[2023-06-05 06:18:58,636] [INFO] DFAST_QC pipeline started.
[2023-06-05 06:18:58,642] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 06:18:58,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg189380a3-2421-481f-ae6c-14e0269ef1b9/dqc_reference
[2023-06-05 06:19:01,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 06:19:01,625] [INFO] Task started: Prodigal
[2023-06-05 06:19:01,625] [INFO] Running command: gunzip -c /var/lib/cwl/stgfad8b941-340e-474b-8c75-84ee0d7e0ec2/GCA_934191625.1_ERR7738559_bin.15_genomic.fna.gz | prodigal -d GCA_934191625.1_ERR7738559_bin.15_genomic.fna/cds.fna -a GCA_934191625.1_ERR7738559_bin.15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 06:19:06,101] [INFO] Task succeeded: Prodigal
[2023-06-05 06:19:06,102] [INFO] Task started: HMMsearch
[2023-06-05 06:19:06,102] [INFO] Running command: hmmsearch --tblout GCA_934191625.1_ERR7738559_bin.15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg189380a3-2421-481f-ae6c-14e0269ef1b9/dqc_reference/reference_markers.hmm GCA_934191625.1_ERR7738559_bin.15_genomic.fna/protein.faa > /dev/null
[2023-06-05 06:19:06,346] [INFO] Task succeeded: HMMsearch
[2023-06-05 06:19:06,361] [INFO] Found 6/6 markers.
[2023-06-05 06:19:06,389] [INFO] Query marker FASTA was written to GCA_934191625.1_ERR7738559_bin.15_genomic.fna/markers.fasta
[2023-06-05 06:19:06,390] [INFO] Task started: Blastn
[2023-06-05 06:19:06,390] [INFO] Running command: blastn -query GCA_934191625.1_ERR7738559_bin.15_genomic.fna/markers.fasta -db /var/lib/cwl/stg189380a3-2421-481f-ae6c-14e0269ef1b9/dqc_reference/reference_markers.fasta -out GCA_934191625.1_ERR7738559_bin.15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:19:06,966] [INFO] Task succeeded: Blastn
[2023-06-05 06:19:06,970] [INFO] Selected 11 target genomes.
[2023-06-05 06:19:06,971] [INFO] Target genome list was writen to GCA_934191625.1_ERR7738559_bin.15_genomic.fna/target_genomes.txt
[2023-06-05 06:19:06,975] [INFO] Task started: fastANI
[2023-06-05 06:19:06,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgfad8b941-340e-474b-8c75-84ee0d7e0ec2/GCA_934191625.1_ERR7738559_bin.15_genomic.fna.gz --refList GCA_934191625.1_ERR7738559_bin.15_genomic.fna/target_genomes.txt --output GCA_934191625.1_ERR7738559_bin.15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 06:19:11,776] [INFO] Task succeeded: fastANI
[2023-06-05 06:19:11,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg189380a3-2421-481f-ae6c-14e0269ef1b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 06:19:11,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg189380a3-2421-481f-ae6c-14e0269ef1b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 06:19:11,790] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 06:19:11,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 06:19:11,790] [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 petauri	strain=159469	GCA_002154895.1	1940789	1940789	type	True	90.3551	578	687	95	below_threshold
Lactococcus garvieae subsp. garvieae	strain=CCUG 32208T	GCA_008692985.1	1890280	1363	type	True	89.6977	531	687	95	below_threshold
Lactococcus garvieae	strain=DSM 20684	GCA_002441675.1	1363	1363	type	True	89.604	528	687	95	below_threshold
Lactococcus garvieae	strain=NBRC 100934	GCA_000739975.1	1363	1363	type	True	89.5586	537	687	95	below_threshold
Lactococcus garvieae	strain=FDAARGOS_929	GCA_016026695.1	1363	1363	type	True	89.4721	551	687	95	below_threshold
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	89.2366	553	687	95	below_threshold
Lactococcus formosensis	strain=NBRC 109475	GCA_018403745.1	1281486	1281486	type	True	89.1657	553	687	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 06:19:11,792] [INFO] DFAST Taxonomy check result was written to GCA_934191625.1_ERR7738559_bin.15_genomic.fna/tc_result.tsv
[2023-06-05 06:19:11,792] [INFO] ===== Taxonomy check completed =====
[2023-06-05 06:19:11,793] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 06:19:11,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg189380a3-2421-481f-ae6c-14e0269ef1b9/dqc_reference/checkm_data
[2023-06-05 06:19:11,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 06:19:11,821] [INFO] Task started: CheckM
[2023-06-05 06:19:11,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934191625.1_ERR7738559_bin.15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934191625.1_ERR7738559_bin.15_genomic.fna/checkm_input GCA_934191625.1_ERR7738559_bin.15_genomic.fna/checkm_result
[2023-06-05 06:19:32,498] [INFO] Task succeeded: CheckM
[2023-06-05 06:19:32,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 06:19:32,521] [INFO] ===== Completeness check finished =====
[2023-06-05 06:19:32,521] [INFO] ===== Start GTDB Search =====
[2023-06-05 06:19:32,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934191625.1_ERR7738559_bin.15_genomic.fna/markers.fasta)
[2023-06-05 06:19:32,522] [INFO] Task started: Blastn
[2023-06-05 06:19:32,522] [INFO] Running command: blastn -query GCA_934191625.1_ERR7738559_bin.15_genomic.fna/markers.fasta -db /var/lib/cwl/stg189380a3-2421-481f-ae6c-14e0269ef1b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_934191625.1_ERR7738559_bin.15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:19:33,319] [INFO] Task succeeded: Blastn
[2023-06-05 06:19:33,324] [INFO] Selected 7 target genomes.
[2023-06-05 06:19:33,325] [INFO] Target genome list was writen to GCA_934191625.1_ERR7738559_bin.15_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 06:19:33,330] [INFO] Task started: fastANI
[2023-06-05 06:19:33,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgfad8b941-340e-474b-8c75-84ee0d7e0ec2/GCA_934191625.1_ERR7738559_bin.15_genomic.fna.gz --refList GCA_934191625.1_ERR7738559_bin.15_genomic.fna/target_genomes_gtdb.txt --output GCA_934191625.1_ERR7738559_bin.15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 06:19:36,810] [INFO] Task succeeded: fastANI
[2023-06-05 06:19:36,821] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 06:19:36,822] [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_002154895.1	s__Lactococcus petauri	90.3551	578	687	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	89.5586	537	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.58	0.89	0.85	26	-
GCF_018403745.1	s__Lactococcus formosensis	89.1657	553	687	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	82.9395	396	687	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	82.3469	439	687	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	78.7332	119	687	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	78.598	130	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.76	97.45	0.91	0.82	70	-
--------------------------------------------------------------------------------
[2023-06-05 06:19:36,824] [INFO] GTDB search result was written to GCA_934191625.1_ERR7738559_bin.15_genomic.fna/result_gtdb.tsv
[2023-06-05 06:19:36,824] [INFO] ===== GTDB Search completed =====
[2023-06-05 06:19:36,827] [INFO] DFAST_QC result json was written to GCA_934191625.1_ERR7738559_bin.15_genomic.fna/dqc_result.json
[2023-06-05 06:19:36,827] [INFO] DFAST_QC completed!
[2023-06-05 06:19:36,828] [INFO] Total running time: 0h0m38s