[2024-01-24 13:31:35,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a871891-8f12-49a3-83ab-74d39c62793b/dqc_reference
[2024-01-24 13:31:36,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,739] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,739] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9ffc3dd-5acf-4fec-86bb-eb99ecb11850/GCF_001281265.1_ASM128126v1_genomic.fna.gz | prodigal -d GCF_001281265.1_ASM128126v1_genomic.fna/cds.fna -a GCF_001281265.1_ASM128126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:39,973] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:39,973] [INFO] Task started: HMMsearch
[2024-01-24 13:31:39,973] [INFO] Running command: hmmsearch --tblout GCF_001281265.1_ASM128126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a871891-8f12-49a3-83ab-74d39c62793b/dqc_reference/reference_markers.hmm GCF_001281265.1_ASM128126v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:40,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:40,221] [INFO] Found 6/6 markers.
[2024-01-24 13:31:40,242] [INFO] Query marker FASTA was written to GCF_001281265.1_ASM128126v1_genomic.fna/markers.fasta
[2024-01-24 13:31:40,242] [INFO] Task started: Blastn
[2024-01-24 13:31:40,242] [INFO] Running command: blastn -query GCF_001281265.1_ASM128126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a871891-8f12-49a3-83ab-74d39c62793b/dqc_reference/reference_markers.fasta -out GCF_001281265.1_ASM128126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:40,921] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:40,924] [INFO] Selected 8 target genomes.
[2024-01-24 13:31:40,924] [INFO] Target genome list was writen to GCF_001281265.1_ASM128126v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:40,940] [INFO] Task started: fastANI
[2024-01-24 13:31:40,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9ffc3dd-5acf-4fec-86bb-eb99ecb11850/GCF_001281265.1_ASM128126v1_genomic.fna.gz --refList GCF_001281265.1_ASM128126v1_genomic.fna/target_genomes.txt --output GCF_001281265.1_ASM128126v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:43,991] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:43,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a871891-8f12-49a3-83ab-74d39c62793b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:43,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a871891-8f12-49a3-83ab-74d39c62793b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:43,998] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:43,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:43,998] [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
Apilactobacillus kunkeei	strain=YH-15	GCA_001281265.1	148814	148814	suspected-type	True	100.0	496	496	95	conclusive
Apilactobacillus kunkeei	strain=DSM 12361	GCA_001433825.1	148814	148814	suspected-type	True	99.9845	486	496	95	conclusive
Apilactobacillus waqarii	strain=HBW1	GCA_019061205.1	2851006	2851006	type	True	93.5675	446	496	95	below_threshold
Apilactobacillus nanyangensis	strain=HN36-1	GCA_016861915.1	2799579	2799579	type	True	92.5874	414	496	95	below_threshold
Apilactobacillus zhangqiuensis	strain=F502-1	GCA_019656215.1	2841031	2841031	type	True	91.3456	441	496	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:43,999] [INFO] DFAST Taxonomy check result was written to GCF_001281265.1_ASM128126v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:44,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:44,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:44,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a871891-8f12-49a3-83ab-74d39c62793b/dqc_reference/checkm_data
[2024-01-24 13:31:44,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:44,026] [INFO] Task started: CheckM
[2024-01-24 13:31:44,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001281265.1_ASM128126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001281265.1_ASM128126v1_genomic.fna/checkm_input GCF_001281265.1_ASM128126v1_genomic.fna/checkm_result
[2024-01-24 13:32:02,089] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:02,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:02,110] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:02,111] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:02,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001281265.1_ASM128126v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:02,112] [INFO] Task started: Blastn
[2024-01-24 13:32:02,112] [INFO] Running command: blastn -query GCF_001281265.1_ASM128126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a871891-8f12-49a3-83ab-74d39c62793b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001281265.1_ASM128126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:02,921] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:02,924] [INFO] Selected 6 target genomes.
[2024-01-24 13:32:02,925] [INFO] Target genome list was writen to GCF_001281265.1_ASM128126v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:02,928] [INFO] Task started: fastANI
[2024-01-24 13:32:02,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9ffc3dd-5acf-4fec-86bb-eb99ecb11850/GCF_001281265.1_ASM128126v1_genomic.fna.gz --refList GCF_001281265.1_ASM128126v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001281265.1_ASM128126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:05,273] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:05,282] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:05,282] [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_001281265.1	s__Apilactobacillus kunkeei	100.0	496	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	97.63	95.32	0.94	0.90	8	conclusive
GCF_001308195.1	s__Apilactobacillus kunkeei_C	94.6262	448	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	95.16	95.16	0.91	0.91	2	-
GCF_005930975.1	s__Apilactobacillus kunkeei_E	94.14	437	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001949975.2	s__Apilactobacillus kunkeei_A	93.9228	446	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	96.15	95.05	0.91	0.88	13	-
GCF_005930915.1	s__Apilactobacillus kunkeei_D	92.5362	426	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.78	97.92	0.96	0.94	5	-
GCF_001308205.1	s__Apilactobacillus kunkeei_B	91.1918	431	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:05,283] [INFO] GTDB search result was written to GCF_001281265.1_ASM128126v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:05,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:05,287] [INFO] DFAST_QC result json was written to GCF_001281265.1_ASM128126v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:05,288] [INFO] DFAST_QC completed!
[2024-01-24 13:32:05,288] [INFO] Total running time: 0h0m30s