[2024-01-24 13:49:00,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b867e1f-fceb-4245-897a-8c98b2c78515/dqc_reference
[2024-01-24 13:49:01,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,698] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg840cafa9-20f9-41ce-89ec-bfcc47cd3b05/GCF_001050475.1_ASM105047v1_genomic.fna.gz | prodigal -d GCF_001050475.1_ASM105047v1_genomic.fna/cds.fna -a GCF_001050475.1_ASM105047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:07,692] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:07,693] [INFO] Task started: HMMsearch
[2024-01-24 13:49:07,693] [INFO] Running command: hmmsearch --tblout GCF_001050475.1_ASM105047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b867e1f-fceb-4245-897a-8c98b2c78515/dqc_reference/reference_markers.hmm GCF_001050475.1_ASM105047v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:07,950] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:07,952] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg840cafa9-20f9-41ce-89ec-bfcc47cd3b05/GCF_001050475.1_ASM105047v1_genomic.fna.gz]
[2024-01-24 13:49:07,980] [INFO] Query marker FASTA was written to GCF_001050475.1_ASM105047v1_genomic.fna/markers.fasta
[2024-01-24 13:49:07,981] [INFO] Task started: Blastn
[2024-01-24 13:49:07,981] [INFO] Running command: blastn -query GCF_001050475.1_ASM105047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b867e1f-fceb-4245-897a-8c98b2c78515/dqc_reference/reference_markers.fasta -out GCF_001050475.1_ASM105047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:08,567] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:08,571] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:08,571] [INFO] Target genome list was writen to GCF_001050475.1_ASM105047v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:08,601] [INFO] Task started: fastANI
[2024-01-24 13:49:08,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg840cafa9-20f9-41ce-89ec-bfcc47cd3b05/GCF_001050475.1_ASM105047v1_genomic.fna.gz --refList GCF_001050475.1_ASM105047v1_genomic.fna/target_genomes.txt --output GCF_001050475.1_ASM105047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:15,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:15,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b867e1f-fceb-4245-897a-8c98b2c78515/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:15,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b867e1f-fceb-4245-897a-8c98b2c78515/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:15,899] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:15,900] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:15,900] [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
Companilactobacillus ginsenosidimutans	strain=EMML 3041	GCA_001050475.1	1007676	1007676	type	True	100.0	857	863	95	conclusive
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	81.6981	387	863	95	below_threshold
Companilactobacillus furfuricola	strain=JCM 18764	GCA_003946325.1	1462575	1462575	type	True	80.9098	365	863	95	below_threshold
Companilactobacillus zhongbaensis	strain=M1575	GCA_003946515.1	2486009	2486009	type	True	80.4296	393	863	95	below_threshold
Companilactobacillus versmoldensis	strain=KCTC 3814	GCA_000260455.1	194326	194326	type	True	80.3824	356	863	95	below_threshold
Companilactobacillus versmoldensis	strain=DSM 14857	GCA_001434295.1	194326	194326	type	True	80.339	361	863	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	79.5252	196	863	95	below_threshold
Companilactobacillus insicii	strain=DSM 29801	GCA_003946015.1	1732567	1732567	type	True	79.169	186	863	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	79.0555	194	863	95	below_threshold
Companilactobacillus suantsaicola	strain=BCRC 81127	GCA_004745525.1	2487723	2487723	type	True	78.9379	180	863	95	below_threshold
Companilactobacillus nantensis	strain=DSM 16982	GCA_001435815.1	305793	305793	type	True	78.8945	198	863	95	below_threshold
Companilactobacillus heilongjiangensis	strain=S4-3	GCA_005405325.1	1074467	1074467	type	True	78.8899	207	863	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	78.852	176	863	95	below_threshold
Companilactobacillus pabuli	strain=NFFJ11	GCA_014058425.1	2714036	2714036	type	True	78.8368	210	863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:15,902] [INFO] DFAST Taxonomy check result was written to GCF_001050475.1_ASM105047v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:15,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:15,903] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:15,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b867e1f-fceb-4245-897a-8c98b2c78515/dqc_reference/checkm_data
[2024-01-24 13:49:15,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:15,937] [INFO] Task started: CheckM
[2024-01-24 13:49:15,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050475.1_ASM105047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050475.1_ASM105047v1_genomic.fna/checkm_input GCF_001050475.1_ASM105047v1_genomic.fna/checkm_result
[2024-01-24 13:49:41,199] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:41,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:41,222] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:41,223] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:41,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050475.1_ASM105047v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:41,224] [INFO] Task started: Blastn
[2024-01-24 13:49:41,224] [INFO] Running command: blastn -query GCF_001050475.1_ASM105047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b867e1f-fceb-4245-897a-8c98b2c78515/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050475.1_ASM105047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:41,955] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:41,958] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:41,958] [INFO] Target genome list was writen to GCF_001050475.1_ASM105047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:42,001] [INFO] Task started: fastANI
[2024-01-24 13:49:42,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg840cafa9-20f9-41ce-89ec-bfcc47cd3b05/GCF_001050475.1_ASM105047v1_genomic.fna.gz --refList GCF_001050475.1_ASM105047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001050475.1_ASM105047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:48,342] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:48,357] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:48,357] [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_001050475.1	s__Companilactobacillus ginsenosidimutans	100.0	860	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003946505.1	s__Companilactobacillus mishanensis	81.6718	389	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	98.34	97.53	0.96	0.93	4	-
GCF_003946325.1	s__Companilactobacillus furfuricola	80.9268	364	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946515.1	s__Companilactobacillus zhongbaensis	80.4296	393	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434295.1	s__Companilactobacillus versmoldensis	80.3553	360	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_001434665.1	s__Companilactobacillus tucceti	80.1581	211	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971585.1	s__Companilactobacillus allii	79.4888	199	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000831645.3	s__Companilactobacillus heilongjiangensis	79.3772	213	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003946015.1	s__Companilactobacillus insicii	79.1447	187	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946575.1	s__Companilactobacillus jidongensis	79.0637	211	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014058425.1	s__Companilactobacillus pabuli	78.999	211	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.23	98.09	0.94	0.87	5	-
GCF_004745525.1	s__Companilactobacillus suantsaicola	78.9379	180	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435815.1	s__Companilactobacillus nantensis	78.8937	198	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:48,359] [INFO] GTDB search result was written to GCF_001050475.1_ASM105047v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:48,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:48,363] [INFO] DFAST_QC result json was written to GCF_001050475.1_ASM105047v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:48,363] [INFO] DFAST_QC completed!
[2024-01-24 13:49:48,363] [INFO] Total running time: 0h0m48s