[2024-01-24 13:49:41,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:41,312] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:41,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg40b2150f-1663-43c3-8926-6676bbbaef1a/dqc_reference
[2024-01-24 13:49:42,557] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,558] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,558] [INFO] Running command: gunzip -c /var/lib/cwl/stg5af0c444-6d68-4027-8a65-28b76e5853cc/GCF_001591745.1_ASM159174v1_genomic.fna.gz | prodigal -d GCF_001591745.1_ASM159174v1_genomic.fna/cds.fna -a GCF_001591745.1_ASM159174v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:46,427] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:46,427] [INFO] Task started: HMMsearch
[2024-01-24 13:49:46,427] [INFO] Running command: hmmsearch --tblout GCF_001591745.1_ASM159174v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40b2150f-1663-43c3-8926-6676bbbaef1a/dqc_reference/reference_markers.hmm GCF_001591745.1_ASM159174v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:46,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:46,728] [INFO] Found 6/6 markers.
[2024-01-24 13:49:46,753] [INFO] Query marker FASTA was written to GCF_001591745.1_ASM159174v1_genomic.fna/markers.fasta
[2024-01-24 13:49:46,754] [INFO] Task started: Blastn
[2024-01-24 13:49:46,754] [INFO] Running command: blastn -query GCF_001591745.1_ASM159174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b2150f-1663-43c3-8926-6676bbbaef1a/dqc_reference/reference_markers.fasta -out GCF_001591745.1_ASM159174v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:47,426] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:47,430] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:47,431] [INFO] Target genome list was writen to GCF_001591745.1_ASM159174v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:47,458] [INFO] Task started: fastANI
[2024-01-24 13:49:47,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af0c444-6d68-4027-8a65-28b76e5853cc/GCF_001591745.1_ASM159174v1_genomic.fna.gz --refList GCF_001591745.1_ASM159174v1_genomic.fna/target_genomes.txt --output GCF_001591745.1_ASM159174v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:55,950] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:55,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40b2150f-1663-43c3-8926-6676bbbaef1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:55,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40b2150f-1663-43c3-8926-6676bbbaef1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:55,958] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:55,959] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:55,959] [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 plantarum	strain=DSM 20686	GCA_002441715.1	1365	1365	type	True	99.9953	635	637	95	conclusive
Lactococcus paracarnosus	strain=TMW 2.1615	GCA_006770285.1	2749962	2749962	type	True	80.3752	304	637	95	below_threshold
Lactococcus piscium	strain=DSM 6634	GCA_002441695.1	1364	1364	suspected-type	True	80.2079	315	637	95	below_threshold
Lactococcus carnosus	strain=TMW 2.1612	GCA_006770265.1	2749961	2749961	type	True	79.9388	316	637	95	below_threshold
Lactococcus raffinolactis	strain=NBRC 100932	GCA_001591765.1	1366	1366	type	True	79.5367	193	637	95	below_threshold
Lactococcus laudensis	strain=LMG 28353	GCA_019586025.1	1494461	1494461	type	True	79.477	209	637	95	below_threshold
Lactococcus protaetiae	strain=KACC 19320	GCA_006965445.1	2592653	2592653	type	True	76.9675	52	637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,963] [INFO] DFAST Taxonomy check result was written to GCF_001591745.1_ASM159174v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:55,964] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:55,964] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:55,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40b2150f-1663-43c3-8926-6676bbbaef1a/dqc_reference/checkm_data
[2024-01-24 13:49:55,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:55,992] [INFO] Task started: CheckM
[2024-01-24 13:49:55,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591745.1_ASM159174v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591745.1_ASM159174v1_genomic.fna/checkm_input GCF_001591745.1_ASM159174v1_genomic.fna/checkm_result
[2024-01-24 13:50:15,773] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:15,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:15,797] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:15,797] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:15,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591745.1_ASM159174v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:15,798] [INFO] Task started: Blastn
[2024-01-24 13:50:15,799] [INFO] Running command: blastn -query GCF_001591745.1_ASM159174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b2150f-1663-43c3-8926-6676bbbaef1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591745.1_ASM159174v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:16,590] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:16,596] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:16,596] [INFO] Target genome list was writen to GCF_001591745.1_ASM159174v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:16,616] [INFO] Task started: fastANI
[2024-01-24 13:50:16,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af0c444-6d68-4027-8a65-28b76e5853cc/GCF_001591745.1_ASM159174v1_genomic.fna.gz --refList GCF_001591745.1_ASM159174v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591745.1_ASM159174v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:25,982] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:25,990] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:25,990] [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_002441715.1	s__Lactococcus_A plantarum	99.9953	635	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.99	99.98	1.00	0.99	3	conclusive
GCF_006770285.1	s__Lactococcus_A paracarnosus	80.3752	304	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.90	99.90	0.97	0.97	2	-
GCF_002441695.1	s__Lactococcus_A piscium	80.1976	316	637	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	79.9388	316	637	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_013449735.1	s__Lactococcus_A laudensis	79.8414	213	637	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_002441885.1	s__Lactococcus_A chungangensis	79.7664	207	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.24	98.46	0.92	0.88	4	-
GCF_001591765.1	s__Lactococcus_A raffinolactis	79.5367	193	637	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	79.0895	160	637	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 13:50:25,992] [INFO] GTDB search result was written to GCF_001591745.1_ASM159174v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:25,992] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:25,995] [INFO] DFAST_QC result json was written to GCF_001591745.1_ASM159174v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:25,996] [INFO] DFAST_QC completed!
[2024-01-24 13:50:25,996] [INFO] Total running time: 0h0m45s