[2024-01-24 13:36:46,204] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:46,206] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:46,206] [INFO] DQC Reference Directory: /var/lib/cwl/stgf843437b-0a9e-468e-a35a-24427ea17b0d/dqc_reference
[2024-01-24 13:36:47,489] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,490] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,491] [INFO] Running command: gunzip -c /var/lib/cwl/stgc69563f6-c37e-4f77-8111-108843a9f3e5/GCF_014595945.1_ASM1459594v1_genomic.fna.gz | prodigal -d GCF_014595945.1_ASM1459594v1_genomic.fna/cds.fna -a GCF_014595945.1_ASM1459594v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:52,923] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:52,924] [INFO] Task started: HMMsearch
[2024-01-24 13:36:52,924] [INFO] Running command: hmmsearch --tblout GCF_014595945.1_ASM1459594v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf843437b-0a9e-468e-a35a-24427ea17b0d/dqc_reference/reference_markers.hmm GCF_014595945.1_ASM1459594v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:53,159] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:53,160] [INFO] Found 6/6 markers.
[2024-01-24 13:36:53,187] [INFO] Query marker FASTA was written to GCF_014595945.1_ASM1459594v1_genomic.fna/markers.fasta
[2024-01-24 13:36:53,188] [INFO] Task started: Blastn
[2024-01-24 13:36:53,188] [INFO] Running command: blastn -query GCF_014595945.1_ASM1459594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf843437b-0a9e-468e-a35a-24427ea17b0d/dqc_reference/reference_markers.fasta -out GCF_014595945.1_ASM1459594v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:53,793] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:53,796] [INFO] Selected 23 target genomes.
[2024-01-24 13:36:53,796] [INFO] Target genome list was writen to GCF_014595945.1_ASM1459594v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:53,892] [INFO] Task started: fastANI
[2024-01-24 13:36:53,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgc69563f6-c37e-4f77-8111-108843a9f3e5/GCF_014595945.1_ASM1459594v1_genomic.fna.gz --refList GCF_014595945.1_ASM1459594v1_genomic.fna/target_genomes.txt --output GCF_014595945.1_ASM1459594v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:08,384] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:08,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf843437b-0a9e-468e-a35a-24427ea17b0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:08,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf843437b-0a9e-468e-a35a-24427ea17b0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:08,395] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:08,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:08,395] [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 aidingensis	strain=YIM 98829	GCA_014595945.1	2747607	2747607	type	True	100.0	934	935	95	conclusive
Alkalibacillus haloalkaliphilus	strain=NBRC 103110	GCA_007991275.1	94136	94136	type	True	78.4716	251	935	95	below_threshold
Alkalibacillus almallahensis	strain=CECT 8373	GCA_011761495.1	1379154	1379154	type	True	77.7079	155	935	95	below_threshold
Halalkalibacillus halophilus	strain=DSM 18494	GCA_000423105.1	392827	392827	type	True	77.5703	136	935	95	below_threshold
Piscibacillus halophilus	strain=DSM 21633	GCA_900110685.1	571933	571933	type	True	77.4812	133	935	95	below_threshold
Tenuibacillus multivorans	strain=CGMCC 1.3442	GCA_900103915.1	237069	237069	type	True	77.2822	138	935	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.2416	60	935	95	below_threshold
Tenuibacillus multivorans	strain=NBRC 100370	GCA_007989445.1	237069	237069	type	True	77.1269	135	935	95	below_threshold
Allobacillus salarius	strain=SKP4-8	GCA_007559425.1	1955272	1955272	type	True	77.0779	86	935	95	below_threshold
Allobacillus saliphilus	strain=SKP8-2	GCA_018138385.1	2912308	2912308	type	True	77.0047	83	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:08,397] [INFO] DFAST Taxonomy check result was written to GCF_014595945.1_ASM1459594v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:08,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:08,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:08,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf843437b-0a9e-468e-a35a-24427ea17b0d/dqc_reference/checkm_data
[2024-01-24 13:37:08,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:08,429] [INFO] Task started: CheckM
[2024-01-24 13:37:08,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014595945.1_ASM1459594v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014595945.1_ASM1459594v1_genomic.fna/checkm_input GCF_014595945.1_ASM1459594v1_genomic.fna/checkm_result
[2024-01-24 13:37:32,525] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:32,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:32,545] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:32,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:32,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014595945.1_ASM1459594v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:32,546] [INFO] Task started: Blastn
[2024-01-24 13:37:32,546] [INFO] Running command: blastn -query GCF_014595945.1_ASM1459594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf843437b-0a9e-468e-a35a-24427ea17b0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014595945.1_ASM1459594v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:33,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:33,279] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:33,279] [INFO] Target genome list was writen to GCF_014595945.1_ASM1459594v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:33,330] [INFO] Task started: fastANI
[2024-01-24 13:37:33,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgc69563f6-c37e-4f77-8111-108843a9f3e5/GCF_014595945.1_ASM1459594v1_genomic.fna.gz --refList GCF_014595945.1_ASM1459594v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014595945.1_ASM1459594v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:42,862] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:42,873] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:42,873] [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_014595945.1	s__Alkalibacillus sp014595945	100.0	934	935	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_007991275.1	s__Alkalibacillus haloalkaliphilus	78.4564	252	935	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	78.3847	238	935	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	77.7028	153	935	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_003843875.1	s__Aquisalibacillus elongatus	77.5951	133	935	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	77.5887	136	935	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_900110685.1	s__Piscibacillus halophilus	77.4812	133	935	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_004402015.1	s__Filobacillus milosensis	77.4492	147	935	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_900103915.1	s__Tenuibacillus multivorans	77.2645	139	935	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_005870085.1	s__BH258 sp005870085	77.1945	66	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559425.1	s__Allobacillus sp007559425	77.0779	86	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018138385.1	s__Allobacillus sp018138385	77.0047	83	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:42,875] [INFO] GTDB search result was written to GCF_014595945.1_ASM1459594v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:42,876] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:42,879] [INFO] DFAST_QC result json was written to GCF_014595945.1_ASM1459594v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:42,880] [INFO] DFAST_QC completed!
[2024-01-24 13:37:42,880] [INFO] Total running time: 0h0m57s