[2024-01-24 11:12:35,276] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:35,277] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:35,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg06b7dfcc-f217-4a61-8491-02daf7b29722/dqc_reference
[2024-01-24 11:12:36,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:36,519] [INFO] Task started: Prodigal
[2024-01-24 11:12:36,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg3530d635-ed7d-4d3d-be4e-ae377b321baa/GCF_024609325.1_ASM2460932v1_genomic.fna.gz | prodigal -d GCF_024609325.1_ASM2460932v1_genomic.fna/cds.fna -a GCF_024609325.1_ASM2460932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:46,868] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:46,868] [INFO] Task started: HMMsearch
[2024-01-24 11:12:46,868] [INFO] Running command: hmmsearch --tblout GCF_024609325.1_ASM2460932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06b7dfcc-f217-4a61-8491-02daf7b29722/dqc_reference/reference_markers.hmm GCF_024609325.1_ASM2460932v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:47,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:47,143] [INFO] Found 6/6 markers.
[2024-01-24 11:12:47,172] [INFO] Query marker FASTA was written to GCF_024609325.1_ASM2460932v1_genomic.fna/markers.fasta
[2024-01-24 11:12:47,172] [INFO] Task started: Blastn
[2024-01-24 11:12:47,173] [INFO] Running command: blastn -query GCF_024609325.1_ASM2460932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06b7dfcc-f217-4a61-8491-02daf7b29722/dqc_reference/reference_markers.fasta -out GCF_024609325.1_ASM2460932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:47,881] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:47,885] [INFO] Selected 19 target genomes.
[2024-01-24 11:12:47,886] [INFO] Target genome list was writen to GCF_024609325.1_ASM2460932v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:47,908] [INFO] Task started: fastANI
[2024-01-24 11:12:47,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg3530d635-ed7d-4d3d-be4e-ae377b321baa/GCF_024609325.1_ASM2460932v1_genomic.fna.gz --refList GCF_024609325.1_ASM2460932v1_genomic.fna/target_genomes.txt --output GCF_024609325.1_ASM2460932v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:03,695] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:03,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06b7dfcc-f217-4a61-8491-02daf7b29722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:03,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06b7dfcc-f217-4a61-8491-02daf7b29722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:03,708] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:03,708] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:03,708] [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	86.2519	863	1103	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.0597	262	1103	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	76.04	56	1103	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	75.7687	58	1103	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.5452	91	1103	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	75.4324	118	1103	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	75.4187	106	1103	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	75.1645	59	1103	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.1462	72	1103	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.1421	86	1103	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	75.0455	60	1103	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.0368	69	1103	95	below_threshold
Streptosporangium becharense	strain=DSM 46887	GCA_014204985.1	1816182	1816182	type	True	75.0143	62	1103	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	74.9103	61	1103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:03,710] [INFO] DFAST Taxonomy check result was written to GCF_024609325.1_ASM2460932v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:03,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:03,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:03,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06b7dfcc-f217-4a61-8491-02daf7b29722/dqc_reference/checkm_data
[2024-01-24 11:13:03,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:03,752] [INFO] Task started: CheckM
[2024-01-24 11:13:03,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024609325.1_ASM2460932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024609325.1_ASM2460932v1_genomic.fna/checkm_input GCF_024609325.1_ASM2460932v1_genomic.fna/checkm_result
[2024-01-24 11:13:39,081] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:39,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:39,105] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:39,106] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:39,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024609325.1_ASM2460932v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:39,107] [INFO] Task started: Blastn
[2024-01-24 11:13:39,107] [INFO] Running command: blastn -query GCF_024609325.1_ASM2460932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06b7dfcc-f217-4a61-8491-02daf7b29722/dqc_reference/reference_markers_gtdb.fasta -out GCF_024609325.1_ASM2460932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:40,310] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:40,316] [INFO] Selected 10 target genomes.
[2024-01-24 11:13:40,317] [INFO] Target genome list was writen to GCF_024609325.1_ASM2460932v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:40,326] [INFO] Task started: fastANI
[2024-01-24 11:13:40,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg3530d635-ed7d-4d3d-be4e-ae377b321baa/GCF_024609325.1_ASM2460932v1_genomic.fna.gz --refList GCF_024609325.1_ASM2460932v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024609325.1_ASM2460932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:48,572] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:48,587] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:13:48,587] [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	86.2519	863	1103	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	84.9714	597	1103	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	83.5975	760	1103	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	83.2697	730	1103	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.39	97.91	0.89	0.88	4	-
GCA_016721195.1	s__Geothrix sp016721195	82.669	726	1103	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903857495.1	s__Geothrix sp903857495	82.6033	661	1103	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.99	99.97	0.99	0.98	50	-
GCA_016195985.1	s__Geothrix sp016195985	82.1875	715	1103	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	81.7013	573	1103	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.09	98.86	0.88	0.85	6	-
GCA_003158505.1	s__Geothrix sp003158505	81.5798	582	1103	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.60	99.60	0.90	0.90	2	-
GCA_903873655.1	s__Geothrix sp903873655	81.1811	526	1103	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 11:13:48,589] [INFO] GTDB search result was written to GCF_024609325.1_ASM2460932v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:48,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:48,593] [INFO] DFAST_QC result json was written to GCF_024609325.1_ASM2460932v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:48,593] [INFO] DFAST_QC completed!
[2024-01-24 11:13:48,593] [INFO] Total running time: 0h1m13s