[2024-01-24 14:56:18,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:18,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:18,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c640d39-8a57-4a17-a732-f92728ad9218/dqc_reference
[2024-01-24 14:56:19,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:19,320] [INFO] Task started: Prodigal
[2024-01-24 14:56:19,321] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a4912aa-7193-4ec1-95b9-1dd7a01a1f1e/GCF_005280205.1_ASM528020v1_genomic.fna.gz | prodigal -d GCF_005280205.1_ASM528020v1_genomic.fna/cds.fna -a GCF_005280205.1_ASM528020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:28,682] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:28,682] [INFO] Task started: HMMsearch
[2024-01-24 14:56:28,682] [INFO] Running command: hmmsearch --tblout GCF_005280205.1_ASM528020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c640d39-8a57-4a17-a732-f92728ad9218/dqc_reference/reference_markers.hmm GCF_005280205.1_ASM528020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:28,939] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:28,941] [INFO] Found 6/6 markers.
[2024-01-24 14:56:28,980] [INFO] Query marker FASTA was written to GCF_005280205.1_ASM528020v1_genomic.fna/markers.fasta
[2024-01-24 14:56:28,980] [INFO] Task started: Blastn
[2024-01-24 14:56:28,981] [INFO] Running command: blastn -query GCF_005280205.1_ASM528020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c640d39-8a57-4a17-a732-f92728ad9218/dqc_reference/reference_markers.fasta -out GCF_005280205.1_ASM528020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:29,583] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:29,587] [INFO] Selected 20 target genomes.
[2024-01-24 14:56:29,587] [INFO] Target genome list was writen to GCF_005280205.1_ASM528020v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:29,602] [INFO] Task started: fastANI
[2024-01-24 14:56:29,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4912aa-7193-4ec1-95b9-1dd7a01a1f1e/GCF_005280205.1_ASM528020v1_genomic.fna.gz --refList GCF_005280205.1_ASM528020v1_genomic.fna/target_genomes.txt --output GCF_005280205.1_ASM528020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:46,549] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:46,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c640d39-8a57-4a17-a732-f92728ad9218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:46,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c640d39-8a57-4a17-a732-f92728ad9218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:46,565] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:46,566] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:46,566] [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
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	100.0	1511	1513	95	conclusive
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	100.0	1511	1513	95	conclusive
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	79.6078	487	1513	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	79.3123	182	1513	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	79.0302	415	1513	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	78.3748	128	1513	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	78.2794	262	1513	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.5471	200	1513	95	below_threshold
Mesobacillus foraminis	strain=CV53	GCA_013618915.1	279826	279826	type	True	77.4918	107	1513	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	77.4662	145	1513	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	77.4252	145	1513	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	77.3912	150	1513	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.3723	153	1513	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.3578	125	1513	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	77.323	71	1513	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	77.3227	136	1513	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.1895	108	1513	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.1884	114	1513	95	below_threshold
Lederbergia citri	strain=FJAT-49780	GCA_018343625.1	2833580	2833580	type	True	76.9648	95	1513	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	76.5962	64	1513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:46,568] [INFO] DFAST Taxonomy check result was written to GCF_005280205.1_ASM528020v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:46,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:46,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:46,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c640d39-8a57-4a17-a732-f92728ad9218/dqc_reference/checkm_data
[2024-01-24 14:56:46,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:46,616] [INFO] Task started: CheckM
[2024-01-24 14:56:46,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005280205.1_ASM528020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005280205.1_ASM528020v1_genomic.fna/checkm_input GCF_005280205.1_ASM528020v1_genomic.fna/checkm_result
[2024-01-24 14:57:18,946] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:18,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:18,969] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:18,969] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:18,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005280205.1_ASM528020v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:18,970] [INFO] Task started: Blastn
[2024-01-24 14:57:18,970] [INFO] Running command: blastn -query GCF_005280205.1_ASM528020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c640d39-8a57-4a17-a732-f92728ad9218/dqc_reference/reference_markers_gtdb.fasta -out GCF_005280205.1_ASM528020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:19,722] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:19,726] [INFO] Selected 22 target genomes.
[2024-01-24 14:57:19,726] [INFO] Target genome list was writen to GCF_005280205.1_ASM528020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:19,761] [INFO] Task started: fastANI
[2024-01-24 14:57:19,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4912aa-7193-4ec1-95b9-1dd7a01a1f1e/GCF_005280205.1_ASM528020v1_genomic.fna.gz --refList GCF_005280205.1_ASM528020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005280205.1_ASM528020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:37,070] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:37,087] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:37,087] [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_005280205.1	s__Robertmurraya yapensis	100.0	1511	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_005116465.1	s__Robertmurraya kyonggiensis	90.485	1227	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000311725.1	s__Robertmurraya massiliosenegalensis	79.6445	485	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014837155.1	s__Litchfieldia sp014837155	79.5291	173	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502275.1	s__Robertmurraya siralis	79.0302	415	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	99.13	99.00	0.93	0.92	3	-
GCA_002480735.1	s__Robertmurraya sp002480735	78.4597	274	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586445.1	s__Robertmurraya sp003586445	78.3316	194	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917645.1	s__Robertmurraya sp009917645	78.0507	197	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019219025.1	s__Neobacillus sp019219025	77.7304	150	1513	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_001591565.1	s__Priestia flexa	77.7057	102	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
GCF_001439605.1	s__Cytobacillus praedii	77.5639	200	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_001591645.1	s__Robertmurraya korlensis	77.5417	190	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524525.1	s__Robertmurraya sp011524525	77.5038	141	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902168435.1	s__Bacillus_BU marasmi	77.4467	146	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509555.1	s__Cytobacillus sp001509555	77.365	169	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242895.2	s__Bacillus_BU sp000242895	77.3623	145	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248975.1	s__Neobacillus endophyticus	77.3435	137	1513	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_002863585.1	s__Bacillus_AI deserti_A	77.2725	89	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970685.1	s__Domibacillus indicus	77.2553	51	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866655.1	s__Neobacillus sp001866655	77.1657	175	1513	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_902374955.1	s__Bacillus_AD massilioanorexius	77.0624	105	1513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:37,089] [INFO] GTDB search result was written to GCF_005280205.1_ASM528020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:37,090] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:37,095] [INFO] DFAST_QC result json was written to GCF_005280205.1_ASM528020v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:37,095] [INFO] DFAST_QC completed!
[2024-01-24 14:57:37,095] [INFO] Total running time: 0h1m19s