[2024-01-24 13:48:59,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg17755b40-bd58-49ba-92d6-b12ecec3bcaa/dqc_reference
[2024-01-24 13:49:01,155] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,156] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,156] [INFO] Running command: gunzip -c /var/lib/cwl/stg5394054e-0137-4ad8-b4f7-932c63949661/GCF_000586375.1_ATCC_33152_genomic.fna.gz | prodigal -d GCF_000586375.1_ATCC_33152_genomic.fna/cds.fna -a GCF_000586375.1_ATCC_33152_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:08,772] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:08,772] [INFO] Task started: HMMsearch
[2024-01-24 13:49:08,773] [INFO] Running command: hmmsearch --tblout GCF_000586375.1_ATCC_33152_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17755b40-bd58-49ba-92d6-b12ecec3bcaa/dqc_reference/reference_markers.hmm GCF_000586375.1_ATCC_33152_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:09,061] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:09,063] [INFO] Found 6/6 markers.
[2024-01-24 13:49:09,096] [INFO] Query marker FASTA was written to GCF_000586375.1_ATCC_33152_genomic.fna/markers.fasta
[2024-01-24 13:49:09,097] [INFO] Task started: Blastn
[2024-01-24 13:49:09,097] [INFO] Running command: blastn -query GCF_000586375.1_ATCC_33152_genomic.fna/markers.fasta -db /var/lib/cwl/stg17755b40-bd58-49ba-92d6-b12ecec3bcaa/dqc_reference/reference_markers.fasta -out GCF_000586375.1_ATCC_33152_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:09,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:09,774] [INFO] Selected 10 target genomes.
[2024-01-24 13:49:09,775] [INFO] Target genome list was writen to GCF_000586375.1_ATCC_33152_genomic.fna/target_genomes.txt
[2024-01-24 13:49:09,779] [INFO] Task started: fastANI
[2024-01-24 13:49:09,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg5394054e-0137-4ad8-b4f7-932c63949661/GCF_000586375.1_ATCC_33152_genomic.fna.gz --refList GCF_000586375.1_ATCC_33152_genomic.fna/target_genomes.txt --output GCF_000586375.1_ATCC_33152_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:15,958] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:15,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17755b40-bd58-49ba-92d6-b12ecec3bcaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:15,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17755b40-bd58-49ba-92d6-b12ecec3bcaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:15,966] [INFO] Found 7 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:49:15,966] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:15,966] [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 pneumophila subsp. pneumophila	strain=ATCC 33152	GCA_000586375.1	91891	446	type	True	99.9989	1123	1135	95	conclusive
Legionella pneumophila subsp. pneumophila	strain=FDAARGOS_202	GCA_002082955.2	91891	446	type	True	99.975	1126	1135	95	conclusive
Legionella pneumophila subsp. pneumophila	strain=PartS-Lpneumophila-RM8376	GCA_022870105.1	91891	446	type	True	99.9741	1126	1135	95	conclusive
Legionella pneumophila	strain=FDAARGOS_779	GCA_006364635.1	446	446	type	True	99.97	1125	1135	95	conclusive
Legionella pneumophila	strain=ATCC 33152	GCA_001582475.1	446	446	type	True	99.9249	1090	1135	95	conclusive
Legionella pneumophila	strain=NCTC11192	GCA_900452735.1	446	446	type	True	99.9001	1125	1135	95	conclusive
Legionella rowbothamii	strain=LLAP6	GCA_900639985.1	96229	96229	type	True	78.1004	140	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:15,969] [INFO] DFAST Taxonomy check result was written to GCF_000586375.1_ATCC_33152_genomic.fna/tc_result.tsv
[2024-01-24 13:49:15,970] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:15,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:15,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17755b40-bd58-49ba-92d6-b12ecec3bcaa/dqc_reference/checkm_data
[2024-01-24 13:49:15,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:16,011] [INFO] Task started: CheckM
[2024-01-24 13:49:16,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000586375.1_ATCC_33152_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000586375.1_ATCC_33152_genomic.fna/checkm_input GCF_000586375.1_ATCC_33152_genomic.fna/checkm_result
[2024-01-24 13:49:45,950] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:45,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:45,972] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:45,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:45,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000586375.1_ATCC_33152_genomic.fna/markers.fasta)
[2024-01-24 13:49:45,973] [INFO] Task started: Blastn
[2024-01-24 13:49:45,973] [INFO] Running command: blastn -query GCF_000586375.1_ATCC_33152_genomic.fna/markers.fasta -db /var/lib/cwl/stg17755b40-bd58-49ba-92d6-b12ecec3bcaa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000586375.1_ATCC_33152_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:47,070] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:47,074] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:47,074] [INFO] Target genome list was writen to GCF_000586375.1_ATCC_33152_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:47,103] [INFO] Task started: fastANI
[2024-01-24 13:49:47,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg5394054e-0137-4ad8-b4f7-932c63949661/GCF_000586375.1_ATCC_33152_genomic.fna.gz --refList GCF_000586375.1_ATCC_33152_genomic.fna/target_genomes_gtdb.txt --output GCF_000586375.1_ATCC_33152_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:56,747] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:56,759] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:56,760] [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_000008485.1	s__Legionella pneumophila	99.9134	1124	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.85	95.56	0.93	0.84	789	conclusive
GCA_000586315.1	s__Legionella fraseri	92.0693	962	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.50	96.27	0.94	0.87	43	-
GCF_900637585.1	s__Legionella pascullei	91.2644	1005	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.92	99.72	1.00	0.99	8	-
GCF_001467525.1	s__Legionella anisa	80.3927	215	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_000770585.1	s__Legionella norrlandica	80.2107	532	1135	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	79.1305	265	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
GCF_011764505.1	s__Legionella sp011764505	78.3346	186	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900452415.1	s__Legionella cincinnatiensis	78.2446	197	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000423305.1	s__Legionella moravica	78.1954	251	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.09	96.46	0.96	0.86	5	-
GCF_001467955.1	s__Legionella quateirensis	77.7919	262	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.97	99.97	0.99	0.99	3	-
GCF_001465875.1	s__Legionella saoudiensis	77.7659	135	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004283175.1	s__Legionella longbeachae	77.2829	169	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.77	99.22	0.96	0.94	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:56,761] [INFO] GTDB search result was written to GCF_000586375.1_ATCC_33152_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:56,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:56,769] [INFO] DFAST_QC result json was written to GCF_000586375.1_ATCC_33152_genomic.fna/dqc_result.json
[2024-01-24 13:49:56,769] [INFO] DFAST_QC completed!
[2024-01-24 13:49:56,769] [INFO] Total running time: 0h0m57s