[2024-01-24 15:10:22,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:22,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:22,525] [INFO] DQC Reference Directory: /var/lib/cwl/stged815ad6-26ba-447d-a86d-278f82b2e142/dqc_reference
[2024-01-24 15:10:24,122] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,123] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,123] [INFO] Running command: gunzip -c /var/lib/cwl/stg1fd97cd4-f14e-446d-ac53-fd6ee1d04491/GCF_003611735.1_ASM361173v1_genomic.fna.gz | prodigal -d GCF_003611735.1_ASM361173v1_genomic.fna/cds.fna -a GCF_003611735.1_ASM361173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:33,216] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:33,216] [INFO] Task started: HMMsearch
[2024-01-24 15:11:33,217] [INFO] Running command: hmmsearch --tblout GCF_003611735.1_ASM361173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged815ad6-26ba-447d-a86d-278f82b2e142/dqc_reference/reference_markers.hmm GCF_003611735.1_ASM361173v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:33,630] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:33,632] [INFO] Found 6/6 markers.
[2024-01-24 15:11:33,715] [INFO] Query marker FASTA was written to GCF_003611735.1_ASM361173v1_genomic.fna/markers.fasta
[2024-01-24 15:11:33,716] [INFO] Task started: Blastn
[2024-01-24 15:11:33,716] [INFO] Running command: blastn -query GCF_003611735.1_ASM361173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged815ad6-26ba-447d-a86d-278f82b2e142/dqc_reference/reference_markers.fasta -out GCF_003611735.1_ASM361173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:34,563] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:34,566] [INFO] Selected 12 target genomes.
[2024-01-24 15:11:34,567] [INFO] Target genome list was writen to GCF_003611735.1_ASM361173v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:34,571] [INFO] Task started: fastANI
[2024-01-24 15:11:34,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fd97cd4-f14e-446d-ac53-fd6ee1d04491/GCF_003611735.1_ASM361173v1_genomic.fna.gz --refList GCF_003611735.1_ASM361173v1_genomic.fna/target_genomes.txt --output GCF_003611735.1_ASM361173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:58,613] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:58,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged815ad6-26ba-447d-a86d-278f82b2e142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:58,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged815ad6-26ba-447d-a86d-278f82b2e142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:58,625] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:58,626] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:58,626] [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
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	100.0	3102	3123	95	conclusive
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	93.6188	2304	3123	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	90.3198	2382	3123	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	90.1827	2244	3123	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	89.8941	2243	3123	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	88.9014	2118	3123	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	75.0571	149	3123	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	74.9501	105	3123	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	74.8924	401	3123	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	74.8841	101	3123	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	74.8692	288	3123	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	74.8647	101	3123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:58,628] [INFO] DFAST Taxonomy check result was written to GCF_003611735.1_ASM361173v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:58,628] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:58,629] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:58,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged815ad6-26ba-447d-a86d-278f82b2e142/dqc_reference/checkm_data
[2024-01-24 15:11:58,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:58,722] [INFO] Task started: CheckM
[2024-01-24 15:11:58,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003611735.1_ASM361173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003611735.1_ASM361173v1_genomic.fna/checkm_input GCF_003611735.1_ASM361173v1_genomic.fna/checkm_result
[2024-01-24 15:15:51,545] [INFO] Task succeeded: CheckM
[2024-01-24 15:15:51,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 15:15:51,571] [INFO] ===== Completeness check finished =====
[2024-01-24 15:15:51,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:15:51,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003611735.1_ASM361173v1_genomic.fna/markers.fasta)
[2024-01-24 15:15:51,572] [INFO] Task started: Blastn
[2024-01-24 15:15:51,573] [INFO] Running command: blastn -query GCF_003611735.1_ASM361173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged815ad6-26ba-447d-a86d-278f82b2e142/dqc_reference/reference_markers_gtdb.fasta -out GCF_003611735.1_ASM361173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:52,931] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:52,935] [INFO] Selected 7 target genomes.
[2024-01-24 15:15:52,935] [INFO] Target genome list was writen to GCF_003611735.1_ASM361173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:15:52,974] [INFO] Task started: fastANI
[2024-01-24 15:15:52,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fd97cd4-f14e-446d-ac53-fd6ee1d04491/GCF_003611735.1_ASM361173v1_genomic.fna.gz --refList GCF_003611735.1_ASM361173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003611735.1_ASM361173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:16:17,685] [INFO] Task succeeded: fastANI
[2024-01-24 15:16:17,699] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:16:17,699] [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_003611735.1	s__Corallococcus sicarius	100.0	3102	3123	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003611675.1	s__Corallococcus sp003611675	93.7858	2388	3123	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014930455.1	s__Corallococcus sp014930455	90.3546	2377	3123	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612115.1	s__Corallococcus sp003612115	90.2369	2340	3123	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.04	99.04	0.92	0.92	2	-
GCF_003611635.1	s__Corallococcus terminator	89.8894	2242	3123	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173515.1	s__Corallococcus sp004173515	89.4726	2126	3123	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668875.1	s__Corallococcus interemptor	88.2632	2241	3123	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.20	99.20	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:16:17,701] [INFO] GTDB search result was written to GCF_003611735.1_ASM361173v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:16:17,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:16:17,704] [INFO] DFAST_QC result json was written to GCF_003611735.1_ASM361173v1_genomic.fna/dqc_result.json
[2024-01-24 15:16:17,705] [INFO] DFAST_QC completed!
[2024-01-24 15:16:17,705] [INFO] Total running time: 0h5m55s