[2024-01-24 14:11:51,135] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:51,138] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:51,138] [INFO] DQC Reference Directory: /var/lib/cwl/stgae4e1843-df97-49d9-8762-f53933c7bc96/dqc_reference
[2024-01-24 14:11:52,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,548] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,549] [INFO] Running command: gunzip -c /var/lib/cwl/stg061a84b5-8749-4c68-bb9f-4f2e05c6ad12/GCF_023921225.1_ASM2392122v1_genomic.fna.gz | prodigal -d GCF_023921225.1_ASM2392122v1_genomic.fna/cds.fna -a GCF_023921225.1_ASM2392122v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:00,598] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:00,599] [INFO] Task started: HMMsearch
[2024-01-24 14:12:00,599] [INFO] Running command: hmmsearch --tblout GCF_023921225.1_ASM2392122v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae4e1843-df97-49d9-8762-f53933c7bc96/dqc_reference/reference_markers.hmm GCF_023921225.1_ASM2392122v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:00,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:01,001] [INFO] Found 6/6 markers.
[2024-01-24 14:12:01,034] [INFO] Query marker FASTA was written to GCF_023921225.1_ASM2392122v1_genomic.fna/markers.fasta
[2024-01-24 14:12:01,035] [INFO] Task started: Blastn
[2024-01-24 14:12:01,035] [INFO] Running command: blastn -query GCF_023921225.1_ASM2392122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae4e1843-df97-49d9-8762-f53933c7bc96/dqc_reference/reference_markers.fasta -out GCF_023921225.1_ASM2392122v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:01,826] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:01,829] [INFO] Selected 14 target genomes.
[2024-01-24 14:12:01,830] [INFO] Target genome list was writen to GCF_023921225.1_ASM2392122v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:01,840] [INFO] Task started: fastANI
[2024-01-24 14:12:01,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg061a84b5-8749-4c68-bb9f-4f2e05c6ad12/GCF_023921225.1_ASM2392122v1_genomic.fna.gz --refList GCF_023921225.1_ASM2392122v1_genomic.fna/target_genomes.txt --output GCF_023921225.1_ASM2392122v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:11,753] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:11,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae4e1843-df97-49d9-8762-f53933c7bc96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:11,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae4e1843-df97-49d9-8762-f53933c7bc96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:11,764] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:11,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:11,764] [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 lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	100.0	1223	1235	95	conclusive
Legionella rowbothamii	strain=LLAP6	GCA_900639985.1	96229	96229	type	True	86.9469	973	1235	95	below_threshold
Legionella saoudiensis	strain=LS-1	GCA_001465875.1	1750561	1750561	type	True	84.6658	882	1235	95	below_threshold
Legionella drancourtii	strain=LLAP12	GCA_000162755.2	168933	168933	type	True	79.3639	400	1235	95	below_threshold
Legionella bononiensis	strain=30cs62	GCA_016786415.1	2793102	2793102	type	True	78.9006	160	1235	95	below_threshold
Legionella antarctica	strain=TUM19329	GCA_011764505.1	2708020	2708020	type	True	78.7993	169	1235	95	below_threshold
Legionella longbeachae	strain=FDAARGOS_1481	GCA_019930685.1	450	450	type	True	78.7576	211	1235	95	below_threshold
Legionella steelei	strain=IMVS3376	GCA_001468005.1	947033	947033	type	True	78.6812	266	1235	95	below_threshold
Legionella bozemanae	strain=WIGA	GCA_001467045.1	447	447	type	True	78.3605	252	1235	95	below_threshold
Legionella tucsonensis	strain=ATCC 49180	GCA_001468035.1	40335	40335	type	True	78.1773	228	1235	95	below_threshold
Legionella tucsonensis	strain=1087-AZ-H	GCA_900640035.1	40335	40335	type	True	78.084	226	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:11,766] [INFO] DFAST Taxonomy check result was written to GCF_023921225.1_ASM2392122v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:11,767] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:11,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:11,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae4e1843-df97-49d9-8762-f53933c7bc96/dqc_reference/checkm_data
[2024-01-24 14:12:11,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:11,811] [INFO] Task started: CheckM
[2024-01-24 14:12:11,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023921225.1_ASM2392122v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023921225.1_ASM2392122v1_genomic.fna/checkm_input GCF_023921225.1_ASM2392122v1_genomic.fna/checkm_result
[2024-01-24 14:12:42,160] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:42,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:42,185] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:42,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:42,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023921225.1_ASM2392122v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:42,186] [INFO] Task started: Blastn
[2024-01-24 14:12:42,186] [INFO] Running command: blastn -query GCF_023921225.1_ASM2392122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae4e1843-df97-49d9-8762-f53933c7bc96/dqc_reference/reference_markers_gtdb.fasta -out GCF_023921225.1_ASM2392122v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:45,067] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:45,071] [INFO] Selected 17 target genomes.
[2024-01-24 14:12:45,072] [INFO] Target genome list was writen to GCF_023921225.1_ASM2392122v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:45,145] [INFO] Task started: fastANI
[2024-01-24 14:12:45,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg061a84b5-8749-4c68-bb9f-4f2e05c6ad12/GCF_023921225.1_ASM2392122v1_genomic.fna.gz --refList GCF_023921225.1_ASM2392122v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023921225.1_ASM2392122v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:12:57,765] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:57,842] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:12:57,843] [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_900639985.1	s__Legionella rowbothamii	86.9214	975	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001465875.1	s__Legionella saoudiensis	84.6739	883	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000162755.2	s__Legionella drancourtii	79.3703	399	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236165.1	s__Legionella dumoffii	78.9275	221	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.81	99.55	0.97	0.94	4	-
GCF_001467525.1	s__Legionella anisa	78.9059	260	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_011764505.1	s__Legionella sp011764505	78.8946	167	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016786215.1	s__Legionella sp016786215	78.8651	169	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
GCF_001468005.1	s__Legionella steelei	78.6053	271	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.95	98.94	0.93	0.93	3	-
GCF_900635815.1	s__Legionella cherrii	78.533	242	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.61	0.99	0.97	4	-
GCA_004283175.1	s__Legionella longbeachae	78.3356	200	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.77	99.22	0.96	0.94	9	-
GCF_001468135.1	s__Legionella santicrucis	78.2903	249	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.96	99.96	0.98	0.98	2	-
GCF_000423305.1	s__Legionella moravica	78.2577	147	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.09	96.46	0.96	0.86	5	-
GCF_900156395.1	s__Legionella gormanii	78.2412	254	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.78	98.94	0.98	0.92	6	-
GCF_001648595.1	s__Legionella bozemanae	78.2394	249	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_001468035.1	s__Legionella tucsonensis	78.1773	228	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001468065.1	s__Legionella steigerwaltii	78.0984	252	1235	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.99	0.99	0.99	3	-
GCA_002352055.1	s__Legionella sp002352055	77.8356	131	1235	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 14:12:57,844] [INFO] GTDB search result was written to GCF_023921225.1_ASM2392122v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:12:57,845] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:12:57,849] [INFO] DFAST_QC result json was written to GCF_023921225.1_ASM2392122v1_genomic.fna/dqc_result.json
[2024-01-24 14:12:57,850] [INFO] DFAST_QC completed!
[2024-01-24 14:12:57,850] [INFO] Total running time: 0h1m7s