[2024-01-25 20:16:35,547] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:35,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:35,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg95e6cbe4-0224-4158-8909-725bd541a3db/dqc_reference
[2024-01-25 20:16:36,666] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:36,667] [INFO] Task started: Prodigal
[2024-01-25 20:16:36,667] [INFO] Running command: gunzip -c /var/lib/cwl/stg72c05e0e-47b8-4666-8c6f-9e937c188905/GCF_002019765.1_ASM201976v1_genomic.fna.gz | prodigal -d GCF_002019765.1_ASM201976v1_genomic.fna/cds.fna -a GCF_002019765.1_ASM201976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:44,480] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:44,480] [INFO] Task started: HMMsearch
[2024-01-25 20:16:44,480] [INFO] Running command: hmmsearch --tblout GCF_002019765.1_ASM201976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95e6cbe4-0224-4158-8909-725bd541a3db/dqc_reference/reference_markers.hmm GCF_002019765.1_ASM201976v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:44,705] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:44,706] [INFO] Found 6/6 markers.
[2024-01-25 20:16:44,738] [INFO] Query marker FASTA was written to GCF_002019765.1_ASM201976v1_genomic.fna/markers.fasta
[2024-01-25 20:16:44,739] [INFO] Task started: Blastn
[2024-01-25 20:16:44,739] [INFO] Running command: blastn -query GCF_002019765.1_ASM201976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95e6cbe4-0224-4158-8909-725bd541a3db/dqc_reference/reference_markers.fasta -out GCF_002019765.1_ASM201976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:45,337] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:45,340] [INFO] Selected 33 target genomes.
[2024-01-25 20:16:45,340] [INFO] Target genome list was writen to GCF_002019765.1_ASM201976v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:45,359] [INFO] Task started: fastANI
[2024-01-25 20:16:45,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg72c05e0e-47b8-4666-8c6f-9e937c188905/GCF_002019765.1_ASM201976v1_genomic.fna.gz --refList GCF_002019765.1_ASM201976v1_genomic.fna/target_genomes.txt --output GCF_002019765.1_ASM201976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:07,933] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:07,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95e6cbe4-0224-4158-8909-725bd541a3db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:07,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95e6cbe4-0224-4158-8909-725bd541a3db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:07,948] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:17:07,948] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:17:07,948] [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
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	79.2159	71	1352	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	79.0838	85	1352	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	79.0398	60	1352	95	below_threshold
Alkalihalobacillus patagoniensis	strain=DSM 16117	GCA_002019705.1	228576	228576	type	True	78.9413	252	1352	95	below_threshold
Alkalihalobacillus xiaoxiensis	strain=DSM 21943	GCA_016907895.1	766895	766895	type	True	78.7395	285	1352	95	below_threshold
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	78.6917	58	1352	95	below_threshold
Anaerobacillus alkalilacustris	strain=DSM 18345	GCA_001866005.1	393763	393763	type	True	77.8164	57	1352	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	77.5392	78	1352	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	77.0973	86	1352	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	77.0561	73	1352	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.6596	76	1352	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:07,949] [INFO] DFAST Taxonomy check result was written to GCF_002019765.1_ASM201976v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:07,950] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:07,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:07,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95e6cbe4-0224-4158-8909-725bd541a3db/dqc_reference/checkm_data
[2024-01-25 20:17:07,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:07,993] [INFO] Task started: CheckM
[2024-01-25 20:17:07,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019765.1_ASM201976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019765.1_ASM201976v1_genomic.fna/checkm_input GCF_002019765.1_ASM201976v1_genomic.fna/checkm_result
[2024-01-25 20:17:35,543] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:35,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:35,570] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:35,570] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:35,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019765.1_ASM201976v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:35,571] [INFO] Task started: Blastn
[2024-01-25 20:17:35,571] [INFO] Running command: blastn -query GCF_002019765.1_ASM201976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95e6cbe4-0224-4158-8909-725bd541a3db/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019765.1_ASM201976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:36,567] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:36,570] [INFO] Selected 19 target genomes.
[2024-01-25 20:17:36,570] [INFO] Target genome list was writen to GCF_002019765.1_ASM201976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:36,587] [INFO] Task started: fastANI
[2024-01-25 20:17:36,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg72c05e0e-47b8-4666-8c6f-9e937c188905/GCF_002019765.1_ASM201976v1_genomic.fna.gz --refList GCF_002019765.1_ASM201976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019765.1_ASM201976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:53,209] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:53,218] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:53,218] [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_002019765.1	s__Bacillus_H oshimensis	99.9921	1348	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	98.95	98.65	0.95	0.93	6	conclusive
GCF_007725405.1	s__Bacillus_H miscanthi	91.1279	1218	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	99.10	99.10	0.94	0.93	3	-
GCF_900197585.1	s__Bacillus_H sp900197585	80.4068	584	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000005825.2	s__Bacillus_S pseudofirmus	79.4476	78	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_002019795.1	s__Bacillus_AO alkalicellulosilyticus	78.9876	60	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019705.1	s__Bacillus_H patagoniensis	78.9415	249	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002109385.1	s__Bacillus_L krulwichiae	78.8723	85	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001866075.3	s__Anaerobacillus isosaccharinicus	78.8496	59	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907895.1	s__Bacillus_H xiaoxiensis	78.7421	285	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	97.73	97.69	0.93	0.93	4	-
GCA_001310375.1	s__Bacillus_H sp001310375	78.4807	221	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	77.6348	77	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513095.1	s__Bacillus_L wakoensis	77.3124	70	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	77.168	88	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_000474275.2	s__Bacillus_S marmarensis	77.0561	73	1352	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:53,219] [INFO] GTDB search result was written to GCF_002019765.1_ASM201976v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:53,220] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:53,222] [INFO] DFAST_QC result json was written to GCF_002019765.1_ASM201976v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:53,223] [INFO] DFAST_QC completed!
[2024-01-25 20:17:53,223] [INFO] Total running time: 0h1m18s