[2024-01-25 18:05:50,687] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:50,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:50,692] [INFO] DQC Reference Directory: /var/lib/cwl/stgfad265d6-c8c6-45ee-97ed-7dbb7bf19783/dqc_reference
[2024-01-25 18:05:51,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:51,876] [INFO] Task started: Prodigal
[2024-01-25 18:05:51,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg98a88bea-a8f2-4983-8419-e50d57f8cfe0/GCF_016786415.1_ASM1678641v1_genomic.fna.gz | prodigal -d GCF_016786415.1_ASM1678641v1_genomic.fna/cds.fna -a GCF_016786415.1_ASM1678641v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:05:59,467] [INFO] Task succeeded: Prodigal
[2024-01-25 18:05:59,467] [INFO] Task started: HMMsearch
[2024-01-25 18:05:59,467] [INFO] Running command: hmmsearch --tblout GCF_016786415.1_ASM1678641v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfad265d6-c8c6-45ee-97ed-7dbb7bf19783/dqc_reference/reference_markers.hmm GCF_016786415.1_ASM1678641v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:05:59,719] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:05:59,720] [INFO] Found 6/6 markers.
[2024-01-25 18:05:59,751] [INFO] Query marker FASTA was written to GCF_016786415.1_ASM1678641v1_genomic.fna/markers.fasta
[2024-01-25 18:05:59,751] [INFO] Task started: Blastn
[2024-01-25 18:05:59,751] [INFO] Running command: blastn -query GCF_016786415.1_ASM1678641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfad265d6-c8c6-45ee-97ed-7dbb7bf19783/dqc_reference/reference_markers.fasta -out GCF_016786415.1_ASM1678641v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:00,354] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:00,372] [INFO] Selected 9 target genomes.
[2024-01-25 18:06:00,372] [INFO] Target genome list was writen to GCF_016786415.1_ASM1678641v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:00,376] [INFO] Task started: fastANI
[2024-01-25 18:06:00,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg98a88bea-a8f2-4983-8419-e50d57f8cfe0/GCF_016786415.1_ASM1678641v1_genomic.fna.gz --refList GCF_016786415.1_ASM1678641v1_genomic.fna/target_genomes.txt --output GCF_016786415.1_ASM1678641v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:08,489] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:08,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfad265d6-c8c6-45ee-97ed-7dbb7bf19783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:08,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfad265d6-c8c6-45ee-97ed-7dbb7bf19783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:08,495] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:08,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:08,495] [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 bononiensis	strain=30cs62	GCA_016786415.1	2793102	2793102	type	True	100.0	1358	1361	95	conclusive
Legionella quateirensis	strain=ATCC 49507	GCA_001467955.1	45072	45072	type	True	91.4466	1111	1361	95	below_threshold
Legionella quateirensis	strain=NCTC12376	GCA_900452695.1	45072	45072	type	True	91.3468	1134	1361	95	below_threshold
Legionella moravica	strain=NCTC12239	GCA_900452715.1	39962	39962	type	True	84.1455	874	1361	95	below_threshold
Legionella moravica	strain=DSM 19234	GCA_000423305.1	39962	39962	type	True	83.9533	875	1361	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:08,496] [INFO] DFAST Taxonomy check result was written to GCF_016786415.1_ASM1678641v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:08,497] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:08,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:08,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfad265d6-c8c6-45ee-97ed-7dbb7bf19783/dqc_reference/checkm_data
[2024-01-25 18:06:08,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:08,539] [INFO] Task started: CheckM
[2024-01-25 18:06:08,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016786415.1_ASM1678641v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016786415.1_ASM1678641v1_genomic.fna/checkm_input GCF_016786415.1_ASM1678641v1_genomic.fna/checkm_result
[2024-01-25 18:06:35,956] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:35,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:35,975] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:35,975] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:35,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016786415.1_ASM1678641v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:35,976] [INFO] Task started: Blastn
[2024-01-25 18:06:35,976] [INFO] Running command: blastn -query GCF_016786415.1_ASM1678641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfad265d6-c8c6-45ee-97ed-7dbb7bf19783/dqc_reference/reference_markers_gtdb.fasta -out GCF_016786415.1_ASM1678641v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:36,917] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:36,921] [INFO] Selected 10 target genomes.
[2024-01-25 18:06:36,921] [INFO] Target genome list was writen to GCF_016786415.1_ASM1678641v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:36,926] [INFO] Task started: fastANI
[2024-01-25 18:06:36,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg98a88bea-a8f2-4983-8419-e50d57f8cfe0/GCF_016786415.1_ASM1678641v1_genomic.fna.gz --refList GCF_016786415.1_ASM1678641v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016786415.1_ASM1678641v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:45,359] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:45,366] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:45,367] [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_016786215.1	s__Legionella sp016786215	99.9315	1316	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	conclusive
GCF_001467955.1	s__Legionella quateirensis	91.4313	1112	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.97	99.97	0.99	0.99	3	-
GCF_000423305.1	s__Legionella moravica	83.97	873	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.09	96.46	0.96	0.86	5	-
GCF_014109805.1	s__Legionella sp014109805	80.2648	221	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014109825.1	s__Legionella sp014109825	80.1677	196	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467535.1	s__Legionella worsleiensis	80.1089	462	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000236165.1	s__Legionella dumoffii	79.961	222	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.81	99.55	0.97	0.94	4	-
GCF_900156395.1	s__Legionella gormanii	79.5582	242	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.78	98.94	0.98	0.92	6	-
GCF_000373765.1	s__Legionella shakespearei	78.9308	300	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.95	0.97	0.97	2	-
GCF_011764505.1	s__Legionella sp011764505	78.6792	284	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:45,369] [INFO] GTDB search result was written to GCF_016786415.1_ASM1678641v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:45,370] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:45,372] [INFO] DFAST_QC result json was written to GCF_016786415.1_ASM1678641v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:45,372] [INFO] DFAST_QC completed!
[2024-01-25 18:06:45,372] [INFO] Total running time: 0h0m55s