[2024-01-24 14:13:01,562] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,564] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,564] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8f67add-9e96-4b75-af15-f8ba642b3a60/dqc_reference
[2024-01-24 14:13:02,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,818] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcbcb8e7-2519-4edf-988e-fbbcd6b86457/GCF_002441825.1_ASM244182v1_genomic.fna.gz | prodigal -d GCF_002441825.1_ASM244182v1_genomic.fna/cds.fna -a GCF_002441825.1_ASM244182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:08,103] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:08,104] [INFO] Task started: HMMsearch
[2024-01-24 14:13:08,104] [INFO] Running command: hmmsearch --tblout GCF_002441825.1_ASM244182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8f67add-9e96-4b75-af15-f8ba642b3a60/dqc_reference/reference_markers.hmm GCF_002441825.1_ASM244182v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:08,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:08,384] [INFO] Found 6/6 markers.
[2024-01-24 14:13:08,408] [INFO] Query marker FASTA was written to GCF_002441825.1_ASM244182v1_genomic.fna/markers.fasta
[2024-01-24 14:13:08,408] [INFO] Task started: Blastn
[2024-01-24 14:13:08,408] [INFO] Running command: blastn -query GCF_002441825.1_ASM244182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f67add-9e96-4b75-af15-f8ba642b3a60/dqc_reference/reference_markers.fasta -out GCF_002441825.1_ASM244182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:09,001] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:09,004] [INFO] Selected 10 target genomes.
[2024-01-24 14:13:09,005] [INFO] Target genome list was writen to GCF_002441825.1_ASM244182v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:09,028] [INFO] Task started: fastANI
[2024-01-24 14:13:09,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbcb8e7-2519-4edf-988e-fbbcd6b86457/GCF_002441825.1_ASM244182v1_genomic.fna.gz --refList GCF_002441825.1_ASM244182v1_genomic.fna/target_genomes.txt --output GCF_002441825.1_ASM244182v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:14,341] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:14,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8f67add-9e96-4b75-af15-f8ba642b3a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:14,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8f67add-9e96-4b75-af15-f8ba642b3a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:14,355] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:13:14,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:14,356] [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. tructae	strain=DSM 21502	GCA_002441825.1	542833	1359	type	True	100.0	843	844	95	conclusive
Lactococcus cremoris subsp. cremoris	strain=NBRC 100676	GCA_001591705.1	2816960	1359	type	True	97.7248	630	844	95	conclusive
Lactococcus cremoris	strain=LMG6897	GCA_001622295.1	1359	1359	type	True	97.6436	594	844	95	conclusive
Lactococcus cremoris	strain=ATCC 19257	GCA_002441765.1	1359	1359	type	True	97.5537	590	844	95	conclusive
Lactococcus cremoris	strain=ATCC 19257	GCA_004354515.1	1359	1359	type	True	97.4793	616	844	95	conclusive
Lactococcus lactis subsp. hordniae	strain=NBRC 100931	GCA_001591725.1	203404	1358	type	True	87.5276	579	844	95	below_threshold
Lactococcus lactis subsp. hordniae	strain=DSM 20450	GCA_002441785.1	203404	1358	type	True	87.5053	584	844	95	below_threshold
Lactococcus lactis subsp. hordniae	strain=CCUG 32210T	GCA_008692945.1	203404	1358	type	True	87.4274	595	844	95	below_threshold
Lactococcus protaetiae	strain=KACC 19320	GCA_006965445.1	2592653	2592653	type	True	79.1181	301	844	95	below_threshold
Lactococcus paracarnosus	strain=TMW 2.1615	GCA_006770285.1	2749962	2749962	type	True	77.4472	61	844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:14,358] [INFO] DFAST Taxonomy check result was written to GCF_002441825.1_ASM244182v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:14,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:14,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:14,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8f67add-9e96-4b75-af15-f8ba642b3a60/dqc_reference/checkm_data
[2024-01-24 14:13:14,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:14,398] [INFO] Task started: CheckM
[2024-01-24 14:13:14,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002441825.1_ASM244182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002441825.1_ASM244182v1_genomic.fna/checkm_input GCF_002441825.1_ASM244182v1_genomic.fna/checkm_result
[2024-01-24 14:13:38,202] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:38,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:38,233] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:38,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:38,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002441825.1_ASM244182v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:38,234] [INFO] Task started: Blastn
[2024-01-24 14:13:38,234] [INFO] Running command: blastn -query GCF_002441825.1_ASM244182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f67add-9e96-4b75-af15-f8ba642b3a60/dqc_reference/reference_markers_gtdb.fasta -out GCF_002441825.1_ASM244182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:39,012] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:39,015] [INFO] Selected 14 target genomes.
[2024-01-24 14:13:39,015] [INFO] Target genome list was writen to GCF_002441825.1_ASM244182v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:39,040] [INFO] Task started: fastANI
[2024-01-24 14:13:39,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbcb8e7-2519-4edf-988e-fbbcd6b86457/GCF_002441825.1_ASM244182v1_genomic.fna.gz --refList GCF_002441825.1_ASM244182v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002441825.1_ASM244182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:45,515] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:45,525] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:45,526] [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	97.7248	630	844	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	87.4529	629	844	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	81.7638	337	844	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	80.7133	367	844	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	79.3225	169	844	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	79.1034	302	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.72	98.72	0.90	0.90	2	-
GCF_009601055.1	s__Lactococcus sp009601055	78.4659	168	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	100.00	99.99	0.99	0.98	3	-
GCF_018403745.1	s__Lactococcus formosensis	78.4654	132	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.20	97.52	0.88	0.85	8	-
GCF_002441655.1	s__Lactococcus fujiensis	77.9256	152	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	99.84	99.84	0.99	0.99	2	-
GCF_018403765.1	s__Lactococcus nasutitermitis	77.8383	177	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:45,527] [INFO] GTDB search result was written to GCF_002441825.1_ASM244182v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:45,528] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:45,532] [INFO] DFAST_QC result json was written to GCF_002441825.1_ASM244182v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:45,533] [INFO] DFAST_QC completed!
[2024-01-24 14:13:45,533] [INFO] Total running time: 0h0m44s