[2024-01-24 10:57:06,589] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:06,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:06,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg75869d13-3a16-4fa2-9af7-4e1e226245eb/dqc_reference
[2024-01-24 10:57:07,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:07,850] [INFO] Task started: Prodigal
[2024-01-24 10:57:07,851] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0b30a3a-dc41-46e0-a12c-006d23717ea0/GCF_010975035.1_ASM1097503v1_genomic.fna.gz | prodigal -d GCF_010975035.1_ASM1097503v1_genomic.fna/cds.fna -a GCF_010975035.1_ASM1097503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:14,435] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:14,436] [INFO] Task started: HMMsearch
[2024-01-24 10:57:14,436] [INFO] Running command: hmmsearch --tblout GCF_010975035.1_ASM1097503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75869d13-3a16-4fa2-9af7-4e1e226245eb/dqc_reference/reference_markers.hmm GCF_010975035.1_ASM1097503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:14,694] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:14,695] [INFO] Found 6/6 markers.
[2024-01-24 10:57:14,723] [INFO] Query marker FASTA was written to GCF_010975035.1_ASM1097503v1_genomic.fna/markers.fasta
[2024-01-24 10:57:14,723] [INFO] Task started: Blastn
[2024-01-24 10:57:14,723] [INFO] Running command: blastn -query GCF_010975035.1_ASM1097503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75869d13-3a16-4fa2-9af7-4e1e226245eb/dqc_reference/reference_markers.fasta -out GCF_010975035.1_ASM1097503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:15,328] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:15,332] [INFO] Selected 20 target genomes.
[2024-01-24 10:57:15,333] [INFO] Target genome list was writen to GCF_010975035.1_ASM1097503v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:16,037] [INFO] Task started: fastANI
[2024-01-24 10:57:16,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0b30a3a-dc41-46e0-a12c-006d23717ea0/GCF_010975035.1_ASM1097503v1_genomic.fna.gz --refList GCF_010975035.1_ASM1097503v1_genomic.fna/target_genomes.txt --output GCF_010975035.1_ASM1097503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:32,797] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:32,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75869d13-3a16-4fa2-9af7-4e1e226245eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:32,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75869d13-3a16-4fa2-9af7-4e1e226245eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:32,815] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:32,815] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:57:32,815] [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
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	100.0	1040	1043	95	inconclusive
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	95.4074	911	1043	95	inconclusive
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.2759	346	1043	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.1457	288	1043	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	78.0255	279	1043	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	78.0123	289	1043	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.9913	259	1043	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.8754	265	1043	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	77.8676	259	1043	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	77.8535	256	1043	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	77.8165	290	1043	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.7531	309	1043	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	77.7085	212	1043	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	77.63	287	1043	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	77.5715	252	1043	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.4221	139	1043	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	77.3357	136	1043	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.2204	130	1043	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	77.1568	93	1043	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.6281	70	1043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:32,816] [INFO] DFAST Taxonomy check result was written to GCF_010975035.1_ASM1097503v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:32,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:32,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:32,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75869d13-3a16-4fa2-9af7-4e1e226245eb/dqc_reference/checkm_data
[2024-01-24 10:57:32,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:32,850] [INFO] Task started: CheckM
[2024-01-24 10:57:32,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010975035.1_ASM1097503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010975035.1_ASM1097503v1_genomic.fna/checkm_input GCF_010975035.1_ASM1097503v1_genomic.fna/checkm_result
[2024-01-24 10:57:58,766] [INFO] Task succeeded: CheckM
[2024-01-24 10:57:58,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:57:58,795] [INFO] ===== Completeness check finished =====
[2024-01-24 10:57:58,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:57:58,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010975035.1_ASM1097503v1_genomic.fna/markers.fasta)
[2024-01-24 10:57:58,797] [INFO] Task started: Blastn
[2024-01-24 10:57:58,797] [INFO] Running command: blastn -query GCF_010975035.1_ASM1097503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75869d13-3a16-4fa2-9af7-4e1e226245eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_010975035.1_ASM1097503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:59,654] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:59,658] [INFO] Selected 29 target genomes.
[2024-01-24 10:57:59,658] [INFO] Target genome list was writen to GCF_010975035.1_ASM1097503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:57:59,752] [INFO] Task started: fastANI
[2024-01-24 10:57:59,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0b30a3a-dc41-46e0-a12c-006d23717ea0/GCF_010975035.1_ASM1097503v1_genomic.fna.gz --refList GCF_010975035.1_ASM1097503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010975035.1_ASM1097503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:25,525] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:25,547] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:25,547] [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_010975035.1	s__Neobacillus thermocopriae	100.0	1040	1043	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	conclusive
GCF_002860255.1	s__Neobacillus cucumis_A	78.3047	263	1043	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_001510715.1	s__Neobacillus sp001510715	78.1531	288	1043	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_001591805.1	s__Neobacillus novalis	78.0935	278	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014656545.1	s__Neobacillus sp014656545	78.0122	278	1043	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_016765675.1	s__Neobacillus sp016765675	78.0099	226	1043	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_018613415.1	s__Neobacillus sp018613415	77.9883	257	1043	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_016908975.1	s__Neobacillus cucumis	77.9402	258	1043	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_001866655.1	s__Neobacillus sp001866655	77.9294	243	1043	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_002585305.1	s__Neobacillus sp002585305	77.9211	269	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_016107705.1	s__Neobacillus cucumis_B	77.9173	245	1043	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_007678255.1	s__Neobacillus sp007678255	77.877	286	1043	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_001048695.1	s__Neobacillus massiliamazoniensis	77.8589	256	1043	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_000612625.1	s__Neobacillus jeddahensis	77.8165	290	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	0.99	0.99	3	-
GCF_011250555.1	s__Neobacillus sp011250555	77.8157	296	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000482325.1	s__Neobacillus sp000482325	77.7969	251	1043	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_000686805.1	s__Neobacillus sp000686805	77.7244	297	1043	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_001591485.1	s__Neobacillus fumarioli	77.7204	212	1043	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_002559145.1	s__Neobacillus sp002559145	77.7115	254	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.43	95.43	0.81	0.81	2	-
GCF_013396335.1	s__Neobacillus sp013396335	77.6604	248	1043	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_002567005.1	s__Neobacillus sp002567005	77.6321	287	1043	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	-
GCA_019219025.1	s__Neobacillus sp019219025	77.6253	296	1043	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_016464375.1	s__Neobacillus renqingensis	77.619	245	1043	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_002272245.1	s__Neobacillus sp002272245	77.6076	232	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.06	97.06	0.86	0.86	2	-
GCF_001591445.1	s__Neobacillus drentensis	77.5628	251	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002860125.1	s__Bacillus_BJ canaveralius	77.3955	91	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	99.48	99.12	0.94	0.92	4	-
GCF_900156875.1	s__Robertmurraya dakarensis	77.3357	136	1043	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_003989135.1	s__Peribacillus cavernae	77.0583	65	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:25,549] [INFO] GTDB search result was written to GCF_010975035.1_ASM1097503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:25,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:25,554] [INFO] DFAST_QC result json was written to GCF_010975035.1_ASM1097503v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:25,555] [INFO] DFAST_QC completed!
[2024-01-24 10:58:25,555] [INFO] Total running time: 0h1m19s