[2024-01-24 12:44:53,760] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:53,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:53,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a46f78c-0f02-484a-8c22-e67c3adbf65a/dqc_reference
[2024-01-24 12:44:55,136] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:55,137] [INFO] Task started: Prodigal
[2024-01-24 12:44:55,137] [INFO] Running command: gunzip -c /var/lib/cwl/stg2afceafe-3023-47de-82be-3203d7d92a34/GCF_000970685.1_ASM97068v1_genomic.fna.gz | prodigal -d GCF_000970685.1_ASM97068v1_genomic.fna/cds.fna -a GCF_000970685.1_ASM97068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:04,285] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:04,285] [INFO] Task started: HMMsearch
[2024-01-24 12:45:04,285] [INFO] Running command: hmmsearch --tblout GCF_000970685.1_ASM97068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a46f78c-0f02-484a-8c22-e67c3adbf65a/dqc_reference/reference_markers.hmm GCF_000970685.1_ASM97068v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:04,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:04,588] [INFO] Found 6/6 markers.
[2024-01-24 12:45:04,626] [INFO] Query marker FASTA was written to GCF_000970685.1_ASM97068v1_genomic.fna/markers.fasta
[2024-01-24 12:45:04,626] [INFO] Task started: Blastn
[2024-01-24 12:45:04,626] [INFO] Running command: blastn -query GCF_000970685.1_ASM97068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a46f78c-0f02-484a-8c22-e67c3adbf65a/dqc_reference/reference_markers.fasta -out GCF_000970685.1_ASM97068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:05,237] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:05,240] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:05,240] [INFO] Target genome list was writen to GCF_000970685.1_ASM97068v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:05,247] [INFO] Task started: fastANI
[2024-01-24 12:45:05,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg2afceafe-3023-47de-82be-3203d7d92a34/GCF_000970685.1_ASM97068v1_genomic.fna.gz --refList GCF_000970685.1_ASM97068v1_genomic.fna/target_genomes.txt --output GCF_000970685.1_ASM97068v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:15,616] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:15,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a46f78c-0f02-484a-8c22-e67c3adbf65a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:15,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a46f78c-0f02-484a-8c22-e67c3adbf65a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:15,632] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:15,632] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:15,632] [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
Domibacillus indicus	strain=SD 111	GCA_000970685.1	1437523	1437523	type	True	100.0	1182	1185	95	conclusive
Domibacillus tundrae	strain=PAMC 80007	GCA_000970675.1	1587527	1587527	type	True	81.5656	600	1185	95	below_threshold
Domibacillus iocasae	strain=DSM 29979	GCA_001750285.1	1714016	1714016	type	True	81.2426	629	1185	95	below_threshold
Domibacillus robiginosus	strain=WS 4628	GCA_000966195.1	1071054	1071054	type	True	80.5768	606	1185	95	below_threshold
Domibacillus enclensis	strain=NIO-1016	GCA_000966185.1	1017273	1017273	type	True	80.1498	523	1185	95	below_threshold
Domibacillus enclensis	strain=DSM 25145	GCA_002237775.1	1017273	1017273	type	True	79.9887	550	1185	95	below_threshold
Domibacillus enclensis	strain=NIO-1016	GCA_900156125.1	1017273	1017273	type	True	79.9887	550	1185	95	below_threshold
Domibacillus antri	strain=XD80	GCA_001936625.1	1714264	1714264	type	True	79.2637	373	1185	95	below_threshold
Domibacillus epiphyticus	strain=SAB 38	GCA_001975785.1	1714355	1714355	type	True	79.0769	312	1185	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.7661	58	1185	95	below_threshold
Bacillus aerolatus	strain=CX253	GCA_009183655.1	2653354	2653354	type	True	77.1314	122	1185	95	below_threshold
Bacillus thermotolerans	strain=SGZ-8	GCA_000812025.2	1221996	1221996	type	True	76.919	83	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:15,634] [INFO] DFAST Taxonomy check result was written to GCF_000970685.1_ASM97068v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:15,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:15,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:15,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a46f78c-0f02-484a-8c22-e67c3adbf65a/dqc_reference/checkm_data
[2024-01-24 12:45:15,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:15,677] [INFO] Task started: CheckM
[2024-01-24 12:45:15,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000970685.1_ASM97068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000970685.1_ASM97068v1_genomic.fna/checkm_input GCF_000970685.1_ASM97068v1_genomic.fna/checkm_result
[2024-01-24 12:45:47,058] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:47,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:47,085] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:47,085] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:47,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000970685.1_ASM97068v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:47,086] [INFO] Task started: Blastn
[2024-01-24 12:45:47,086] [INFO] Running command: blastn -query GCF_000970685.1_ASM97068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a46f78c-0f02-484a-8c22-e67c3adbf65a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000970685.1_ASM97068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:47,908] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:47,912] [INFO] Selected 18 target genomes.
[2024-01-24 12:45:47,913] [INFO] Target genome list was writen to GCF_000970685.1_ASM97068v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:47,926] [INFO] Task started: fastANI
[2024-01-24 12:45:47,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg2afceafe-3023-47de-82be-3203d7d92a34/GCF_000970685.1_ASM97068v1_genomic.fna.gz --refList GCF_000970685.1_ASM97068v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000970685.1_ASM97068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:00,118] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:00,126] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:00,126] [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_000970685.1	s__Domibacillus indicus	100.0	1182	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000970675.1	s__Domibacillus tundrae	81.5592	602	1185	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_001750285.1	s__Domibacillus iocasae	81.2642	627	1185	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_000966195.1	s__Domibacillus robiginosus	80.5527	608	1185	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_900156125.1	s__Domibacillus enclensis	79.9887	550	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	100.00	99.99	1.00	1.00	3	-
GCF_001936625.1	s__Domibacillus antri	79.2768	372	1185	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_001975785.1	s__Domibacillus epiphyticus	79.0769	312	1185	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_000294775.2	s__Cytobacillus oceanisediminis_B	77.2759	82	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
GCF_009183655.1	s__Pseudobacillus aerolatus	77.1856	122	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:00,128] [INFO] GTDB search result was written to GCF_000970685.1_ASM97068v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:00,131] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:00,135] [INFO] DFAST_QC result json was written to GCF_000970685.1_ASM97068v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:00,135] [INFO] DFAST_QC completed!
[2024-01-24 12:46:00,136] [INFO] Total running time: 0h1m6s