[2024-01-24 13:13:51,532] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:51,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:51,535] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdfca59a-a086-44d9-ae1b-2fe1394b99c1/dqc_reference
[2024-01-24 13:13:52,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:52,884] [INFO] Task started: Prodigal
[2024-01-24 13:13:52,885] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d23420f-47e8-4efb-b278-05a587f30c4e/GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna.gz | prodigal -d GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/cds.fna -a GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:59,241] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:59,241] [INFO] Task started: HMMsearch
[2024-01-24 13:13:59,241] [INFO] Running command: hmmsearch --tblout GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdfca59a-a086-44d9-ae1b-2fe1394b99c1/dqc_reference/reference_markers.hmm GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:59,510] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:59,511] [INFO] Found 6/6 markers.
[2024-01-24 13:13:59,547] [INFO] Query marker FASTA was written to GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/markers.fasta
[2024-01-24 13:13:59,548] [INFO] Task started: Blastn
[2024-01-24 13:13:59,548] [INFO] Running command: blastn -query GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdfca59a-a086-44d9-ae1b-2fe1394b99c1/dqc_reference/reference_markers.fasta -out GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:00,429] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:00,433] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:00,433] [INFO] Target genome list was writen to GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:00,440] [INFO] Task started: fastANI
[2024-01-24 13:14:00,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d23420f-47e8-4efb-b278-05a587f30c4e/GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna.gz --refList GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/target_genomes.txt --output GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:09,892] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:09,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdfca59a-a086-44d9-ae1b-2fe1394b99c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:09,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdfca59a-a086-44d9-ae1b-2fe1394b99c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:09,904] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:14:09,904] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:09,904] [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 lansingensis	strain=1677-MI-H	GCA_900640195.1	45067	45067	type	True	100.0	934	937	95	conclusive
Legionella lansingensis	strain=NCTC12830	GCA_900187355.1	45067	45067	type	True	99.9858	936	937	95	conclusive
Legionella lansingensis	strain=ATCC 49751	GCA_001467795.1	45067	45067	type	True	99.9764	920	937	95	conclusive
Legionella lansingensis	strain=ATCC 49751	GCA_000622185.1	45067	45067	type	True	99.9721	927	937	95	conclusive
Legionella brunensis	strain=ATCC 43878	GCA_001467025.1	29422	29422	type	True	78.2039	286	937	95	below_threshold
Legionella clemsonensis	strain=CDC-D5610	GCA_002240035.1	1867846	1867846	type	True	77.9695	212	937	95	below_threshold
Legionella hackeliae	strain=ATCC35250	GCA_000953655.1	449	449	type	True	77.7998	229	937	95	below_threshold
Legionella jamestowniensis	strain=DSM 19215	GCA_900114725.1	455	455	type	True	77.7015	214	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,910] [INFO] DFAST Taxonomy check result was written to GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:09,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:09,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:09,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdfca59a-a086-44d9-ae1b-2fe1394b99c1/dqc_reference/checkm_data
[2024-01-24 13:14:09,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:09,955] [INFO] Task started: CheckM
[2024-01-24 13:14:09,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/checkm_input GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/checkm_result
[2024-01-24 13:14:37,344] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:37,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:37,433] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:37,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:37,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:37,435] [INFO] Task started: Blastn
[2024-01-24 13:14:37,435] [INFO] Running command: blastn -query GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdfca59a-a086-44d9-ae1b-2fe1394b99c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:38,684] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:38,688] [INFO] Selected 19 target genomes.
[2024-01-24 13:14:38,689] [INFO] Target genome list was writen to GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:38,943] [INFO] Task started: fastANI
[2024-01-24 13:14:38,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d23420f-47e8-4efb-b278-05a587f30c4e/GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna.gz --refList GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:50,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:50,936] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:50,936] [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_900187355.1	s__Tatlockia lansingensis	99.9858	936	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.99	99.98	1.00	1.00	4	conclusive
GCF_001467025.1	s__Tatlockia brunensis	78.2039	286	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900637635.1	s__Tatlockia jordanis	78.0943	175	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.59	0.99	0.98	6	-
GCF_002240035.1	s__Tatlockia clemsonensis	77.9745	213	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467745.1	s__Tatlockia jamestowniensis	77.8325	211	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.71	99.16	0.98	0.95	4	-
GCF_000953655.1	s__Tatlockia hackeliae	77.7866	230	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.95	99.91	0.98	0.96	3	-
GCF_000512355.1	s__Legionella_A oakridgensis	77.638	73	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	99.85	99.51	0.97	0.90	5	-
GCF_001467585.1	s__Tatlockia drozanskii	77.6228	114	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.88	99.79	0.97	0.95	3	-
GCF_900640175.1	s__Tatlockia sp900640175	77.5119	140	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900452415.1	s__Legionella cincinnatiensis	77.4925	87	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000756815.1	s__Tatlockia massiliensis	77.481	116	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000308315.1	s__Tatlockia tunisiensis	77.3235	157	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637685.1	s__Legionella sainthelensi	77.2326	64	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.79	95.71	0.95	0.89	8	-
GCF_001468135.1	s__Legionella santicrucis	77.1488	75	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.96	99.96	0.98	0.98	2	-
GCF_900635815.1	s__Legionella cherrii	77.0399	86	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.61	0.99	0.97	4	-
GCF_001468005.1	s__Legionella steelei	76.9763	90	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.95	98.94	0.93	0.93	3	-
GCF_003184185.1	s__Legionella qingyii	76.8967	72	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.76	0.97	0.97	3	-
GCF_016786215.1	s__Legionella sp016786215	76.8403	66	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
GCF_001467955.1	s__Legionella quateirensis	76.832	81	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.97	99.97	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:50,938] [INFO] GTDB search result was written to GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:50,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:50,944] [INFO] DFAST_QC result json was written to GCF_900640195.1_Leg_lansingensis_1677-MI-H.v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:50,944] [INFO] DFAST_QC completed!
[2024-01-24 13:14:50,944] [INFO] Total running time: 0h0m59s