[2024-01-24 14:22:29,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:29,386] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:29,386] [INFO] DQC Reference Directory: /var/lib/cwl/stge8f99450-7703-4f2a-b5dd-e172226a7a1c/dqc_reference
[2024-01-24 14:22:30,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:30,613] [INFO] Task started: Prodigal
[2024-01-24 14:22:30,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg949f06e9-086a-41a9-9793-ab941616ba07/GCF_004402015.1_ASM440201v1_genomic.fna.gz | prodigal -d GCF_004402015.1_ASM440201v1_genomic.fna/cds.fna -a GCF_004402015.1_ASM440201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:36,702] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:36,702] [INFO] Task started: HMMsearch
[2024-01-24 14:22:36,703] [INFO] Running command: hmmsearch --tblout GCF_004402015.1_ASM440201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8f99450-7703-4f2a-b5dd-e172226a7a1c/dqc_reference/reference_markers.hmm GCF_004402015.1_ASM440201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:36,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:36,964] [INFO] Found 6/6 markers.
[2024-01-24 14:22:36,993] [INFO] Query marker FASTA was written to GCF_004402015.1_ASM440201v1_genomic.fna/markers.fasta
[2024-01-24 14:22:36,993] [INFO] Task started: Blastn
[2024-01-24 14:22:36,994] [INFO] Running command: blastn -query GCF_004402015.1_ASM440201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8f99450-7703-4f2a-b5dd-e172226a7a1c/dqc_reference/reference_markers.fasta -out GCF_004402015.1_ASM440201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:37,591] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:37,595] [INFO] Selected 28 target genomes.
[2024-01-24 14:22:37,595] [INFO] Target genome list was writen to GCF_004402015.1_ASM440201v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:37,609] [INFO] Task started: fastANI
[2024-01-24 14:22:37,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg949f06e9-086a-41a9-9793-ab941616ba07/GCF_004402015.1_ASM440201v1_genomic.fna.gz --refList GCF_004402015.1_ASM440201v1_genomic.fna/target_genomes.txt --output GCF_004402015.1_ASM440201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:53,148] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:53,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8f99450-7703-4f2a-b5dd-e172226a7a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:53,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8f99450-7703-4f2a-b5dd-e172226a7a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:53,160] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:53,160] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:53,160] [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
Piscibacillus halophilus	strain=DSM 21633	GCA_900110685.1	571933	571933	type	True	78.9269	341	1050	95	below_threshold
Tenuibacillus multivorans	strain=NBRC 100370	GCA_007989445.1	237069	237069	type	True	78.442	294	1050	95	below_threshold
Tenuibacillus multivorans	strain=CGMCC 1.3442	GCA_900103915.1	237069	237069	type	True	78.4366	296	1050	95	below_threshold
Alkalibacillus almallahensis	strain=CECT 8373	GCA_011761495.1	1379154	1379154	type	True	77.5439	108	1050	95	below_threshold
Alkalibacillus aidingensis	strain=YIM 98829	GCA_014595945.1	2747607	2747607	type	True	77.425	148	1050	95	below_threshold
Salinibacillus xinjiangensis	strain=J4	GCA_009649735.1	1229268	1229268	type	True	77.3623	56	1050	95	below_threshold
Alkalibacillus haloalkaliphilus	strain=NBRC 103110	GCA_007991275.1	94136	94136	type	True	77.1571	147	1050	95	below_threshold
Halalkalibacillus halophilus	strain=DSM 18494	GCA_000423105.1	392827	392827	type	True	77.1563	123	1050	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.0132	55	1050	95	below_threshold
Pontibacillus marinus	strain=DSM 16465	GCA_000425225.1	273164	273164	type	True	76.7232	62	1050	95	below_threshold
Pontibacillus marinus	strain=BH030004	GCA_000775605.1	273164	273164	type	True	76.6532	56	1050	95	below_threshold
Pontibacillus yanchengensis	strain=Y32	GCA_000770635.1	462910	462910	type	True	76.4063	57	1050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:53,162] [INFO] DFAST Taxonomy check result was written to GCF_004402015.1_ASM440201v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:53,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:53,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:53,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8f99450-7703-4f2a-b5dd-e172226a7a1c/dqc_reference/checkm_data
[2024-01-24 14:22:53,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:53,196] [INFO] Task started: CheckM
[2024-01-24 14:22:53,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004402015.1_ASM440201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004402015.1_ASM440201v1_genomic.fna/checkm_input GCF_004402015.1_ASM440201v1_genomic.fna/checkm_result
[2024-01-24 14:23:17,716] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:17,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:17,739] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:17,739] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:17,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004402015.1_ASM440201v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:17,740] [INFO] Task started: Blastn
[2024-01-24 14:23:17,740] [INFO] Running command: blastn -query GCF_004402015.1_ASM440201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8f99450-7703-4f2a-b5dd-e172226a7a1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004402015.1_ASM440201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:18,522] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:18,526] [INFO] Selected 22 target genomes.
[2024-01-24 14:23:18,526] [INFO] Target genome list was writen to GCF_004402015.1_ASM440201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:18,572] [INFO] Task started: fastANI
[2024-01-24 14:23:18,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg949f06e9-086a-41a9-9793-ab941616ba07/GCF_004402015.1_ASM440201v1_genomic.fna.gz --refList GCF_004402015.1_ASM440201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004402015.1_ASM440201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:30,213] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:30,224] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:30,225] [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_004402015.1	s__Filobacillus milosensis	100.0	1047	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Filobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001311865.1	s__Piscibacillus salipiscarius	79.1113	309	1050	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_900110685.1	s__Piscibacillus halophilus	78.9279	342	1050	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	78.8768	304	1050	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_900103915.1	s__Tenuibacillus multivorans	78.4297	294	1050	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_011761495.1	s__Alkalibacillus almallahensis	77.53	107	1050	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	77.4412	144	1050	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_009649735.1	s__Salinibacillus xinjiangensis	77.3623	56	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991275.1	s__Alkalibacillus haloalkaliphilus	77.1571	147	1050	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	77.1351	123	1050	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_003268595.1	s__Paraliobacillus_A zengyii	77.0675	53	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_000425225.1	s__Pontibacillus marinus	76.6955	61	1050	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_000770635.1	s__Pontibacillus yanchengensis	76.441	56	1050	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 14:23:30,226] [INFO] GTDB search result was written to GCF_004402015.1_ASM440201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:30,227] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:30,230] [INFO] DFAST_QC result json was written to GCF_004402015.1_ASM440201v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:30,230] [INFO] DFAST_QC completed!
[2024-01-24 14:23:30,230] [INFO] Total running time: 0h1m1s