[2024-01-24 13:27:58,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,726] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1bf2808-deaa-4bbc-81e7-2e44efdb1f9e/dqc_reference
[2024-01-24 13:27:59,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,992] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,992] [INFO] Running command: gunzip -c /var/lib/cwl/stgecbb83fc-35a5-4798-bc53-e82ab91f8082/GCF_019930885.1_ASM1993088v1_genomic.fna.gz | prodigal -d GCF_019930885.1_ASM1993088v1_genomic.fna/cds.fna -a GCF_019930885.1_ASM1993088v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:09,729] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:09,729] [INFO] Task started: HMMsearch
[2024-01-24 13:28:09,729] [INFO] Running command: hmmsearch --tblout GCF_019930885.1_ASM1993088v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1bf2808-deaa-4bbc-81e7-2e44efdb1f9e/dqc_reference/reference_markers.hmm GCF_019930885.1_ASM1993088v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:10,039] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:10,041] [INFO] Found 6/6 markers.
[2024-01-24 13:28:10,085] [INFO] Query marker FASTA was written to GCF_019930885.1_ASM1993088v1_genomic.fna/markers.fasta
[2024-01-24 13:28:10,086] [INFO] Task started: Blastn
[2024-01-24 13:28:10,086] [INFO] Running command: blastn -query GCF_019930885.1_ASM1993088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1bf2808-deaa-4bbc-81e7-2e44efdb1f9e/dqc_reference/reference_markers.fasta -out GCF_019930885.1_ASM1993088v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:10,756] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:10,759] [INFO] Selected 10 target genomes.
[2024-01-24 13:28:10,759] [INFO] Target genome list was writen to GCF_019930885.1_ASM1993088v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:10,767] [INFO] Task started: fastANI
[2024-01-24 13:28:10,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgecbb83fc-35a5-4798-bc53-e82ab91f8082/GCF_019930885.1_ASM1993088v1_genomic.fna.gz --refList GCF_019930885.1_ASM1993088v1_genomic.fna/target_genomes.txt --output GCF_019930885.1_ASM1993088v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:22,403] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:22,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1bf2808-deaa-4bbc-81e7-2e44efdb1f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:22,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1bf2808-deaa-4bbc-81e7-2e44efdb1f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:22,412] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:28:22,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:22,412] [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 anisa	strain=FDAARGOS_1480	GCA_019930885.1	28082	28082	type	True	100.0	1481	1481	95	conclusive
Legionella anisa	strain=FDAARGOS_200	GCA_002082905.2	28082	28082	type	True	99.997	1477	1481	95	conclusive
Legionella anisa	strain=WA-316-C3	GCA_001467525.1	28082	28082	type	True	99.9526	1406	1481	95	conclusive
Legionella anisa	strain=WA-316-C3	GCA_900639785.1	28082	28082	type	True	99.6523	1284	1481	95	conclusive
Legionella tucsonensis	strain=ATCC 49180	GCA_001468035.1	40335	40335	type	True	89.2393	944	1481	95	below_threshold
Legionella bozemanae	strain=WIGA	GCA_001467045.1	447	447	type	True	89.025	1046	1481	95	below_threshold
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	79.0066	275	1481	95	below_threshold
Legionella rowbothamii	strain=LLAP6	GCA_900639985.1	96229	96229	type	True	78.2862	277	1481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:22,414] [INFO] DFAST Taxonomy check result was written to GCF_019930885.1_ASM1993088v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:22,414] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:22,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:22,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1bf2808-deaa-4bbc-81e7-2e44efdb1f9e/dqc_reference/checkm_data
[2024-01-24 13:28:22,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:22,461] [INFO] Task started: CheckM
[2024-01-24 13:28:22,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019930885.1_ASM1993088v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019930885.1_ASM1993088v1_genomic.fna/checkm_input GCF_019930885.1_ASM1993088v1_genomic.fna/checkm_result
[2024-01-24 13:28:58,936] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:58,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:58,959] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:58,959] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:58,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019930885.1_ASM1993088v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:58,960] [INFO] Task started: Blastn
[2024-01-24 13:28:58,960] [INFO] Running command: blastn -query GCF_019930885.1_ASM1993088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1bf2808-deaa-4bbc-81e7-2e44efdb1f9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019930885.1_ASM1993088v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:59,960] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:59,966] [INFO] Selected 5 target genomes.
[2024-01-24 13:28:59,966] [INFO] Target genome list was writen to GCF_019930885.1_ASM1993088v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:59,973] [INFO] Task started: fastANI
[2024-01-24 13:28:59,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgecbb83fc-35a5-4798-bc53-e82ab91f8082/GCF_019930885.1_ASM1993088v1_genomic.fna.gz --refList GCF_019930885.1_ASM1993088v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019930885.1_ASM1993088v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:05,943] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:05,955] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:05,955] [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_001467525.1	s__Legionella anisa	99.9526	1406	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	conclusive
GCF_014109805.1	s__Legionella sp014109805	90.5553	1111	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468035.1	s__Legionella tucsonensis	89.2395	944	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001648595.1	s__Legionella bozemanae	89.0441	1039	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_001467945.1	s__Legionella parisiensis	88.2749	1103	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.98	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:05,957] [INFO] GTDB search result was written to GCF_019930885.1_ASM1993088v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:05,957] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:05,961] [INFO] DFAST_QC result json was written to GCF_019930885.1_ASM1993088v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:05,961] [INFO] DFAST_QC completed!
[2024-01-24 13:29:05,961] [INFO] Total running time: 0h1m7s