[2024-01-24 14:54:53,579] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:53,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:53,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg524cf05c-30c2-4f28-90aa-32dd74bffb2e/dqc_reference
[2024-01-24 14:54:54,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:54,828] [INFO] Task started: Prodigal
[2024-01-24 14:54:54,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg60f79553-20c6-465d-aa17-1f3c68f111ea/GCF_007989445.1_ASM798944v1_genomic.fna.gz | prodigal -d GCF_007989445.1_ASM798944v1_genomic.fna/cds.fna -a GCF_007989445.1_ASM798944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:00,567] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:00,567] [INFO] Task started: HMMsearch
[2024-01-24 14:55:00,567] [INFO] Running command: hmmsearch --tblout GCF_007989445.1_ASM798944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg524cf05c-30c2-4f28-90aa-32dd74bffb2e/dqc_reference/reference_markers.hmm GCF_007989445.1_ASM798944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:00,819] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:00,820] [INFO] Found 6/6 markers.
[2024-01-24 14:55:00,854] [INFO] Query marker FASTA was written to GCF_007989445.1_ASM798944v1_genomic.fna/markers.fasta
[2024-01-24 14:55:00,854] [INFO] Task started: Blastn
[2024-01-24 14:55:00,854] [INFO] Running command: blastn -query GCF_007989445.1_ASM798944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg524cf05c-30c2-4f28-90aa-32dd74bffb2e/dqc_reference/reference_markers.fasta -out GCF_007989445.1_ASM798944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:01,446] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:01,449] [INFO] Selected 18 target genomes.
[2024-01-24 14:55:01,450] [INFO] Target genome list was writen to GCF_007989445.1_ASM798944v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:01,513] [INFO] Task started: fastANI
[2024-01-24 14:55:01,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg60f79553-20c6-465d-aa17-1f3c68f111ea/GCF_007989445.1_ASM798944v1_genomic.fna.gz --refList GCF_007989445.1_ASM798944v1_genomic.fna/target_genomes.txt --output GCF_007989445.1_ASM798944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:10,682] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:10,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg524cf05c-30c2-4f28-90aa-32dd74bffb2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:10,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg524cf05c-30c2-4f28-90aa-32dd74bffb2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:10,691] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:55:10,691] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:10,691] [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
Tenuibacillus multivorans	strain=NBRC 100370	GCA_007989445.1	237069	237069	type	True	100.0	956	957	95	conclusive
Tenuibacillus multivorans	strain=CGMCC 1.3442	GCA_900103915.1	237069	237069	type	True	99.9987	955	957	95	conclusive
Piscibacillus halophilus	strain=DSM 21633	GCA_900110685.1	571933	571933	type	True	78.3234	292	957	95	below_threshold
Alkalibacillus aidingensis	strain=YIM 98829	GCA_014595945.1	2747607	2747607	type	True	77.1628	127	957	95	below_threshold
Alkalibacillus haloalkaliphilus	strain=NBRC 103110	GCA_007991275.1	94136	94136	type	True	76.8697	124	957	95	below_threshold
Halalkalibacillus halophilus	strain=DSM 18494	GCA_000423105.1	392827	392827	type	True	76.6999	95	957	95	below_threshold
Gracilibacillus massiliensis	strain=Awa-1	GCA_001458115.1	1564956	1564956	type	True	76.659	53	957	95	below_threshold
Salinibacillus kushneri	strain=CGMCC 1.3566	GCA_900111405.1	237682	237682	type	True	76.6167	54	957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:10,693] [INFO] DFAST Taxonomy check result was written to GCF_007989445.1_ASM798944v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:10,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:10,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:10,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg524cf05c-30c2-4f28-90aa-32dd74bffb2e/dqc_reference/checkm_data
[2024-01-24 14:55:10,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:10,731] [INFO] Task started: CheckM
[2024-01-24 14:55:10,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989445.1_ASM798944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989445.1_ASM798944v1_genomic.fna/checkm_input GCF_007989445.1_ASM798944v1_genomic.fna/checkm_result
[2024-01-24 14:55:35,568] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:35,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:35,590] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:35,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:35,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989445.1_ASM798944v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:35,591] [INFO] Task started: Blastn
[2024-01-24 14:55:35,592] [INFO] Running command: blastn -query GCF_007989445.1_ASM798944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg524cf05c-30c2-4f28-90aa-32dd74bffb2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989445.1_ASM798944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:36,485] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:36,489] [INFO] Selected 22 target genomes.
[2024-01-24 14:55:36,489] [INFO] Target genome list was writen to GCF_007989445.1_ASM798944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:36,507] [INFO] Task started: fastANI
[2024-01-24 14:55:36,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg60f79553-20c6-465d-aa17-1f3c68f111ea/GCF_007989445.1_ASM798944v1_genomic.fna.gz --refList GCF_007989445.1_ASM798944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989445.1_ASM798944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:49,685] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:49,695] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:49,695] [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_900103915.1	s__Tenuibacillus multivorans	99.9987	955	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Tenuibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004402015.1	s__Filobacillus milosensis	78.4029	295	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Filobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110685.1	s__Piscibacillus halophilus	78.3362	291	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Piscibacillus	95.0	99.37	99.37	0.93	0.93	2	-
GCF_003843875.1	s__Aquisalibacillus elongatus	78.1695	275	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Aquisalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001311865.1	s__Piscibacillus salipiscarius	78.1146	235	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Piscibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595945.1	s__Alkalibacillus sp014595945	77.1654	126	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000269905.1	s__Alkalibacillus haloalkaliphilus_A	76.9546	112	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991275.1	s__Alkalibacillus haloalkaliphilus	76.8697	124	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423105.1	s__Halalkalibacillus halophilus	76.6984	94	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Halalkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111405.1	s__Salinibacillus kushneri	76.5584	53	957	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:49,697] [INFO] GTDB search result was written to GCF_007989445.1_ASM798944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:49,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:49,701] [INFO] DFAST_QC result json was written to GCF_007989445.1_ASM798944v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:49,701] [INFO] DFAST_QC completed!
[2024-01-24 14:55:49,701] [INFO] Total running time: 0h0m56s