[2024-01-25 20:02:05,463] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:05,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:05,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg442ac1d7-3155-4786-b412-afe0868bb014/dqc_reference
[2024-01-25 20:02:06,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:06,676] [INFO] Task started: Prodigal
[2024-01-25 20:02:06,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg580975d3-4647-4b53-bdbd-858588f3cccd/GCF_020075705.1_ASM2007570v1_genomic.fna.gz | prodigal -d GCF_020075705.1_ASM2007570v1_genomic.fna/cds.fna -a GCF_020075705.1_ASM2007570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:16,190] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:16,190] [INFO] Task started: HMMsearch
[2024-01-25 20:02:16,190] [INFO] Running command: hmmsearch --tblout GCF_020075705.1_ASM2007570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg442ac1d7-3155-4786-b412-afe0868bb014/dqc_reference/reference_markers.hmm GCF_020075705.1_ASM2007570v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:16,477] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:16,478] [INFO] Found 6/6 markers.
[2024-01-25 20:02:16,519] [INFO] Query marker FASTA was written to GCF_020075705.1_ASM2007570v1_genomic.fna/markers.fasta
[2024-01-25 20:02:16,520] [INFO] Task started: Blastn
[2024-01-25 20:02:16,520] [INFO] Running command: blastn -query GCF_020075705.1_ASM2007570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg442ac1d7-3155-4786-b412-afe0868bb014/dqc_reference/reference_markers.fasta -out GCF_020075705.1_ASM2007570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:17,083] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:17,086] [INFO] Selected 22 target genomes.
[2024-01-25 20:02:17,087] [INFO] Target genome list was writen to GCF_020075705.1_ASM2007570v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:17,101] [INFO] Task started: fastANI
[2024-01-25 20:02:17,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg580975d3-4647-4b53-bdbd-858588f3cccd/GCF_020075705.1_ASM2007570v1_genomic.fna.gz --refList GCF_020075705.1_ASM2007570v1_genomic.fna/target_genomes.txt --output GCF_020075705.1_ASM2007570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:35,333] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:35,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg442ac1d7-3155-4786-b412-afe0868bb014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:35,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg442ac1d7-3155-4786-b412-afe0868bb014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:35,346] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:02:35,346] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:02:35,346] [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
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	80.4968	789	1837	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	80.4332	811	1837	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	80.383	804	1837	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	78.962	411	1837	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	78.8853	409	1837	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	78.7625	408	1837	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	78.5823	427	1837	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	78.5722	411	1837	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	78.3246	325	1837	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	77.2758	144	1837	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.0428	113	1837	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	76.9486	108	1837	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.9065	107	1837	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	76.8577	104	1837	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_002009555.1	38875	38875	type	True	76.8264	96	1837	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.6747	98	1837	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.5845	105	1837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:35,352] [INFO] DFAST Taxonomy check result was written to GCF_020075705.1_ASM2007570v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:35,353] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:35,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:35,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg442ac1d7-3155-4786-b412-afe0868bb014/dqc_reference/checkm_data
[2024-01-25 20:02:35,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:35,414] [INFO] Task started: CheckM
[2024-01-25 20:02:35,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020075705.1_ASM2007570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020075705.1_ASM2007570v1_genomic.fna/checkm_input GCF_020075705.1_ASM2007570v1_genomic.fna/checkm_result
[2024-01-25 20:03:08,113] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:08,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:08,140] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:08,141] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:08,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020075705.1_ASM2007570v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:08,141] [INFO] Task started: Blastn
[2024-01-25 20:03:08,141] [INFO] Running command: blastn -query GCF_020075705.1_ASM2007570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg442ac1d7-3155-4786-b412-afe0868bb014/dqc_reference/reference_markers_gtdb.fasta -out GCF_020075705.1_ASM2007570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:08,942] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:08,945] [INFO] Selected 14 target genomes.
[2024-01-25 20:03:08,945] [INFO] Target genome list was writen to GCF_020075705.1_ASM2007570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:08,961] [INFO] Task started: fastANI
[2024-01-25 20:03:08,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg580975d3-4647-4b53-bdbd-858588f3cccd/GCF_020075705.1_ASM2007570v1_genomic.fna.gz --refList GCF_020075705.1_ASM2007570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020075705.1_ASM2007570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:24,900] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:24,909] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:03:24,909] [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_003259415.1	s__Metabacillus sp003259415	93.729	1401	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217835.1	s__Metabacillus litoralis_A	80.518	766	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_017497975.1	s__Metabacillus sp017497975	80.4907	790	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720625.1	s__Metabacillus sp004801455	80.4608	806	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000981385.1	s__Metabacillus sp000981385	79.2597	584	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908395.1	s__Metabacillus crassostreae	78.9919	406	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667825.1	s__Metabacillus litoralis_B	78.7182	403	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_007994985.1	s__Metabacillus litoralis	78.5699	428	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889165.1	s__Metabacillus weihaiensis	78.3351	323	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	97.24	97.24	0.88	0.88	2	-
GCF_001866655.1	s__Neobacillus sp001866655	77.3566	186	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107705.1	s__Neobacillus cucumis_B	77.1264	155	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008764245.1	s__Lederbergia ruris	76.8883	63	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	98.48	98.48	0.86	0.86	2	-
GCF_017809215.1	s__Heyndrickxia oleronia	76.8708	101	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	98.68	97.33	0.92	0.89	7	-
GCF_900112415.1	s__Bacillus_A sp900112415	76.7544	137	1837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.00	99.00	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:24,910] [INFO] GTDB search result was written to GCF_020075705.1_ASM2007570v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:24,911] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:24,914] [INFO] DFAST_QC result json was written to GCF_020075705.1_ASM2007570v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:24,914] [INFO] DFAST_QC completed!
[2024-01-25 20:03:24,914] [INFO] Total running time: 0h1m19s