[2024-01-24 14:54:56,360] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,365] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1cf3cd7-a96a-46fc-8e4d-92a0159b40db/dqc_reference
[2024-01-24 14:54:57,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,771] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,771] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bed3934-4c74-4df1-8de4-5476ade84d38/GCF_002009555.1_ASM200955v1_genomic.fna.gz | prodigal -d GCF_002009555.1_ASM200955v1_genomic.fna/cds.fna -a GCF_002009555.1_ASM200955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:06,588] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:06,589] [INFO] Task started: HMMsearch
[2024-01-24 14:55:06,589] [INFO] Running command: hmmsearch --tblout GCF_002009555.1_ASM200955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1cf3cd7-a96a-46fc-8e4d-92a0159b40db/dqc_reference/reference_markers.hmm GCF_002009555.1_ASM200955v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:06,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:06,916] [INFO] Found 6/6 markers.
[2024-01-24 14:55:06,972] [INFO] Query marker FASTA was written to GCF_002009555.1_ASM200955v1_genomic.fna/markers.fasta
[2024-01-24 14:55:06,973] [INFO] Task started: Blastn
[2024-01-24 14:55:06,973] [INFO] Running command: blastn -query GCF_002009555.1_ASM200955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1cf3cd7-a96a-46fc-8e4d-92a0159b40db/dqc_reference/reference_markers.fasta -out GCF_002009555.1_ASM200955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:07,607] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:07,610] [INFO] Selected 17 target genomes.
[2024-01-24 14:55:07,610] [INFO] Target genome list was writen to GCF_002009555.1_ASM200955v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:07,618] [INFO] Task started: fastANI
[2024-01-24 14:55:07,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bed3934-4c74-4df1-8de4-5476ade84d38/GCF_002009555.1_ASM200955v1_genomic.fna.gz --refList GCF_002009555.1_ASM200955v1_genomic.fna/target_genomes.txt --output GCF_002009555.1_ASM200955v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:23,377] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:23,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1cf3cd7-a96a-46fc-8e4d-92a0159b40db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:23,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1cf3cd7-a96a-46fc-8e4d-92a0159b40db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:23,393] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:55:23,393] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:23,393] [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
Heyndrickxia oleronia	strain=DSM 9356	GCA_002009555.1	38875	38875	type	True	100.0	1388	1411	95	conclusive
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	99.9766	1407	1411	95	conclusive
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	99.9678	1406	1411	95	conclusive
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	80.213	83	1411	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	80.2017	85	1411	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	79.2915	371	1411	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	79.2869	396	1411	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	77.5899	245	1411	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.4154	123	1411	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.3037	112	1411	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.2277	100	1411	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.2189	102	1411	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.1257	88	1411	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.0892	86	1411	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.6467	85	1411	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.4757	80	1411	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	76.1779	87	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:23,395] [INFO] DFAST Taxonomy check result was written to GCF_002009555.1_ASM200955v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:23,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:23,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:23,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1cf3cd7-a96a-46fc-8e4d-92a0159b40db/dqc_reference/checkm_data
[2024-01-24 14:55:23,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:23,464] [INFO] Task started: CheckM
[2024-01-24 14:55:23,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002009555.1_ASM200955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002009555.1_ASM200955v1_genomic.fna/checkm_input GCF_002009555.1_ASM200955v1_genomic.fna/checkm_result
[2024-01-24 14:55:55,423] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:55,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:55,448] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:55,448] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:55,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002009555.1_ASM200955v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:55,449] [INFO] Task started: Blastn
[2024-01-24 14:55:55,449] [INFO] Running command: blastn -query GCF_002009555.1_ASM200955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1cf3cd7-a96a-46fc-8e4d-92a0159b40db/dqc_reference/reference_markers_gtdb.fasta -out GCF_002009555.1_ASM200955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:56,263] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:56,268] [INFO] Selected 23 target genomes.
[2024-01-24 14:55:56,268] [INFO] Target genome list was writen to GCF_002009555.1_ASM200955v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:56,326] [INFO] Task started: fastANI
[2024-01-24 14:55:56,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bed3934-4c74-4df1-8de4-5476ade84d38/GCF_002009555.1_ASM200955v1_genomic.fna.gz --refList GCF_002009555.1_ASM200955v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002009555.1_ASM200955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:14,573] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:14,598] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:14,599] [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_017809215.1	s__Heyndrickxia oleronia	99.9766	1407	1411	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	conclusive
GCF_016908465.1	s__Ureibacillus composti	80.213	83	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016772275.1	s__Heyndrickxia vini	79.2536	460	1411	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_016756695.1	s__Heyndrickxia sporothermodurans	79.2464	417	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	99.73	97.95	0.95	0.84	38	-
GCF_001420715.1	s__Margalitia shackletonii	79.1019	288	1411	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	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	78.9815	501	1411	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	-
GCA_002261155.1	s__FJAT-46582 sp002261155	77.9613	69	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343615.1	s__Margalitia sp018343615	77.8378	228	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019219025.1	s__Neobacillus sp019219025	77.6424	111	1411	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_002844575.1	s__Margalitia camelliae	77.5931	246	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.53	99.53	0.93	0.93	2	-
GCF_007995155.1	s__Cytobacillus dafuensis	77.4398	122	1411	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_002019635.1	s__Metabacillus halosaccharovorans	77.1859	110	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_000813125.1	s__Mesobacillus selenatarsenatis	77.1821	55	1411	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_002797375.1	s__FJAT-46582 sp002797375	77.1356	85	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	96.55	96.55	0.91	0.91	2	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	77.1257	88	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343665.1	s__Cytobacillus sp018343665	77.0721	121	1411	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_002560985.1	s__Bacillus_A sp002560985	76.9948	76	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010975035.1	s__Neobacillus thermocopriae	76.7904	87	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.41	95.38	0.92	0.91	3	-
GCF_000832985.1	s__Priestia megaterium	76.5767	92	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.5311	96.82	95.69	0.88	0.73	151	-
GCF_016909075.1	s__Priestia iocasae	76.4184	79	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424685.1	s__Mesobacillus boroniphilus_A	76.3398	70	1411	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	-
GCA_016841285.1	s__Calidifontibacillus sp016841285	76.2047	65	1411	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:14,600] [INFO] GTDB search result was written to GCF_002009555.1_ASM200955v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:14,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:14,606] [INFO] DFAST_QC result json was written to GCF_002009555.1_ASM200955v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:14,606] [INFO] DFAST_QC completed!
[2024-01-24 14:56:14,606] [INFO] Total running time: 0h1m18s