[2024-01-24 12:13:27,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:27,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:27,493] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a2369ae-3f87-4a4e-a0c8-2f295078945a/dqc_reference
[2024-01-24 12:13:28,965] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:28,966] [INFO] Task started: Prodigal
[2024-01-24 12:13:28,966] [INFO] Running command: gunzip -c /var/lib/cwl/stg466fab40-214c-4236-9284-6c1bf7db04ea/GCF_007991275.1_ASM799127v1_genomic.fna.gz | prodigal -d GCF_007991275.1_ASM799127v1_genomic.fna/cds.fna -a GCF_007991275.1_ASM799127v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:34,636] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:34,637] [INFO] Task started: HMMsearch
[2024-01-24 12:13:34,637] [INFO] Running command: hmmsearch --tblout GCF_007991275.1_ASM799127v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a2369ae-3f87-4a4e-a0c8-2f295078945a/dqc_reference/reference_markers.hmm GCF_007991275.1_ASM799127v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:35,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:35,038] [INFO] Found 6/6 markers.
[2024-01-24 12:13:35,075] [INFO] Query marker FASTA was written to GCF_007991275.1_ASM799127v1_genomic.fna/markers.fasta
[2024-01-24 12:13:35,075] [INFO] Task started: Blastn
[2024-01-24 12:13:35,075] [INFO] Running command: blastn -query GCF_007991275.1_ASM799127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a2369ae-3f87-4a4e-a0c8-2f295078945a/dqc_reference/reference_markers.fasta -out GCF_007991275.1_ASM799127v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:35,732] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:35,735] [INFO] Selected 23 target genomes.
[2024-01-24 12:13:35,735] [INFO] Target genome list was writen to GCF_007991275.1_ASM799127v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:35,790] [INFO] Task started: fastANI
[2024-01-24 12:13:35,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg466fab40-214c-4236-9284-6c1bf7db04ea/GCF_007991275.1_ASM799127v1_genomic.fna.gz --refList GCF_007991275.1_ASM799127v1_genomic.fna/target_genomes.txt --output GCF_007991275.1_ASM799127v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:49,604] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:49,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a2369ae-3f87-4a4e-a0c8-2f295078945a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:49,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a2369ae-3f87-4a4e-a0c8-2f295078945a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:49,620] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:49,621] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:49,621] [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
Alkalibacillus haloalkaliphilus	strain=NBRC 103110	GCA_007991275.1	94136	94136	type	True	100.0	939	940	95	conclusive
Alkalibacillus aidingensis	strain=YIM 98829	GCA_014595945.1	2747607	2747607	type	True	78.3357	255	940	95	below_threshold
Alkalibacillus almallahensis	strain=CECT 8373	GCA_011761495.1	1379154	1379154	type	True	77.7124	234	940	95	below_threshold
Piscibacillus halophilus	strain=DSM 21633	GCA_900110685.1	571933	571933	type	True	77.2485	153	940	95	below_threshold
Halalkalibacillus halophilus	strain=DSM 18494	GCA_000423105.1	392827	392827	type	True	77.1268	167	940	95	below_threshold
Tenuibacillus multivorans	strain=CGMCC 1.3442	GCA_900103915.1	237069	237069	type	True	76.9122	119	940	95	below_threshold
Tenuibacillus multivorans	strain=NBRC 100370	GCA_007989445.1	237069	237069	type	True	76.8672	114	940	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	76.1134	51	940	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:49,623] [INFO] DFAST Taxonomy check result was written to GCF_007991275.1_ASM799127v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:49,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:49,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:49,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a2369ae-3f87-4a4e-a0c8-2f295078945a/dqc_reference/checkm_data
[2024-01-24 12:13:49,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:49,654] [INFO] Task started: CheckM
[2024-01-24 12:13:49,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991275.1_ASM799127v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991275.1_ASM799127v1_genomic.fna/checkm_input GCF_007991275.1_ASM799127v1_genomic.fna/checkm_result
[2024-01-24 12:14:13,958] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:13,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:13,982] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:13,983] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:13,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991275.1_ASM799127v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:13,983] [INFO] Task started: Blastn
[2024-01-24 12:14:13,984] [INFO] Running command: blastn -query GCF_007991275.1_ASM799127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a2369ae-3f87-4a4e-a0c8-2f295078945a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991275.1_ASM799127v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:14,823] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:14,828] [INFO] Selected 17 target genomes.
[2024-01-24 12:14:14,828] [INFO] Target genome list was writen to GCF_007991275.1_ASM799127v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:14,847] [INFO] Task started: fastANI
[2024-01-24 12:14:14,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg466fab40-214c-4236-9284-6c1bf7db04ea/GCF_007991275.1_ASM799127v1_genomic.fna.gz --refList GCF_007991275.1_ASM799127v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991275.1_ASM799127v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:24,312] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:24,322] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:24,322] [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_007991275.1	s__Alkalibacillus haloalkaliphilus	100.0	939	940	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000269905.1	s__Alkalibacillus haloalkaliphilus_A	93.1965	715	940	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_014595945.1	s__Alkalibacillus sp014595945	78.3357	255	940	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_011761495.1	s__Alkalibacillus almallahensis	77.7124	234	940	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_004402015.1	s__Filobacillus milosensis	77.2252	140	940	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_003843875.1	s__Aquisalibacillus elongatus	77.2017	151	940	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Aquisalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423105.1	s__Halalkalibacillus halophilus	77.1268	167	940	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_900103915.1	s__Tenuibacillus multivorans	76.9122	119	940	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Tenuibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425225.1	s__Pontibacillus marinus	76.7889	69	940	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009858175.1	s__Pontibacillus sp009858175	76.6371	67	940	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:24,324] [INFO] GTDB search result was written to GCF_007991275.1_ASM799127v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:24,324] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:24,328] [INFO] DFAST_QC result json was written to GCF_007991275.1_ASM799127v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:24,328] [INFO] DFAST_QC completed!
[2024-01-24 12:14:24,328] [INFO] Total running time: 0h0m57s