[2024-01-24 14:14:37,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,470] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgf94ee510-5517-4564-a731-659f08bfd398/dqc_reference
[2024-01-24 14:14:38,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,883] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,883] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf008b90-b5c0-4013-a2a6-3159011f3234/GCF_001591705.1_ASM159170v1_genomic.fna.gz | prodigal -d GCF_001591705.1_ASM159170v1_genomic.fna/cds.fna -a GCF_001591705.1_ASM159170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:43,722] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:43,723] [INFO] Task started: HMMsearch
[2024-01-24 14:14:43,723] [INFO] Running command: hmmsearch --tblout GCF_001591705.1_ASM159170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf94ee510-5517-4564-a731-659f08bfd398/dqc_reference/reference_markers.hmm GCF_001591705.1_ASM159170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:44,061] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:44,063] [INFO] Found 6/6 markers.
[2024-01-24 14:14:44,096] [INFO] Query marker FASTA was written to GCF_001591705.1_ASM159170v1_genomic.fna/markers.fasta
[2024-01-24 14:14:44,097] [INFO] Task started: Blastn
[2024-01-24 14:14:44,097] [INFO] Running command: blastn -query GCF_001591705.1_ASM159170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf94ee510-5517-4564-a731-659f08bfd398/dqc_reference/reference_markers.fasta -out GCF_001591705.1_ASM159170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:46,904] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:46,908] [INFO] Selected 10 target genomes.
[2024-01-24 14:14:46,908] [INFO] Target genome list was writen to GCF_001591705.1_ASM159170v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:46,922] [INFO] Task started: fastANI
[2024-01-24 14:14:46,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf008b90-b5c0-4013-a2a6-3159011f3234/GCF_001591705.1_ASM159170v1_genomic.fna.gz --refList GCF_001591705.1_ASM159170v1_genomic.fna/target_genomes.txt --output GCF_001591705.1_ASM159170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:52,852] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:52,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf94ee510-5517-4564-a731-659f08bfd398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:52,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf94ee510-5517-4564-a731-659f08bfd398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:52,911] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:14:52,911] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:52,912] [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
Lactococcus cremoris subsp. cremoris	strain=NBRC 100676	GCA_001591705.1	2816960	1359	type	True	100.0	715	721	95	conclusive
Lactococcus cremoris	strain=LMG6897	GCA_001622295.1	1359	1359	type	True	99.2728	618	721	95	conclusive
Lactococcus cremoris	strain=ATCC 19257	GCA_004354515.1	1359	1359	type	True	99.2666	648	721	95	conclusive
Lactococcus cremoris	strain=ATCC 19257	GCA_002441765.1	1359	1359	type	True	99.1733	615	721	95	conclusive
Lactococcus cremoris subsp. tructae	strain=DSM 21502	GCA_002441825.1	542833	1359	type	True	97.759	636	721	95	conclusive
Lactococcus lactis subsp. hordniae	strain=NBRC 100931	GCA_001591725.1	203404	1358	type	True	87.437	537	721	95	below_threshold
Lactococcus lactis subsp. hordniae	strain=CCUG 32210T	GCA_008692945.1	203404	1358	type	True	87.4205	538	721	95	below_threshold
Lactococcus lactis subsp. hordniae	strain=DSM 20450	GCA_002441785.1	203404	1358	type	True	87.2743	547	721	95	below_threshold
Lactococcus paracarnosus	strain=TMW 2.1615	GCA_006770285.1	2749962	2749962	type	True	77.3893	56	721	95	below_threshold
Lactococcus carnosus	strain=TMW 2.1612	GCA_006770265.1	2749961	2749961	type	True	77.149	51	721	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:52,914] [INFO] DFAST Taxonomy check result was written to GCF_001591705.1_ASM159170v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:52,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:52,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:52,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf94ee510-5517-4564-a731-659f08bfd398/dqc_reference/checkm_data
[2024-01-24 14:14:52,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:52,975] [INFO] Task started: CheckM
[2024-01-24 14:14:52,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591705.1_ASM159170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591705.1_ASM159170v1_genomic.fna/checkm_input GCF_001591705.1_ASM159170v1_genomic.fna/checkm_result
[2024-01-24 14:15:14,908] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:14,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:14,934] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:14,935] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:14,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591705.1_ASM159170v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:14,936] [INFO] Task started: Blastn
[2024-01-24 14:15:14,936] [INFO] Running command: blastn -query GCF_001591705.1_ASM159170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf94ee510-5517-4564-a731-659f08bfd398/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591705.1_ASM159170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:15,801] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:15,804] [INFO] Selected 16 target genomes.
[2024-01-24 14:15:15,805] [INFO] Target genome list was writen to GCF_001591705.1_ASM159170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:15,818] [INFO] Task started: fastANI
[2024-01-24 14:15:15,818] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf008b90-b5c0-4013-a2a6-3159011f3234/GCF_001591705.1_ASM159170v1_genomic.fna.gz --refList GCF_001591705.1_ASM159170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591705.1_ASM159170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:23,575] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:23,597] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:23,597] [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_001591705.1	s__Lactococcus cremoris	100.0	715	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.76	97.45	0.91	0.82	70	conclusive
GCF_900099625.1	s__Lactococcus lactis	87.8849	567	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.03	0.87	0.82	223	-
GCF_014905395.1	s__Lactococcus taiwanensis	81.8555	311	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.39	0.94	0.93	6	-
GCF_004210295.1	s__Lactococcus sp004210295	80.9292	328	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601015.1	s__Lactococcus hircilactis	79.9673	161	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006965445.1	s__Lactococcus sp006965445	79.2487	275	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.72	98.72	0.90	0.90	2	-
GCF_002441655.1	s__Lactococcus fujiensis	78.635	130	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	99.84	99.84	0.99	0.99	2	-
GCF_018403745.1	s__Lactococcus formosensis	78.616	122	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.20	97.52	0.88	0.85	8	-
GCF_009601055.1	s__Lactococcus sp009601055	78.4377	168	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	100.00	99.99	0.99	0.98	3	-
GCF_000187935.1	s__Streptococcus parauberis	78.3746	56	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.87	98.45	0.89	0.84	24	-
GCF_018403765.1	s__Lactococcus nasutitermitis	78.0641	153	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016758115.1	s__Lactococcus sp002492185	77.9437	115	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.71	98.67	0.89	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:23,599] [INFO] GTDB search result was written to GCF_001591705.1_ASM159170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:23,599] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:23,603] [INFO] DFAST_QC result json was written to GCF_001591705.1_ASM159170v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:23,603] [INFO] DFAST_QC completed!
[2024-01-24 14:15:23,603] [INFO] Total running time: 0h0m46s