[2023-06-27 15:57:06,700] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:57:06,703] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:57:06,703] [INFO] DQC Reference Directory: /var/lib/cwl/stge1c2bfe7-3069-477e-82f0-603b8960b26a/dqc_reference
[2023-06-27 15:57:07,970] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:57:07,971] [INFO] Task started: Prodigal
[2023-06-27 15:57:07,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dfd510a-9048-4ab6-b552-953d2f416016/GCA_002490355.1_ASM249035v1_genomic.fna.gz | prodigal -d GCA_002490355.1_ASM249035v1_genomic.fna/cds.fna -a GCA_002490355.1_ASM249035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:57:12,347] [INFO] Task succeeded: Prodigal
[2023-06-27 15:57:12,347] [INFO] Task started: HMMsearch
[2023-06-27 15:57:12,348] [INFO] Running command: hmmsearch --tblout GCA_002490355.1_ASM249035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1c2bfe7-3069-477e-82f0-603b8960b26a/dqc_reference/reference_markers.hmm GCA_002490355.1_ASM249035v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:57:12,541] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:57:12,543] [INFO] Found 6/6 markers.
[2023-06-27 15:57:12,566] [INFO] Query marker FASTA was written to GCA_002490355.1_ASM249035v1_genomic.fna/markers.fasta
[2023-06-27 15:57:12,567] [INFO] Task started: Blastn
[2023-06-27 15:57:12,567] [INFO] Running command: blastn -query GCA_002490355.1_ASM249035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1c2bfe7-3069-477e-82f0-603b8960b26a/dqc_reference/reference_markers.fasta -out GCA_002490355.1_ASM249035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:57:13,148] [INFO] Task succeeded: Blastn
[2023-06-27 15:57:13,152] [INFO] Selected 21 target genomes.
[2023-06-27 15:57:13,153] [INFO] Target genome list was writen to GCA_002490355.1_ASM249035v1_genomic.fna/target_genomes.txt
[2023-06-27 15:57:13,156] [INFO] Task started: fastANI
[2023-06-27 15:57:13,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dfd510a-9048-4ab6-b552-953d2f416016/GCA_002490355.1_ASM249035v1_genomic.fna.gz --refList GCA_002490355.1_ASM249035v1_genomic.fna/target_genomes.txt --output GCA_002490355.1_ASM249035v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:57:19,812] [INFO] Task succeeded: fastANI
[2023-06-27 15:57:19,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1c2bfe7-3069-477e-82f0-603b8960b26a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:57:19,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1c2bfe7-3069-477e-82f0-603b8960b26a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:57:19,825] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:57:19,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 15:57:19,826] [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 formosensis	strain=NBRC 109475	GCA_018403745.1	1281486	1281486	type	True	83.9547	367	642	95	below_threshold
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	83.8644	364	642	95	below_threshold
Lactococcus petauri	strain=159469	GCA_002154895.1	1940789	1940789	type	True	83.7593	368	642	95	below_threshold
Lactococcus garvieae subsp. garvieae	strain=CCUG 32208T	GCA_008692985.1	1890280	1363	type	True	83.4921	365	642	95	below_threshold
Lactococcus garvieae	strain=DSM 20684	GCA_002441675.1	1363	1363	type	True	83.4876	360	642	95	below_threshold
Lactococcus garvieae	strain=NBRC 100934	GCA_000739975.1	1363	1363	type	True	83.4377	356	642	95	below_threshold
Lactococcus garvieae	strain=FDAARGOS_929	GCA_016026695.1	1363	1363	type	True	83.4089	367	642	95	below_threshold
Lactococcus cremoris	strain=ATCC 19257	GCA_004354515.1	1359	1359	type	True	77.6774	106	642	95	below_threshold
Lactococcus cremoris subsp. cremoris	strain=NBRC 100676	GCA_001591705.1	2816960	1359	type	True	77.6537	103	642	95	below_threshold
Lactococcus cremoris subsp. tructae	strain=DSM 21502	GCA_002441825.1	542833	1359	type	True	77.5968	112	642	95	below_threshold
Lactococcus cremoris	strain=LMG6897	GCA_001622295.1	1359	1359	type	True	77.5622	101	642	95	below_threshold
Lactococcus cremoris	strain=ATCC 19257	GCA_002441765.1	1359	1359	type	True	77.5597	103	642	95	below_threshold
