[2024-01-24 11:21:07,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,413] [INFO] DQC Reference Directory: /var/lib/cwl/stga492e4af-0e78-4f5e-96d4-cf59d9087fe6/dqc_reference
[2024-01-24 11:21:11,972] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,973] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,974] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3809137-e1d5-4332-8cab-e08f58769ec9/GCF_014836495.1_ASM1483649v1_genomic.fna.gz | prodigal -d GCF_014836495.1_ASM1483649v1_genomic.fna/cds.fna -a GCF_014836495.1_ASM1483649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:20,844] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:20,845] [INFO] Task started: HMMsearch
[2024-01-24 11:21:20,845] [INFO] Running command: hmmsearch --tblout GCF_014836495.1_ASM1483649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga492e4af-0e78-4f5e-96d4-cf59d9087fe6/dqc_reference/reference_markers.hmm GCF_014836495.1_ASM1483649v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:21,131] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:21,133] [INFO] Found 6/6 markers.
[2024-01-24 11:21:21,172] [INFO] Query marker FASTA was written to GCF_014836495.1_ASM1483649v1_genomic.fna/markers.fasta
[2024-01-24 11:21:21,173] [INFO] Task started: Blastn
[2024-01-24 11:21:21,173] [INFO] Running command: blastn -query GCF_014836495.1_ASM1483649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga492e4af-0e78-4f5e-96d4-cf59d9087fe6/dqc_reference/reference_markers.fasta -out GCF_014836495.1_ASM1483649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:21,763] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:21,767] [INFO] Selected 26 target genomes.
[2024-01-24 11:21:21,767] [INFO] Target genome list was writen to GCF_014836495.1_ASM1483649v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:21,822] [INFO] Task started: fastANI
[2024-01-24 11:21:21,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3809137-e1d5-4332-8cab-e08f58769ec9/GCF_014836495.1_ASM1483649v1_genomic.fna.gz --refList GCF_014836495.1_ASM1483649v1_genomic.fna/target_genomes.txt --output GCF_014836495.1_ASM1483649v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:39,838] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:39,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga492e4af-0e78-4f5e-96d4-cf59d9087fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:39,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga492e4af-0e78-4f5e-96d4-cf59d9087fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:39,856] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:39,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:39,857] [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
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	100.0	1456	1457	95	conclusive
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	78.6583	371	1457	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	77.7611	112	1457	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	77.6295	136	1457	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.5958	170	1457	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	77.5199	95	1457	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	77.4123	129	1457	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.339	153	1457	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	77.3061	83	1457	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.2884	86	1457	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	77.2844	126	1457	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	77.2585	85	1457	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.199	91	1457	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.1544	164	1457	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	76.969	90	1457	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.856	80	1457	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	76.8054	85	1457	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	76.676	84	1457	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	76.6031	99	1457	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.4604	111	1457	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.4389	86	1457	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.3461	74	1457	95	below_threshold
Anoxybacillus caldiproteolyticus	strain=DSM 15730	GCA_013761245.1	247480	247480	type	True	76.2367	52	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:39,858] [INFO] DFAST Taxonomy check result was written to GCF_014836495.1_ASM1483649v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:39,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:39,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:39,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga492e4af-0e78-4f5e-96d4-cf59d9087fe6/dqc_reference/checkm_data
[2024-01-24 11:21:39,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:39,901] [INFO] Task started: CheckM
[2024-01-24 11:21:39,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836495.1_ASM1483649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836495.1_ASM1483649v1_genomic.fna/checkm_input GCF_014836495.1_ASM1483649v1_genomic.fna/checkm_result
[2024-01-24 11:22:11,449] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:11,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:11,473] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:11,474] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:11,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836495.1_ASM1483649v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:11,475] [INFO] Task started: Blastn
[2024-01-24 11:22:11,475] [INFO] Running command: blastn -query GCF_014836495.1_ASM1483649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga492e4af-0e78-4f5e-96d4-cf59d9087fe6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836495.1_ASM1483649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:12,203] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:12,207] [INFO] Selected 20 target genomes.
[2024-01-24 11:22:12,207] [INFO] Target genome list was writen to GCF_014836495.1_ASM1483649v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:12,222] [INFO] Task started: fastANI
[2024-01-24 11:22:12,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3809137-e1d5-4332-8cab-e08f58769ec9/GCF_014836495.1_ASM1483649v1_genomic.fna.gz --refList GCF_014836495.1_ASM1483649v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836495.1_ASM1483649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:28,401] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:28,419] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:28,420] [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_014836495.1	s__Cytobacillus sp014836495	100.0	1456	1457	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	conclusive
GCF_002276165.1	s__Cytobacillus kochii	92.5863	1313	1457	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_900166665.1	s__Cytobacillus gottheilii_A	78.7324	178	1457	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_002835735.1	s__Cytobacillus horneckiae	78.6588	371	1457	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.87	98.22	0.90	0.90	3	-
GCF_000518885.1	s__Cytobacillus sp000518885	77.7366	155	1457	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_018343665.1	s__Cytobacillus sp018343665	77.6118	157	1457	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_001420595.1	s__Cytobacillus solani	77.5958	170	1457	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_902168435.1	s__Bacillus_BU marasmi	77.5161	96	1457	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	77.5137	138	1457	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_900199725.1	s__Cytobacillus massiliigabonensis	77.4987	150	1457	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_003726095.1	s__Niallia circulans_A	77.4839	124	1457	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.27	98.85	0.92	0.89	8	-
GCF_900117315.1	s__Bacillus_BE massilionigeriensis	77.4123	129	1457	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_004366035.1	s__Cytobacillus oceanisediminis_C	77.3893	148	1457	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001439605.1	s__Cytobacillus praedii	77.3035	170	1457	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_014656545.1	s__Neobacillus sp014656545	77.199	91	1457	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_003667825.1	s__Metabacillus litoralis_B	77.0376	99	1457	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_002871465.1	s__Metabacillus sp002871465	77.0145	94	1457	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_902374955.1	s__Bacillus_AD massilioanorexius	76.8884	94	1457	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	-
GCF_000686805.1	s__Neobacillus sp000686805	76.7385	110	1457	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	76.676	84	1457	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 11:22:28,421] [INFO] GTDB search result was written to GCF_014836495.1_ASM1483649v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:28,421] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:28,428] [INFO] DFAST_QC result json was written to GCF_014836495.1_ASM1483649v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:28,428] [INFO] DFAST_QC completed!
[2024-01-24 11:22:28,428] [INFO] Total running time: 0h1m21s