[2024-01-25 18:56:50,715] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:50,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:50,717] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7c4e467-3823-41ba-be19-7eb0785d6233/dqc_reference
[2024-01-25 18:56:51,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:51,856] [INFO] Task started: Prodigal
[2024-01-25 18:56:51,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg651e2364-3977-4873-ab07-98c29f33adab/GCF_900452565.1_34347_D01_genomic.fna.gz | prodigal -d GCF_900452565.1_34347_D01_genomic.fna/cds.fna -a GCF_900452565.1_34347_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:58,661] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:58,662] [INFO] Task started: HMMsearch
[2024-01-25 18:56:58,662] [INFO] Running command: hmmsearch --tblout GCF_900452565.1_34347_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7c4e467-3823-41ba-be19-7eb0785d6233/dqc_reference/reference_markers.hmm GCF_900452565.1_34347_D01_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:58,885] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:58,887] [INFO] Found 6/6 markers.
[2024-01-25 18:56:58,917] [INFO] Query marker FASTA was written to GCF_900452565.1_34347_D01_genomic.fna/markers.fasta
[2024-01-25 18:56:58,917] [INFO] Task started: Blastn
[2024-01-25 18:56:58,917] [INFO] Running command: blastn -query GCF_900452565.1_34347_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7c4e467-3823-41ba-be19-7eb0785d6233/dqc_reference/reference_markers.fasta -out GCF_900452565.1_34347_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:59,520] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:59,523] [INFO] Selected 16 target genomes.
[2024-01-25 18:56:59,523] [INFO] Target genome list was writen to GCF_900452565.1_34347_D01_genomic.fna/target_genomes.txt
[2024-01-25 18:56:59,539] [INFO] Task started: fastANI
[2024-01-25 18:56:59,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg651e2364-3977-4873-ab07-98c29f33adab/GCF_900452565.1_34347_D01_genomic.fna.gz --refList GCF_900452565.1_34347_D01_genomic.fna/target_genomes.txt --output GCF_900452565.1_34347_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:09,880] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:09,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7c4e467-3823-41ba-be19-7eb0785d6233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:09,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7c4e467-3823-41ba-be19-7eb0785d6233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:09,889] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:57:09,889] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:09,889] [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 hackeliae	strain=NCTC11979	GCA_900452565.1	449	449	type	True	100.0	1191	1192	95	conclusive
Legionella hackeliae	strain=ATCC35250	GCA_000953655.1	449	449	type	True	99.9907	1188	1192	95	conclusive
Legionella bononiensis	strain=30cs62	GCA_016786415.1	2793102	2793102	type	True	80.3636	121	1192	95	below_threshold
Legionella clemsonensis	strain=CDC-D5610	GCA_002240035.1	1867846	1867846	type	True	79.9979	465	1192	95	below_threshold
Legionella jamestowniensis	strain=JA-26-G1-E2	GCA_001467745.1	455	455	type	True	79.7255	468	1192	95	below_threshold
Legionella jamestowniensis	strain=DSM 19215	GCA_900114725.1	455	455	type	True	79.5794	480	1192	95	below_threshold
Legionella jamestowniensis	strain=JA-26-G1-E2	GCA_900640205.1	455	455	type	True	79.5598	490	1192	95	below_threshold
Legionella feeleii	strain=NCTC12022	GCA_900452475.1	453	453	type	True	78.3316	179	1192	95	below_threshold
Legionella lansingensis	strain=ATCC 49751	GCA_000622185.1	45067	45067	type	True	78.1476	216	1192	95	below_threshold
Legionella lansingensis	strain=ATCC 49751	GCA_001467795.1	45067	45067	type	True	78.1192	213	1192	95	below_threshold
Legionella tunisiensis	strain=LegM	GCA_000308315.1	1034944	1034944	type	True	78.0548	180	1192	95	below_threshold
Legionella feeleii	strain=ATCC 35072	GCA_001648615.1	453	453	type	True	77.7707	178	1192	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:09,891] [INFO] DFAST Taxonomy check result was written to GCF_900452565.1_34347_D01_genomic.fna/tc_result.tsv
[2024-01-25 18:57:09,891] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:09,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:09,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7c4e467-3823-41ba-be19-7eb0785d6233/dqc_reference/checkm_data
[2024-01-25 18:57:09,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:09,929] [INFO] Task started: CheckM
[2024-01-25 18:57:09,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900452565.1_34347_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900452565.1_34347_D01_genomic.fna/checkm_input GCF_900452565.1_34347_D01_genomic.fna/checkm_result
[2024-01-25 18:57:35,483] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:35,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:35,523] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:35,523] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:35,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900452565.1_34347_D01_genomic.fna/markers.fasta)
[2024-01-25 18:57:35,524] [INFO] Task started: Blastn
[2024-01-25 18:57:35,524] [INFO] Running command: blastn -query GCF_900452565.1_34347_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7c4e467-3823-41ba-be19-7eb0785d6233/dqc_reference/reference_markers_gtdb.fasta -out GCF_900452565.1_34347_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:36,485] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:36,488] [INFO] Selected 15 target genomes.
[2024-01-25 18:57:36,488] [INFO] Target genome list was writen to GCF_900452565.1_34347_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:36,497] [INFO] Task started: fastANI
[2024-01-25 18:57:36,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg651e2364-3977-4873-ab07-98c29f33adab/GCF_900452565.1_34347_D01_genomic.fna.gz --refList GCF_900452565.1_34347_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900452565.1_34347_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:45,072] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:45,082] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:45,083] [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_000953655.1	s__Tatlockia hackeliae	99.9907	1188	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.95	99.91	0.98	0.96	3	conclusive
GCF_001468065.1	s__Legionella steigerwaltii	82.0763	134	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002240035.1	s__Tatlockia clemsonensis	80.0094	464	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637635.1	s__Tatlockia jordanis	79.8332	193	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.59	0.99	0.98	6	-
GCF_001467745.1	s__Tatlockia jamestowniensis	79.7086	470	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.71	99.16	0.98	0.95	4	-
GCF_900452385.1	s__Tatlockia donaldsonii	79.5729	194	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467025.1	s__Tatlockia brunensis	79.4006	384	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900187355.1	s__Tatlockia lansingensis	78.5179	218	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.99	99.98	1.00	1.00	4	-
GCF_000953635.1	s__Tatlockia micdadei	78.4412	131	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.75	0.99	0.96	7	-
GCF_001467625.1	s__Tatlockia feeleii	78.1407	181	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.52	98.18	0.97	0.92	5	-
GCF_001467535.1	s__Legionella worsleiensis	78.0833	85	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000308315.1	s__Tatlockia tunisiensis	78.0548	180	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621525.1	s__Tatlockia fairfieldensis	77.5963	121	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.93	99.93	0.99	0.99	2	-
GCA_013697955.1	s__Tatlockia sp013697955	77.3244	96	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:45,084] [INFO] GTDB search result was written to GCF_900452565.1_34347_D01_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:45,085] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:45,088] [INFO] DFAST_QC result json was written to GCF_900452565.1_34347_D01_genomic.fna/dqc_result.json
[2024-01-25 18:57:45,089] [INFO] DFAST_QC completed!
[2024-01-25 18:57:45,089] [INFO] Total running time: 0h0m54s