[2024-01-25 19:42:05,395] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:05,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:05,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg550d7eb7-4e37-4ffa-be0f-870a8e46c8dc/dqc_reference
[2024-01-25 19:42:06,524] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:06,525] [INFO] Task started: Prodigal
[2024-01-25 19:42:06,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c7e3d2a-5196-4635-9ca8-b3c58a91ec14/GCF_001685015.1_ASM168501v1_genomic.fna.gz | prodigal -d GCF_001685015.1_ASM168501v1_genomic.fna/cds.fna -a GCF_001685015.1_ASM168501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:15,110] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:15,110] [INFO] Task started: HMMsearch
[2024-01-25 19:42:15,111] [INFO] Running command: hmmsearch --tblout GCF_001685015.1_ASM168501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg550d7eb7-4e37-4ffa-be0f-870a8e46c8dc/dqc_reference/reference_markers.hmm GCF_001685015.1_ASM168501v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:15,363] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:15,364] [INFO] Found 6/6 markers.
[2024-01-25 19:42:15,404] [INFO] Query marker FASTA was written to GCF_001685015.1_ASM168501v1_genomic.fna/markers.fasta
[2024-01-25 19:42:15,405] [INFO] Task started: Blastn
[2024-01-25 19:42:15,405] [INFO] Running command: blastn -query GCF_001685015.1_ASM168501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg550d7eb7-4e37-4ffa-be0f-870a8e46c8dc/dqc_reference/reference_markers.fasta -out GCF_001685015.1_ASM168501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:15,966] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:15,969] [INFO] Selected 20 target genomes.
[2024-01-25 19:42:15,969] [INFO] Target genome list was writen to GCF_001685015.1_ASM168501v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:15,985] [INFO] Task started: fastANI
[2024-01-25 19:42:15,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c7e3d2a-5196-4635-9ca8-b3c58a91ec14/GCF_001685015.1_ASM168501v1_genomic.fna.gz --refList GCF_001685015.1_ASM168501v1_genomic.fna/target_genomes.txt --output GCF_001685015.1_ASM168501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:29,725] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:29,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg550d7eb7-4e37-4ffa-be0f-870a8e46c8dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:29,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg550d7eb7-4e37-4ffa-be0f-870a8e46c8dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:29,736] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:29,737] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:29,737] [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 wudalianchiensis	strain=FJAT-27215	GCA_001685015.1	1743143	1743143	type	True	100.0	1461	1464	95	conclusive
Bacillus badius	strain=NBRC 15713	GCA_001591605.1	1455	1455	type	True	80.4807	682	1464	95	below_threshold
Bacillus aerolatus	strain=CX253	GCA_009183655.1	2653354	2653354	type	True	79.6581	556	1464	95	below_threshold
Bacillus thermotolerans	strain=SGZ-8	GCA_000812025.2	1221996	1221996	type	True	78.1016	282	1464	95	below_threshold
Bacillus thermotolerans	strain=SgZ-8	GCA_011751085.1	1221996	1221996	type	True	78.06	278	1464	95	below_threshold
Bacillus xiapuensis	strain=FJAT-46582	GCA_002797355.1	2014075	2014075	type	True	77.9049	210	1464	95	below_threshold
Bacillus ectoiniformans	strain=DSM 28970	GCA_016908875.1	1494429	1494429	type	True	77.5983	202	1464	95	below_threshold
Domibacillus robiginosus	strain=WS 4628	GCA_000966195.1	1071054	1071054	type	True	77.0498	111	1464	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	77.0338	63	1464	95	below_threshold
Domibacillus indicus	strain=SD 111	GCA_000970685.1	1437523	1437523	type	True	77.0054	107	1464	95	below_threshold
Domibacillus iocasae	strain=DSM 29979	GCA_001750285.1	1714016	1714016	type	True	76.9553	111	1464	95	below_threshold
Domibacillus epiphyticus	strain=SAB 38	GCA_001975785.1	1714355	1714355	type	True	76.9478	110	1464	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	76.9413	55	1464	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	76.8517	64	1464	95	below_threshold
Domibacillus antri	strain=XD80	GCA_001936625.1	1714264	1714264	type	True	76.8064	109	1464	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.7709	50	1464	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:29,738] [INFO] DFAST Taxonomy check result was written to GCF_001685015.1_ASM168501v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:29,739] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:29,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:29,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg550d7eb7-4e37-4ffa-be0f-870a8e46c8dc/dqc_reference/checkm_data
[2024-01-25 19:42:29,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:29,784] [INFO] Task started: CheckM
[2024-01-25 19:42:29,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001685015.1_ASM168501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001685015.1_ASM168501v1_genomic.fna/checkm_input GCF_001685015.1_ASM168501v1_genomic.fna/checkm_result
[2024-01-25 19:42:58,858] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:58,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:58,880] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:58,881] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:58,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001685015.1_ASM168501v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:58,881] [INFO] Task started: Blastn
[2024-01-25 19:42:58,881] [INFO] Running command: blastn -query GCF_001685015.1_ASM168501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg550d7eb7-4e37-4ffa-be0f-870a8e46c8dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001685015.1_ASM168501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:59,641] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:59,644] [INFO] Selected 12 target genomes.
[2024-01-25 19:42:59,644] [INFO] Target genome list was writen to GCF_001685015.1_ASM168501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:59,649] [INFO] Task started: fastANI
[2024-01-25 19:42:59,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c7e3d2a-5196-4635-9ca8-b3c58a91ec14/GCF_001685015.1_ASM168501v1_genomic.fna.gz --refList GCF_001685015.1_ASM168501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001685015.1_ASM168501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:08,816] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:08,824] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:08,825] [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_001685015.1	s__Pseudobacillus wudalianchiensis	100.0	1461	1464	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	96.18	96.18	0.89	0.89	2	conclusive
GCF_003600835.1	s__Pseudobacillus sp003600835	82.0659	894	1464	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591605.1	s__Pseudobacillus badius	80.4808	682	1464	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	98.55	97.77	0.93	0.89	8	-
GCF_009183655.1	s__Pseudobacillus aerolatus	79.6488	557	1464	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820555.1	s__FJAT-46582 sp016820555	78.1311	266	1464	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	-
GCA_002261155.1	s__FJAT-46582 sp002261155	78.0268	237	1464	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_002797375.1	s__FJAT-46582 sp002797375	78.0151	254	1464	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_002797355.1	s__FJAT-46582 sp002797355	77.8944	209	1464	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_001750285.1	s__Domibacillus iocasae	76.971	112	1464	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_002860165.1	s__Bacillus_BJ sp002860165	76.9682	68	1464	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001936625.1	s__Domibacillus antri	76.7848	110	1464	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_001636345.1	s__Cytobacillus gottheilii	76.7169	87	1464	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	96.50	95.11	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:08,826] [INFO] GTDB search result was written to GCF_001685015.1_ASM168501v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:08,827] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:08,830] [INFO] DFAST_QC result json was written to GCF_001685015.1_ASM168501v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:08,830] [INFO] DFAST_QC completed!
[2024-01-25 19:43:08,830] [INFO] Total running time: 0h1m3s