[2024-01-24 13:30:11,204] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:30:11,207] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:30:11,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg35f8e703-c7d9-4c3f-9a7c-f9bcf9f54bac/dqc_reference
[2024-01-24 13:30:12,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:30:12,506] [INFO] Task started: Prodigal
[2024-01-24 13:30:12,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d06f51e-4161-49cd-9700-8ccaf185fb53/GCF_002441885.1_ASM244188v1_genomic.fna.gz | prodigal -d GCF_002441885.1_ASM244188v1_genomic.fna/cds.fna -a GCF_002441885.1_ASM244188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:30:17,208] [INFO] Task succeeded: Prodigal
[2024-01-24 13:30:17,208] [INFO] Task started: HMMsearch
[2024-01-24 13:30:17,208] [INFO] Running command: hmmsearch --tblout GCF_002441885.1_ASM244188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35f8e703-c7d9-4c3f-9a7c-f9bcf9f54bac/dqc_reference/reference_markers.hmm GCF_002441885.1_ASM244188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:30:17,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:30:17,463] [INFO] Found 6/6 markers.
[2024-01-24 13:30:17,486] [INFO] Query marker FASTA was written to GCF_002441885.1_ASM244188v1_genomic.fna/markers.fasta
[2024-01-24 13:30:17,487] [INFO] Task started: Blastn
[2024-01-24 13:30:17,487] [INFO] Running command: blastn -query GCF_002441885.1_ASM244188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35f8e703-c7d9-4c3f-9a7c-f9bcf9f54bac/dqc_reference/reference_markers.fasta -out GCF_002441885.1_ASM244188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:18,100] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:18,105] [INFO] Selected 10 target genomes.
[2024-01-24 13:30:18,106] [INFO] Target genome list was writen to GCF_002441885.1_ASM244188v1_genomic.fna/target_genomes.txt
[2024-01-24 13:30:18,114] [INFO] Task started: fastANI
[2024-01-24 13:30:18,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d06f51e-4161-49cd-9700-8ccaf185fb53/GCF_002441885.1_ASM244188v1_genomic.fna.gz --refList GCF_002441885.1_ASM244188v1_genomic.fna/target_genomes.txt --output GCF_002441885.1_ASM244188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:30:22,676] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:22,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35f8e703-c7d9-4c3f-9a7c-f9bcf9f54bac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:30:22,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35f8e703-c7d9-4c3f-9a7c-f9bcf9f54bac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:30:22,683] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:30:22,683] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:30:22,684] [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 chungangensis	strain=DSM 22330	GCA_002441885.1	451457	451457	type	True	100.0	701	706	95	conclusive
Lactococcus chungangensis	strain=DSM 22330	GCA_900119835.1	451457	451457	type	True	99.9813	701	706	95	conclusive
Lactococcus laudensis	strain=LMG 28353	GCA_019586025.1	1494461	1494461	type	True	91.8835	533	706	95	below_threshold
Lactococcus laudensis	strain=DSM 28961	GCA_013449735.1	1494461	1494461	type	True	91.8267	537	706	95	below_threshold
Lactococcus raffinolactis	strain=NBRC 100932	GCA_001591765.1	1366	1366	type	True	85.5928	495	706	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:30:22,685] [INFO] DFAST Taxonomy check result was written to GCF_002441885.1_ASM244188v1_genomic.fna/tc_result.tsv
[2024-01-24 13:30:22,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:30:22,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:30:22,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35f8e703-c7d9-4c3f-9a7c-f9bcf9f54bac/dqc_reference/checkm_data
[2024-01-24 13:30:22,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:30:22,715] [INFO] Task started: CheckM
[2024-01-24 13:30:22,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002441885.1_ASM244188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002441885.1_ASM244188v1_genomic.fna/checkm_input GCF_002441885.1_ASM244188v1_genomic.fna/checkm_result
[2024-01-24 13:30:45,688] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:45,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:45,710] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:45,710] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:45,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002441885.1_ASM244188v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:45,711] [INFO] Task started: Blastn
[2024-01-24 13:30:45,712] [INFO] Running command: blastn -query GCF_002441885.1_ASM244188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35f8e703-c7d9-4c3f-9a7c-f9bcf9f54bac/dqc_reference/reference_markers_gtdb.fasta -out GCF_002441885.1_ASM244188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:46,555] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:46,558] [INFO] Selected 9 target genomes.
[2024-01-24 13:30:46,558] [INFO] Target genome list was writen to GCF_002441885.1_ASM244188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:46,566] [INFO] Task started: fastANI
[2024-01-24 13:30:46,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d06f51e-4161-49cd-9700-8ccaf185fb53/GCF_002441885.1_ASM244188v1_genomic.fna.gz --refList GCF_002441885.1_ASM244188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002441885.1_ASM244188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:50,808] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:50,817] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:50,817] [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_002441885.1	s__Lactococcus_A chungangensis	100.0	701	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.24	98.46	0.92	0.88	4	conclusive
GCF_013449735.1	s__Lactococcus_A laudensis	91.8267	537	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	97.98	97.98	0.86	0.86	2	-
GCF_001591765.1	s__Lactococcus_A raffinolactis	85.6238	493	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.11	98.57	0.92	0.88	14	-
GCF_002260845.1	s__Lactococcus_A reticulitermitis	83.9035	458	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002441715.1	s__Lactococcus_A plantarum	79.9114	211	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.99	99.98	1.00	0.99	3	-
GCF_002441695.1	s__Lactococcus_A piscium	79.7057	247	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006770265.1	s__Lactococcus_A carnosus	79.5535	220	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	97.28	95.96	0.91	0.89	5	-
GCF_011170065.1	s__Lactococcus_A insecticola	78.8873	197	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011170085.1	s__Lactococcus_A hodotermopsidis	78.1956	189	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:50,819] [INFO] GTDB search result was written to GCF_002441885.1_ASM244188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:50,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:50,826] [INFO] DFAST_QC result json was written to GCF_002441885.1_ASM244188v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:50,826] [INFO] DFAST_QC completed!
[2024-01-24 13:30:50,826] [INFO] Total running time: 0h0m40s