[2024-01-24 13:40:34,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,907] [INFO] DQC Reference Directory: /var/lib/cwl/stgc242065b-edc5-4bad-9f81-6cae3b6a2c7e/dqc_reference
[2024-01-24 13:40:36,268] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,269] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,269] [INFO] Running command: gunzip -c /var/lib/cwl/stgacefb15d-569b-4490-bfce-bea9fa3dbcf6/GCF_002260845.1_ASM226084v1_genomic.fna.gz | prodigal -d GCF_002260845.1_ASM226084v1_genomic.fna/cds.fna -a GCF_002260845.1_ASM226084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:41,569] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:41,570] [INFO] Task started: HMMsearch
[2024-01-24 13:40:41,570] [INFO] Running command: hmmsearch --tblout GCF_002260845.1_ASM226084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc242065b-edc5-4bad-9f81-6cae3b6a2c7e/dqc_reference/reference_markers.hmm GCF_002260845.1_ASM226084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:41,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:41,856] [INFO] Found 6/6 markers.
[2024-01-24 13:40:41,880] [INFO] Query marker FASTA was written to GCF_002260845.1_ASM226084v1_genomic.fna/markers.fasta
[2024-01-24 13:40:41,880] [INFO] Task started: Blastn
[2024-01-24 13:40:41,880] [INFO] Running command: blastn -query GCF_002260845.1_ASM226084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc242065b-edc5-4bad-9f81-6cae3b6a2c7e/dqc_reference/reference_markers.fasta -out GCF_002260845.1_ASM226084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:42,498] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:42,501] [INFO] Selected 10 target genomes.
[2024-01-24 13:40:42,502] [INFO] Target genome list was writen to GCF_002260845.1_ASM226084v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:42,507] [INFO] Task started: fastANI
[2024-01-24 13:40:42,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgacefb15d-569b-4490-bfce-bea9fa3dbcf6/GCF_002260845.1_ASM226084v1_genomic.fna.gz --refList GCF_002260845.1_ASM226084v1_genomic.fna/target_genomes.txt --output GCF_002260845.1_ASM226084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:47,644] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:47,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc242065b-edc5-4bad-9f81-6cae3b6a2c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:47,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc242065b-edc5-4bad-9f81-6cae3b6a2c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:47,651] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:47,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:47,652] [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 reticulitermitis	strain=Rs-Y01	GCA_002260845.1	2025039	2025039	type	True	100.0	711	712	95	conclusive
Lactococcus laudensis	strain=LMG 28353	GCA_019586025.1	1494461	1494461	type	True	85.0151	479	712	95	below_threshold
Lactococcus raffinolactis	strain=ATCC 43920	GCA_002441745.1	1366	1366	type	True	84.9798	474	712	95	below_threshold
Lactococcus raffinolactis	strain=NBRC 100932	GCA_001591765.1	1366	1366	type	True	84.9765	478	712	95	below_threshold
Lactococcus laudensis	strain=DSM 28961	GCA_013449735.1	1494461	1494461	type	True	84.8579	498	712	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:47,653] [INFO] DFAST Taxonomy check result was written to GCF_002260845.1_ASM226084v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:47,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:47,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:47,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc242065b-edc5-4bad-9f81-6cae3b6a2c7e/dqc_reference/checkm_data
[2024-01-24 13:40:47,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:47,683] [INFO] Task started: CheckM
[2024-01-24 13:40:47,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002260845.1_ASM226084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002260845.1_ASM226084v1_genomic.fna/checkm_input GCF_002260845.1_ASM226084v1_genomic.fna/checkm_result
[2024-01-24 13:41:11,936] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:11,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:11,968] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:11,968] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:11,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002260845.1_ASM226084v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:11,969] [INFO] Task started: Blastn
[2024-01-24 13:41:11,969] [INFO] Running command: blastn -query GCF_002260845.1_ASM226084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc242065b-edc5-4bad-9f81-6cae3b6a2c7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002260845.1_ASM226084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:12,854] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:12,860] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:12,860] [INFO] Target genome list was writen to GCF_002260845.1_ASM226084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:12,868] [INFO] Task started: fastANI
[2024-01-24 13:41:12,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgacefb15d-569b-4490-bfce-bea9fa3dbcf6/GCF_002260845.1_ASM226084v1_genomic.fna.gz --refList GCF_002260845.1_ASM226084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002260845.1_ASM226084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:17,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:17,320] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:17,321] [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_002260845.1	s__Lactococcus_A reticulitermitis	100.0	711	712	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001591765.1	s__Lactococcus_A raffinolactis	84.9765	478	712	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_013449735.1	s__Lactococcus_A laudensis	84.8422	499	712	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	83.7788	464	712	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_002441695.1	s__Lactococcus_A piscium	79.6779	224	712	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	78.9592	162	712	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_011170065.1	s__Lactococcus_A insecticola	78.8931	231	712	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	78.488	233	712	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 13:41:17,322] [INFO] GTDB search result was written to GCF_002260845.1_ASM226084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:17,323] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:17,326] [INFO] DFAST_QC result json was written to GCF_002260845.1_ASM226084v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:17,326] [INFO] DFAST_QC completed!
[2024-01-24 13:41:17,326] [INFO] Total running time: 0h0m42s