-24 11:26:57,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:57,075] [INFO] Task started: CheckM
[2024-01-24 11:26:57,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030268045.1_ASM3026804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030268045.1_ASM3026804v1_genomic.fna/checkm_input GCF_030268045.1_ASM3026804v1_genomic.fna/checkm_result
[2024-01-24 11:27:33,198] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:33,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,219] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:33,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:33,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030268045.1_ASM3026804v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:33,220] [INFO] Task started: Blastn
[2024-01-24 11:27:33,220] [INFO] Running command: blastn -query GCF_030268045.1_ASM3026804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d89deb3-05df-4a54-b347-7c22959e348c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030268045.1_ASM3026804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:34,440] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:34,444] [INFO] Selected 12 target genomes.
[2024-01-24 11:27:34,444] [INFO] Target genome list was writen to GCF_030268045.1_ASM3026804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:34,453] [INFO] Task started: fastANI
[2024-01-24 11:27:34,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg704476c6-9ed0-405c-a610-e5f573ed2c2a/GCF_030268045.1_ASM3026804v1_genomic.fna.gz --refList GCF_030268045.1_ASM3026804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030268045.1_ASM3026804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:43,873] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:43,887] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:43,887] [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_000428885.1	s__Geothrix fermentans	88.7531	868	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538615.1	s__Geothrix sp003538615	87.0729	592	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390615.1	s__Geothrix sp013390615	85.3175	779	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714685.1	s__Geothrix sp016714685	85.0143	739	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.39	97.91	0.89	0.88	4	-
GCA_017859995.1	s__Geothrix sp017859995	84.7224	686	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334395.1	s__Geothrix sp013334395	84.2399	566	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721195.1	s__Geothrix sp016721195	84.0602	756	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903863195.1	s__Geothrix sp903863195	83.936	659	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.63	99.47	0.91	0.90	5	-
GCA_016195985.1	s__Geothrix sp016195985	83.5654	739	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.98	99.98	0.99	0.99	2	-
GCA_903843705.1	s__Geothrix sp903843705	82.9663	619	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.09	98.86	0.88	0.85	6	-
GCA_903884655.1	s__Geothrix sp903884655	82.7668	670	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.96	99.93	0.97	0.97	3	-
GCA_903873655.1	s__Geothrix sp903873655	82.0506	560	1051	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.34	99.01	0.91	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:43,889] [INFO] GTDB search result was written to GCF_030268045.1_ASM3026804v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:43,889] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:43,893] [INFO] DFAST_QC result json was written to GCF_030268045.1_ASM3026804v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:43,893] [INFO] DFAST_QC completed!
[2024-01-24 11:27:43,894] [INFO] Total running time: 0h1m16s