[2024-01-24 15:14:50,129] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:50,130] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:50,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg08a313e8-a58c-437e-b22c-e1e00c248971/dqc_reference
[2024-01-24 15:14:51,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:51,347] [INFO] Task started: Prodigal
[2024-01-24 15:14:51,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg55eae8f6-97c3-4344-b10c-957481e9ddc0/GCF_000621385.1_ASM62138v1_genomic.fna.gz | prodigal -d GCF_000621385.1_ASM62138v1_genomic.fna/cds.fna -a GCF_000621385.1_ASM62138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:14:59,411] [INFO] Task succeeded: Prodigal
[2024-01-24 15:14:59,412] [INFO] Task started: HMMsearch
[2024-01-24 15:14:59,412] [INFO] Running command: hmmsearch --tblout GCF_000621385.1_ASM62138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08a313e8-a58c-437e-b22c-e1e00c248971/dqc_reference/reference_markers.hmm GCF_000621385.1_ASM62138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:14:59,693] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:14:59,695] [INFO] Found 6/6 markers.
[2024-01-24 15:14:59,735] [INFO] Query marker FASTA was written to GCF_000621385.1_ASM62138v1_genomic.fna/markers.fasta
[2024-01-24 15:14:59,735] [INFO] Task started: Blastn
[2024-01-24 15:14:59,735] [INFO] Running command: blastn -query GCF_000621385.1_ASM62138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08a313e8-a58c-437e-b22c-e1e00c248971/dqc_reference/reference_markers.fasta -out GCF_000621385.1_ASM62138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:00,443] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:00,453] [INFO] Selected 10 target genomes.
[2024-01-24 15:15:00,453] [INFO] Target genome list was writen to GCF_000621385.1_ASM62138v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:00,461] [INFO] Task started: fastANI
[2024-01-24 15:15:00,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg55eae8f6-97c3-4344-b10c-957481e9ddc0/GCF_000621385.1_ASM62138v1_genomic.fna.gz --refList GCF_000621385.1_ASM62138v1_genomic.fna/target_genomes.txt --output GCF_000621385.1_ASM62138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:08,874] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:08,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08a313e8-a58c-437e-b22c-e1e00c248971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:08,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08a313e8-a58c-437e-b22c-e1e00c248971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:08,885] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:15:08,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:08,886] [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
Legionella cherrii	strain=DSM 19213	GCA_000621385.1	28084	28084	type	True	100.0	1224	1226	95	conclusive
Legionella cherrii	strain=NCTC11976	GCA_900635815.1	28084	28084	type	True	99.9941	1226	1226	95	conclusive
Legionella cherrii	strain=ORW	GCA_900640085.1	28084	28084	type	True	99.9915	1221	1226	95	conclusive
Legionella cherrii	strain=ORW	GCA_001467035.1	28084	28084	type	True	99.5999	1203	1226	95	conclusive
Legionella steigerwaltii	strain=SC-18-C9	GCA_900640025.1	460	460	type	True	85.5185	991	1226	95	below_threshold
Legionella steelei	strain=IMVS3376	GCA_001468005.1	947033	947033	type	True	83.7329	896	1226	95	below_threshold
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	78.0236	232	1226	95	below_threshold
Legionella pneumophila subsp. pneumophila	strain=PartS-Lpneumophila-RM8376	GCA_022870105.1	91891	446	type	True	77.4504	161	1226	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:08,887] [INFO] DFAST Taxonomy check result was written to GCF_000621385.1_ASM62138v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:08,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:08,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:08,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08a313e8-a58c-437e-b22c-e1e00c248971/dqc_reference/checkm_data
[2024-01-24 15:15:08,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:08,928] [INFO] Task started: CheckM
[2024-01-24 15:15:08,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621385.1_ASM62138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621385.1_ASM62138v1_genomic.fna/checkm_input GCF_000621385.1_ASM62138v1_genomic.fna/checkm_result
[2024-01-24 15:15:39,100] [INFO] Task succeeded: CheckM
[2024-01-24 15:15:39,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:15:39,122] [INFO] ===== Completeness check finished =====
[2024-01-24 15:15:39,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:15:39,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621385.1_ASM62138v1_genomic.fna/markers.fasta)
[2024-01-24 15:15:39,123] [INFO] Task started: Blastn
[2024-01-24 15:15:39,123] [INFO] Running command: blastn -query GCF_000621385.1_ASM62138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08a313e8-a58c-437e-b22c-e1e00c248971/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621385.1_ASM62138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:40,095] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:40,099] [INFO] Selected 9 target genomes.
[2024-01-24 15:15:40,099] [INFO] Target genome list was writen to GCF_000621385.1_ASM62138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:15:40,109] [INFO] Task started: fastANI
[2024-01-24 15:15:40,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg55eae8f6-97c3-4344-b10c-957481e9ddc0/GCF_000621385.1_ASM62138v1_genomic.fna.gz --refList GCF_000621385.1_ASM62138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621385.1_ASM62138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:15:48,472] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:48,484] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:15:48,484] [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_900635815.1	s__Legionella cherrii	99.9941	1226	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.61	0.99	0.97	4	conclusive
GCF_001468065.1	s__Legionella steigerwaltii	85.5745	984	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001468005.1	s__Legionella steelei	83.7368	896	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.95	98.94	0.93	0.93	3	-
GCF_001467525.1	s__Legionella anisa	81.6599	763	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_001648595.1	s__Legionella bozemanae	81.5778	745	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_003184185.1	s__Legionella qingyii	81.2711	752	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.76	0.97	0.97	3	-
GCF_900156395.1	s__Legionella gormanii	81.2512	765	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.78	98.94	0.98	0.92	6	-
GCF_000236165.1	s__Legionella dumoffii	81.1435	717	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.81	99.55	0.97	0.94	4	-
GCF_014109805.1	s__Legionella sp014109805	81.0992	758	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:15:48,486] [INFO] GTDB search result was written to GCF_000621385.1_ASM62138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:15:48,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:15:48,490] [INFO] DFAST_QC result json was written to GCF_000621385.1_ASM62138v1_genomic.fna/dqc_result.json
[2024-01-24 15:15:48,490] [INFO] DFAST_QC completed!
[2024-01-24 15:15:48,490] [INFO] Total running time: 0h0m58s