Lactococcus hircilactis	strain=DSM 28960	GCA_009601015.1	1494462	1494462	type	True	77.2863	62	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 15:57:19,828] [INFO] DFAST Taxonomy check result was written to GCA_002490355.1_ASM249035v1_genomic.fna/tc_result.tsv
[2023-06-27 15:57:19,828] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:57:19,828] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:57:19,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1c2bfe7-3069-477e-82f0-603b8960b26a/dqc_reference/checkm_data
[2023-06-27 15:57:19,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:57:19,854] [INFO] Task started: CheckM
[2023-06-27 15:57:19,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002490355.1_ASM249035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002490355.1_ASM249035v1_genomic.fna/checkm_input GCA_002490355.1_ASM249035v1_genomic.fna/checkm_result
[2023-06-27 15:57:39,465] [INFO] Task succeeded: CheckM
[2023-06-27 15:57:39,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 15:57:39,488] [INFO] ===== Completeness check finished =====
[2023-06-27 15:57:39,489] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:57:39,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002490355.1_ASM249035v1_genomic.fna/markers.fasta)
[2023-06-27 15:57:39,489] [INFO] Task started: Blastn
[2023-06-27 15:57:39,489] [INFO] Running command: blastn -query GCA_002490355.1_ASM249035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1c2bfe7-3069-477e-82f0-603b8960b26a/dqc_reference/reference_markers_gtdb.fasta -out GCA_002490355.1_ASM249035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:57:40,243] [INFO] Task succeeded: Blastn
[2023-06-27 15:57:40,247] [INFO] Selected 12 target genomes.
[2023-06-27 15:57:40,247] [INFO] Target genome list was writen to GCA_002490355.1_ASM249035v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:57:40,266] [INFO] Task started: fastANI
[2023-06-27 15:57:40,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dfd510a-9048-4ab6-b552-953d2f416016/GCA_002490355.1_ASM249035v1_genomic.fna.gz --refList GCA_002490355.1_ASM249035v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002490355.1_ASM249035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:57:45,118] [INFO] Task succeeded: fastANI
[2023-06-27 15:57:45,127] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 15:57:45,127] [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_016758115.1	s__Lactococcus sp002492185	98.6694	563	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.71	98.67	0.89	0.88	5	conclusive
GCF_018403745.1	s__Lactococcus formosensis	83.9547	367	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.20	97.52	0.88	0.85	8	-
GCF_002154895.1	s__Lactococcus petauri	83.7837	367	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.05	96.82	0.88	0.79	32	-
GCF_000739975.1	s__Lactococcus garvieae	83.4048	357	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.58	0.89	0.85	26	-
GCF_016027715.1	s__Lactococcus garvieae_A	81.0868	358	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.50	0.90	0.89	3	-
GCF_004210295.1	s__Lactococcus sp004210295	77.9938	88	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591705.1	s__Lactococcus cremoris	77.6837	102	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.76	97.45	0.91	0.82	70	-
GCF_002441655.1	s__Lactococcus fujiensis	77.6264	72	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	99.84	99.84	0.99	0.99	2	-
GCF_009601055.1	s__Lactococcus sp009601055	77.4408	89	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	100.00	99.99	0.99	0.98	3	-
GCF_009601015.1	s__Lactococcus hircilactis	77.2863	62	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 15:57:45,129] [INFO] GTDB search result was written to GCA_002490355.1_ASM249035v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:57:45,130] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:57:45,134] [INFO] DFAST_QC result json was written to GCA_002490355.1_ASM249035v1_genomic.fna/dqc_result.json
[2023-06-27 15:57:45,134] [INFO] DFAST_QC completed!
[2023-06-27 15:57:45,134] [INFO] Total running time: 0h0m38s