[2024-01-24 11:51:50,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a4b0a4c-1a05-447b-81c4-8c3d62553ffc/dqc_reference
[2024-01-24 11:51:51,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,487] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f9582ec-fb28-41e1-8454-1810aa915aec/GCF_024198175.1_ASM2419817v1_genomic.fna.gz | prodigal -d GCF_024198175.1_ASM2419817v1_genomic.fna/cds.fna -a GCF_024198175.1_ASM2419817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:47,368] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:47,368] [INFO] Task started: HMMsearch
[2024-01-24 11:52:47,369] [INFO] Running command: hmmsearch --tblout GCF_024198175.1_ASM2419817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a4b0a4c-1a05-447b-81c4-8c3d62553ffc/dqc_reference/reference_markers.hmm GCF_024198175.1_ASM2419817v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:47,822] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:47,823] [INFO] Found 6/6 markers.
[2024-01-24 11:52:47,911] [INFO] Query marker FASTA was written to GCF_024198175.1_ASM2419817v1_genomic.fna/markers.fasta
[2024-01-24 11:52:47,912] [INFO] Task started: Blastn
[2024-01-24 11:52:47,912] [INFO] Running command: blastn -query GCF_024198175.1_ASM2419817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a4b0a4c-1a05-447b-81c4-8c3d62553ffc/dqc_reference/reference_markers.fasta -out GCF_024198175.1_ASM2419817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:48,658] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:48,663] [INFO] Selected 18 target genomes.
[2024-01-24 11:52:48,663] [INFO] Target genome list was writen to GCF_024198175.1_ASM2419817v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:48,681] [INFO] Task started: fastANI
[2024-01-24 11:52:48,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f9582ec-fb28-41e1-8454-1810aa915aec/GCF_024198175.1_ASM2419817v1_genomic.fna.gz --refList GCF_024198175.1_ASM2419817v1_genomic.fna/target_genomes.txt --output GCF_024198175.1_ASM2419817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:33,138] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:33,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a4b0a4c-1a05-447b-81c4-8c3d62553ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:33,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a4b0a4c-1a05-447b-81c4-8c3d62553ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:33,158] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:53:33,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:53:33,159] [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
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	87.8361	3050	4203	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	87.4742	3039	4203	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	87.2163	2816	4203	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	84.9594	1874	4203	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	84.7136	2167	4203	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	84.6909	2131	4203	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	84.5565	2140	4203	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	83.9563	2441	4203	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	83.8804	2349	4203	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	83.4028	2201	4203	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	82.6498	2027	4203	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	82.4034	1914	4203	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	75.1025	176	4203	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	75.1006	180	4203	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.0184	636	4203	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.0118	658	4203	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	74.979	135	4203	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.7951	496	4203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:33,161] [INFO] DFAST Taxonomy check result was written to GCF_024198175.1_ASM2419817v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:33,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:33,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:33,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a4b0a4c-1a05-447b-81c4-8c3d62553ffc/dqc_reference/checkm_data
[2024-01-24 11:53:33,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:33,278] [INFO] Task started: CheckM
[2024-01-24 11:53:33,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024198175.1_ASM2419817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024198175.1_ASM2419817v1_genomic.fna/checkm_input GCF_024198175.1_ASM2419817v1_genomic.fna/checkm_result
[2024-01-24 11:58:14,380] [INFO] Task succeeded: CheckM
[2024-01-24 11:58:14,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:58:14,415] [INFO] ===== Completeness check finished =====
[2024-01-24 11:58:14,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:58:14,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024198175.1_ASM2419817v1_genomic.fna/markers.fasta)
[2024-01-24 11:58:14,417] [INFO] Task started: Blastn
[2024-01-24 11:58:14,417] [INFO] Running command: blastn -query GCF_024198175.1_ASM2419817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a4b0a4c-1a05-447b-81c4-8c3d62553ffc/dqc_reference/reference_markers_gtdb.fasta -out GCF_024198175.1_ASM2419817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:15,697] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:15,701] [INFO] Selected 12 target genomes.
[2024-01-24 11:58:15,701] [INFO] Target genome list was writen to GCF_024198175.1_ASM2419817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:58:15,777] [INFO] Task started: fastANI
[2024-01-24 11:58:15,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f9582ec-fb28-41e1-8454-1810aa915aec/GCF_024198175.1_ASM2419817v1_genomic.fna.gz --refList GCF_024198175.1_ASM2419817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024198175.1_ASM2419817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:58:55,410] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:55,430] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:58:55,430] [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_010894435.1	s__Myxococcus trucidator	87.8197	3054	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894405.1	s__Myxococcus caerfyrddinensis	87.4337	3050	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933655.1	s__Myxococcus fallax	87.2105	2819	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301735.1	s__Myxococcus sp017301735	86.4211	2965	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002305895.1	s__Myxococcus macrosporus	85.0345	2265	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.54	98.54	0.93	0.93	2	-
GCF_013372585.1	s__Myxococcus sp013372585	84.8827	2118	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.53	99.53	0.97	0.97	2	-
GCF_900101905.1	s__Myxococcus virescens	84.7022	2170	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	98.11	97.12	0.95	0.93	4	-
GCF_014656495.1	s__Myxococcus sp014656495	84.6336	2187	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900106535.1	s__Myxococcus xanthus	84.5657	2138	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	99.36	96.84	0.98	0.91	10	-
GCF_000280925.3	s__Myxococcus hansupus	84.3017	2200	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111765.1	s__Myxococcus fulvus	83.9259	2417	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.03	95.70	0.96	0.91	4	-
GCF_000331735.1	s__Myxococcus stipitatus	83.3765	2207	4203	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:58:55,462] [INFO] GTDB search result was written to GCF_024198175.1_ASM2419817v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:58:55,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:58:55,469] [INFO] DFAST_QC result json was written to GCF_024198175.1_ASM2419817v1_genomic.fna/dqc_result.json
[2024-01-24 11:58:55,469] [INFO] DFAST_QC completed!
[2024-01-24 11:58:55,470] [INFO] Total running time: 0h7m5s