[2024-01-24 13:31:44,260] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,262] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,262] [INFO] DQC Reference Directory: /var/lib/cwl/stg0febf979-c9ab-4a7b-97e2-d17d8e92f012/dqc_reference
[2024-01-24 13:31:45,585] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,586] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,586] [INFO] Running command: gunzip -c /var/lib/cwl/stg3613b555-5f94-4415-8aa9-b36bfe725597/GCF_004283175.1_ASM428317v1_genomic.fna.gz | prodigal -d GCF_004283175.1_ASM428317v1_genomic.fna/cds.fna -a GCF_004283175.1_ASM428317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:53,784] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:53,784] [INFO] Task started: HMMsearch
[2024-01-24 13:31:53,785] [INFO] Running command: hmmsearch --tblout GCF_004283175.1_ASM428317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0febf979-c9ab-4a7b-97e2-d17d8e92f012/dqc_reference/reference_markers.hmm GCF_004283175.1_ASM428317v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:54,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:54,095] [INFO] Found 6/6 markers.
[2024-01-24 13:31:54,128] [INFO] Query marker FASTA was written to GCF_004283175.1_ASM428317v1_genomic.fna/markers.fasta
[2024-01-24 13:31:54,129] [INFO] Task started: Blastn
[2024-01-24 13:31:54,129] [INFO] Running command: blastn -query GCF_004283175.1_ASM428317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0febf979-c9ab-4a7b-97e2-d17d8e92f012/dqc_reference/reference_markers.fasta -out GCF_004283175.1_ASM428317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:54,852] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:54,856] [INFO] Selected 12 target genomes.
[2024-01-24 13:31:54,856] [INFO] Target genome list was writen to GCF_004283175.1_ASM428317v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:54,870] [INFO] Task started: fastANI
[2024-01-24 13:31:54,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg3613b555-5f94-4415-8aa9-b36bfe725597/GCF_004283175.1_ASM428317v1_genomic.fna.gz --refList GCF_004283175.1_ASM428317v1_genomic.fna/target_genomes.txt --output GCF_004283175.1_ASM428317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:06,587] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:06,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0febf979-c9ab-4a7b-97e2-d17d8e92f012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:06,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0febf979-c9ab-4a7b-97e2-d17d8e92f012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:06,597] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:06,597] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:06,597] [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 longbeachae	strain=NCTC11477	GCA_004283175.1	450	450	type	True	100.0	1355	1356	95	conclusive
Legionella longbeachae	strain=FDAARGOS_1481	GCA_019930685.1	450	450	type	True	99.999	1355	1356	95	conclusive
Legionella sainthelensi	strain=NCTC11988	GCA_900637685.1	28087	28087	type	True	88.7376	1101	1356	95	below_threshold
Legionella sainthelensi	strain=ATCC 35248	GCA_000621685.1	28087	28087	type	True	88.7327	1101	1356	95	below_threshold
Legionella sainthelensi	strain=Mt.St.Helens-4	GCA_001468105.1	28087	28087	type	True	88.7164	1111	1356	95	below_threshold
Legionella sainthelensi	strain=MSH-4	GCA_900640185.1	28087	28087	type	True	88.7056	1085	1356	95	below_threshold
Legionella cincinnatiensis	strain=NCTC12438	GCA_900452415.1	28085	28085	type	True	87.9406	1046	1356	95	below_threshold
Legionella santicrucis	strain=SC-63-C7	GCA_001468135.1	45074	45074	type	True	87.7738	1041	1356	95	below_threshold
Legionella santicrucis	strain=SC-63-C7	GCA_900639975.1	45074	45074	type	True	87.7682	1032	1356	95	below_threshold
Legionella rowbothamii	strain=LLAP6	GCA_900639985.1	96229	96229	type	True	77.7719	247	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:06,599] [INFO] DFAST Taxonomy check result was written to GCF_004283175.1_ASM428317v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:06,601] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:06,601] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:06,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0febf979-c9ab-4a7b-97e2-d17d8e92f012/dqc_reference/checkm_data
[2024-01-24 13:32:06,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:06,644] [INFO] Task started: CheckM
[2024-01-24 13:32:06,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004283175.1_ASM428317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004283175.1_ASM428317v1_genomic.fna/checkm_input GCF_004283175.1_ASM428317v1_genomic.fna/checkm_result
[2024-01-24 13:32:37,509] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:37,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:37,531] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:37,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:37,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004283175.1_ASM428317v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:37,532] [INFO] Task started: Blastn
[2024-01-24 13:32:37,533] [INFO] Running command: blastn -query GCF_004283175.1_ASM428317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0febf979-c9ab-4a7b-97e2-d17d8e92f012/dqc_reference/reference_markers_gtdb.fasta -out GCF_004283175.1_ASM428317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:38,573] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:38,576] [INFO] Selected 5 target genomes.
[2024-01-24 13:32:38,577] [INFO] Target genome list was writen to GCF_004283175.1_ASM428317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:38,582] [INFO] Task started: fastANI
[2024-01-24 13:32:38,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg3613b555-5f94-4415-8aa9-b36bfe725597/GCF_004283175.1_ASM428317v1_genomic.fna.gz --refList GCF_004283175.1_ASM428317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004283175.1_ASM428317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:44,386] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:44,392] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:44,392] [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
GCA_004283175.1	s__Legionella longbeachae	100.0	1355	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.77	99.22	0.96	0.94	9	conclusive
GCF_900637685.1	s__Legionella sainthelensi	88.7444	1100	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.79	95.71	0.95	0.89	8	-
GCF_900452415.1	s__Legionella cincinnatiensis	87.9304	1047	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_001468135.1	s__Legionella santicrucis	87.7632	1043	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001467695.1	s__Legionella gratiana	84.0507	905	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:44,394] [INFO] GTDB search result was written to GCF_004283175.1_ASM428317v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:44,394] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:44,397] [INFO] DFAST_QC result json was written to GCF_004283175.1_ASM428317v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:44,398] [INFO] DFAST_QC completed!
[2024-01-24 13:32:44,398] [INFO] Total running time: 0h1m0s