[2024-01-24 14:22:03,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:03,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:03,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg03790370-01d8-4c1c-9d13-c42bdfb635ab/dqc_reference
[2024-01-24 14:22:05,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,303] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,303] [INFO] Running command: gunzip -c /var/lib/cwl/stge150d35a-6e92-43d3-ae13-2097d34cff79/GCF_002886255.1_ASM288625v1_genomic.fna.gz | prodigal -d GCF_002886255.1_ASM288625v1_genomic.fna/cds.fna -a GCF_002886255.1_ASM288625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:15,557] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:15,558] [INFO] Task started: HMMsearch
[2024-01-24 14:22:15,558] [INFO] Running command: hmmsearch --tblout GCF_002886255.1_ASM288625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03790370-01d8-4c1c-9d13-c42bdfb635ab/dqc_reference/reference_markers.hmm GCF_002886255.1_ASM288625v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:15,881] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:15,883] [INFO] Found 6/6 markers.
[2024-01-24 14:22:15,982] [INFO] Query marker FASTA was written to GCF_002886255.1_ASM288625v1_genomic.fna/markers.fasta
[2024-01-24 14:22:15,982] [INFO] Task started: Blastn
[2024-01-24 14:22:15,982] [INFO] Running command: blastn -query GCF_002886255.1_ASM288625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03790370-01d8-4c1c-9d13-c42bdfb635ab/dqc_reference/reference_markers.fasta -out GCF_002886255.1_ASM288625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:16,630] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:16,636] [INFO] Selected 19 target genomes.
[2024-01-24 14:22:16,637] [INFO] Target genome list was writen to GCF_002886255.1_ASM288625v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:16,644] [INFO] Task started: fastANI
[2024-01-24 14:22:16,644] [INFO] Running command: fastANI --query /var/lib/cwl/stge150d35a-6e92-43d3-ae13-2097d34cff79/GCF_002886255.1_ASM288625v1_genomic.fna.gz --refList GCF_002886255.1_ASM288625v1_genomic.fna/target_genomes.txt --output GCF_002886255.1_ASM288625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:31,739] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:31,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03790370-01d8-4c1c-9d13-c42bdfb635ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:31,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03790370-01d8-4c1c-9d13-c42bdfb635ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:31,749] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:31,749] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:31,749] [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
Alteribacillus bidgolensis	strain=DSM 25260	GCA_002886255.1	930129	930129	type	True	100.0	1566	1567	95	conclusive
Alteribacillus bidgolensis	strain=P4B,CCM 7963,CECT 7998,DSM 25260,IBRC-M 10614,KCTC 13821	GCA_900099745.1	930129	930129	type	True	99.9671	1516	1567	95	conclusive
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	78.5601	66	1567	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	78.4081	52	1567	95	below_threshold
Alteribacillus persepolensis	strain=DSM 21632	GCA_900099605.1	568899	568899	type	True	78.283	362	1567	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	77.3293	78	1567	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.2766	57	1567	95	below_threshold
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	76.1835	59	1567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:31,751] [INFO] DFAST Taxonomy check result was written to GCF_002886255.1_ASM288625v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:31,752] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:31,752] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:31,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03790370-01d8-4c1c-9d13-c42bdfb635ab/dqc_reference/checkm_data
[2024-01-24 14:22:31,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:31,799] [INFO] Task started: CheckM
[2024-01-24 14:22:31,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002886255.1_ASM288625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002886255.1_ASM288625v1_genomic.fna/checkm_input GCF_002886255.1_ASM288625v1_genomic.fna/checkm_result
[2024-01-24 14:23:06,299] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:06,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:06,323] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:06,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:06,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002886255.1_ASM288625v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:06,324] [INFO] Task started: Blastn
[2024-01-24 14:23:06,324] [INFO] Running command: blastn -query GCF_002886255.1_ASM288625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03790370-01d8-4c1c-9d13-c42bdfb635ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_002886255.1_ASM288625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:07,070] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:07,074] [INFO] Selected 19 target genomes.
[2024-01-24 14:23:07,074] [INFO] Target genome list was writen to GCF_002886255.1_ASM288625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:07,088] [INFO] Task started: fastANI
[2024-01-24 14:23:07,088] [INFO] Running command: fastANI --query /var/lib/cwl/stge150d35a-6e92-43d3-ae13-2097d34cff79/GCF_002886255.1_ASM288625v1_genomic.fna.gz --refList GCF_002886255.1_ASM288625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002886255.1_ASM288625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:21,683] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:21,698] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:21,698] [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_002886255.1	s__Alteribacillus bidgolensis	100.0	1566	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Alteribacillus	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_009765375.1	s__Alteribacillus sp009765375	92.307	1137	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Alteribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217835.1	s__Metabacillus litoralis_A	79.3603	67	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_007995155.1	s__Cytobacillus dafuensis	79.1202	58	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002335745.1	s__FJAT-44876 sp002335745	78.5659	63	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__FJAT-44876	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866075.3	s__Anaerobacillus isosaccharinicus	78.4573	68	1567	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_002797315.1	s__C254 sp002797315	78.3768	119	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__C254	95.0	96.15	96.15	0.88	0.88	2	-
GCF_900099605.1	s__Alteribacillus persepolensis	78.277	363	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Alteribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343665.1	s__Cytobacillus sp018343665	78.0728	65	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318295.1	s__Maribacillus taeanensis	77.3309	79	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Maribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017497975.1	s__Metabacillus sp017497975	77.1438	56	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017745675.1	s__Bacillus_BH sp017745675	76.2894	77	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039105.1	s__Desertibacillus haloalkaliphilus	76.2033	60	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__KJ1-10-99;g__Desertibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:21,700] [INFO] GTDB search result was written to GCF_002886255.1_ASM288625v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:21,700] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:21,704] [INFO] DFAST_QC result json was written to GCF_002886255.1_ASM288625v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:21,704] [INFO] DFAST_QC completed!
[2024-01-24 14:23:21,704] [INFO] Total running time: 0h1m18s