[2024-01-24 12:15:20,836] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cfb46ed-1000-4202-b10c-4043423859e6/dqc_reference
[2024-01-24 12:15:22,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:22,275] [INFO] Task started: Prodigal
[2024-01-24 12:15:22,276] [INFO] Running command: gunzip -c /var/lib/cwl/stge59120f6-6a10-4f2d-beb9-2984ea23a14b/GCF_019915265.1_ASM1991526v1_genomic.fna.gz | prodigal -d GCF_019915265.1_ASM1991526v1_genomic.fna/cds.fna -a GCF_019915265.1_ASM1991526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:30,012] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:30,013] [INFO] Task started: HMMsearch
[2024-01-24 12:15:30,013] [INFO] Running command: hmmsearch --tblout GCF_019915265.1_ASM1991526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cfb46ed-1000-4202-b10c-4043423859e6/dqc_reference/reference_markers.hmm GCF_019915265.1_ASM1991526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:30,301] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:30,303] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge59120f6-6a10-4f2d-beb9-2984ea23a14b/GCF_019915265.1_ASM1991526v1_genomic.fna.gz]
[2024-01-24 12:15:30,344] [INFO] Query marker FASTA was written to GCF_019915265.1_ASM1991526v1_genomic.fna/markers.fasta
[2024-01-24 12:15:30,344] [INFO] Task started: Blastn
[2024-01-24 12:15:30,344] [INFO] Running command: blastn -query GCF_019915265.1_ASM1991526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cfb46ed-1000-4202-b10c-4043423859e6/dqc_reference/reference_markers.fasta -out GCF_019915265.1_ASM1991526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:30,977] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:30,980] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:30,981] [INFO] Target genome list was writen to GCF_019915265.1_ASM1991526v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:30,987] [INFO] Task started: fastANI
[2024-01-24 12:15:30,987] [INFO] Running command: fastANI --query /var/lib/cwl/stge59120f6-6a10-4f2d-beb9-2984ea23a14b/GCF_019915265.1_ASM1991526v1_genomic.fna.gz --refList GCF_019915265.1_ASM1991526v1_genomic.fna/target_genomes.txt --output GCF_019915265.1_ASM1991526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:46,311] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:46,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cfb46ed-1000-4202-b10c-4043423859e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:46,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cfb46ed-1000-4202-b10c-4043423859e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:46,328] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:46,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:46,328] [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 aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	100.0	1268	1268	95	conclusive
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	99.7851	1140	1268	95	conclusive
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	79.4347	109	1268	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	78.557	108	1268	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	78.5019	126	1268	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	78.4336	107	1268	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	78.2156	153	1268	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	77.7341	123	1268	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	77.5571	89	1268	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.3384	104	1268	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	76.8365	85	1268	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.8301	97	1268	95	below_threshold
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	76.7491	93	1268	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	76.736	135	1268	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.6006	113	1268	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_002009555.1	38875	38875	type	True	76.4938	91	1268	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.434	115	1268	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	76.2869	111	1268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:46,330] [INFO] DFAST Taxonomy check result was written to GCF_019915265.1_ASM1991526v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:46,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:46,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:46,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cfb46ed-1000-4202-b10c-4043423859e6/dqc_reference/checkm_data
[2024-01-24 12:15:46,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:46,373] [INFO] Task started: CheckM
[2024-01-24 12:15:46,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019915265.1_ASM1991526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019915265.1_ASM1991526v1_genomic.fna/checkm_input GCF_019915265.1_ASM1991526v1_genomic.fna/checkm_result
[2024-01-24 12:16:14,367] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:14,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:14,393] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:14,394] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:14,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019915265.1_ASM1991526v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:14,395] [INFO] Task started: Blastn
[2024-01-24 12:16:14,395] [INFO] Running command: blastn -query GCF_019915265.1_ASM1991526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cfb46ed-1000-4202-b10c-4043423859e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019915265.1_ASM1991526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:15,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:15,191] [INFO] Selected 25 target genomes.
[2024-01-24 12:16:15,191] [INFO] Target genome list was writen to GCF_019915265.1_ASM1991526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:15,218] [INFO] Task started: fastANI
[2024-01-24 12:16:15,219] [INFO] Running command: fastANI --query /var/lib/cwl/stge59120f6-6a10-4f2d-beb9-2984ea23a14b/GCF_019915265.1_ASM1991526v1_genomic.fna.gz --refList GCF_019915265.1_ASM1991526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019915265.1_ASM1991526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:39,002] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:39,028] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:39,028] [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_011008855.1	s__Bacillus_BT aquiflavi	99.7851	1140	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BT	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_001274725.1	s__Cytobacillus globisporus	78.8851	110	1268	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_001636315.1	s__Neobacillus mesonae	78.7017	126	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.98	98.98	0.94	0.94	2	-
GCF_001420715.1	s__Margalitia shackletonii	78.4315	107	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.16	98.74	0.93	0.89	4	-
GCF_017809215.1	s__Heyndrickxia oleronia	78.4314	106	1268	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_007995155.1	s__Cytobacillus dafuensis	78.4074	155	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014217835.1	s__Metabacillus litoralis_A	78.0909	117	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_900117315.1	s__Bacillus_BE massilionigeriensis	77.9066	122	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BE	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018343665.1	s__Cytobacillus sp018343665	77.5488	158	1268	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_009466385.1	s__Bacillus_BN tepidiphilus	77.4896	91	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358205.1	s__Neobacillus salipaludis	77.3384	104	1268	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	77.2303	63	1268	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_900104555.1	s__Litchfieldia salsa	77.0976	82	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	77.0659	121	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011393025.1	s__URHB0009 sp011393025	76.9499	93	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__URHB0009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591465.1	s__Cytobacillus firmus	76.8365	85	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.21	98.02	0.95	0.85	11	-
GCF_017497975.1	s__Metabacillus sp017497975	76.8301	97	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835805.1	s__Niallia nealsonii	76.7898	100	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613315.1	s__Mesobacillus sp018613315	76.7404	79	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874625.1	s__Cytobacillus eiseniae	76.736	135	1268	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_900115925.1	s__CL95 sp900115925	76.7319	97	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__CL95	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018613035.1	s__Cytobacillus sp018613035	76.7189	109	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.97	99.97	0.97	0.97	2	-
GCF_000518885.1	s__Cytobacillus sp000518885	76.6716	121	1268	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_900103525.1	s__Neobacillus sp900103525	76.5321	114	1268	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_001591625.1	s__Metabacillus fastidiosus	76.2728	112	1268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:39,030] [INFO] GTDB search result was written to GCF_019915265.1_ASM1991526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:39,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:39,035] [INFO] DFAST_QC result json was written to GCF_019915265.1_ASM1991526v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:39,035] [INFO] DFAST_QC completed!
[2024-01-24 12:16:39,035] [INFO] Total running time: 0h1m18s