[2023-06-08 02:20:09,954] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:20:09,957] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:20:09,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c21d4f2-f22c-439e-aab6-374857df29ec/dqc_reference
[2023-06-08 02:20:11,291] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:20:11,292] [INFO] Task started: Prodigal
[2023-06-08 02:20:11,292] [INFO] Running command: gunzip -c /var/lib/cwl/stg80a61204-f0fb-43d5-9877-b85f9338868c/GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:20:15,083] [INFO] Task succeeded: Prodigal
[2023-06-08 02:20:15,084] [INFO] Task started: HMMsearch
[2023-06-08 02:20:15,084] [INFO] Running command: hmmsearch --tblout GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c21d4f2-f22c-439e-aab6-374857df29ec/dqc_reference/reference_markers.hmm GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:20:15,333] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:20:15,335] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg80a61204-f0fb-43d5-9877-b85f9338868c/GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 02:20:15,356] [INFO] Query marker FASTA was written to GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 02:20:15,356] [INFO] Task started: Blastn
[2023-06-08 02:20:15,356] [INFO] Running command: blastn -query GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c21d4f2-f22c-439e-aab6-374857df29ec/dqc_reference/reference_markers.fasta -out GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:15,966] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:15,970] [INFO] Selected 10 target genomes.
[2023-06-08 02:20:15,970] [INFO] Target genome list was writen to GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 02:20:15,973] [INFO] Task started: fastANI
[2023-06-08 02:20:15,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg80a61204-f0fb-43d5-9877-b85f9338868c/GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:20:20,326] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:20,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c21d4f2-f22c-439e-aab6-374857df29ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:20:20,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c21d4f2-f22c-439e-aab6-374857df29ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:20:20,334] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2023-06-08 02:20:20,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 02:20:20,334] [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 garvieae	strain=DSM 20684	GCA_002441675.1	1363	1363	type	True	98.1933	415	514	95	conclusive
Lactococcus garvieae	strain=NBRC 100934	GCA_000739975.1	1363	1363	type	True	98.1581	413	514	95	conclusive
Lactococcus garvieae	strain=FDAARGOS_929	GCA_016026695.1	1363	1363	type	True	98.132	424	514	95	conclusive
Lactococcus garvieae subsp. garvieae	strain=CCUG 32208T	GCA_008692985.1	1890280	1363	type	True	98.0443	424	514	95	conclusive
Lactococcus petauri	strain=159469	GCA_002154895.1	1940789	1940789	type	True	93.0097	429	514	95	below_threshold
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	90.9844	417	514	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 02:20:20,336] [INFO] DFAST Taxonomy check result was written to GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 02:20:20,337] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:20:20,337] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:20:20,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c21d4f2-f22c-439e-aab6-374857df29ec/dqc_reference/checkm_data
[2023-06-08 02:20:20,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:20:20,361] [INFO] Task started: CheckM
[2023-06-08 02:20:20,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 02:20:39,991] [INFO] Task succeeded: CheckM
[2023-06-08 02:20:39,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:20:40,029] [INFO] ===== Completeness check finished =====
[2023-06-08 02:20:40,030] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:20:40,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 02:20:40,031] [INFO] Task started: Blastn
[2023-06-08 02:20:40,031] [INFO] Running command: blastn -query GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c21d4f2-f22c-439e-aab6-374857df29ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:40,770] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:40,774] [INFO] Selected 7 target genomes.
[2023-06-08 02:20:40,774] [INFO] Target genome list was writen to GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:20:40,777] [INFO] Task started: fastANI
[2023-06-08 02:20:40,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg80a61204-f0fb-43d5-9877-b85f9338868c/GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:20:43,744] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:43,752] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 02:20:43,753] [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_000739975.1	s__Lactococcus garvieae	98.1581	413	514	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.58	0.89	0.85	26	conclusive
GCF_002154895.1	s__Lactococcus petauri	93.0097	429	514	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.05	96.82	0.88	0.79	32	-
GCF_018403745.1	s__Lactococcus formosensis	90.8515	403	514	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.20	97.52	0.88	0.85	8	-
GCF_016758115.1	s__Lactococcus sp002492185	83.593	319	514	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.71	98.67	0.89	0.88	5	-
GCF_016027715.1	s__Lactococcus garvieae_A	83.0153	323	514	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.50	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-08 02:20:43,755] [INFO] GTDB search result was written to GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 02:20:43,755] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:20:43,759] [INFO] DFAST_QC result json was written to GCA_947072355.1_ERR5094895_bin.1_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 02:20:43,759] [INFO] DFAST_QC completed!
[2023-06-08 02:20:43,759] [INFO] Total running time: 0h0m34s