[2024-01-24 12:44:11,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg918bab33-f333-4280-b976-272661e2a23d/dqc_reference
[2024-01-24 12:44:12,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,669] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg3dd3fe0c-bb4b-4d45-b71a-04f9872437b6/GCF_002209555.1_ASM220955v1_genomic.fna.gz | prodigal -d GCF_002209555.1_ASM220955v1_genomic.fna/cds.fna -a GCF_002209555.1_ASM220955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:33,877] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:33,878] [INFO] Task started: HMMsearch
[2024-01-24 12:44:33,878] [INFO] Running command: hmmsearch --tblout GCF_002209555.1_ASM220955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg918bab33-f333-4280-b976-272661e2a23d/dqc_reference/reference_markers.hmm GCF_002209555.1_ASM220955v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:34,299] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:34,300] [INFO] Found 6/6 markers.
[2024-01-24 12:44:34,354] [INFO] Query marker FASTA was written to GCF_002209555.1_ASM220955v1_genomic.fna/markers.fasta
[2024-01-24 12:44:34,355] [INFO] Task started: Blastn
[2024-01-24 12:44:34,355] [INFO] Running command: blastn -query GCF_002209555.1_ASM220955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg918bab33-f333-4280-b976-272661e2a23d/dqc_reference/reference_markers.fasta -out GCF_002209555.1_ASM220955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:35,411] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:35,414] [INFO] Selected 9 target genomes.
[2024-01-24 12:44:35,414] [INFO] Target genome list was writen to GCF_002209555.1_ASM220955v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:35,427] [INFO] Task started: fastANI
[2024-01-24 12:44:35,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd3fe0c-bb4b-4d45-b71a-04f9872437b6/GCF_002209555.1_ASM220955v1_genomic.fna.gz --refList GCF_002209555.1_ASM220955v1_genomic.fna/target_genomes.txt --output GCF_002209555.1_ASM220955v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:48,520] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:48,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg918bab33-f333-4280-b976-272661e2a23d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:48,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg918bab33-f333-4280-b976-272661e2a23d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:48,530] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:44:48,531] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:48,531] [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
Achromobacter insolitus	strain=LMG 6003	GCA_002209555.1	217204	217204	type	True	100.0	2133	2136	95	conclusive
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	99.9997	2135	2136	95	conclusive
Achromobacter insolitus	strain=LMG 6003	GCA_902859615.1	217204	217204	type	True	99.9948	2114	2136	95	conclusive
Achromobacter insolitus	strain=DSM 23807	GCA_001971645.1	217204	217204	type	True	99.9897	2135	2136	95	conclusive
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	98.9683	2043	2136	95	conclusive
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.1069	1445	2136	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.7476	864	2136	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.7299	293	2136	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.0407	273	2136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:48,533] [INFO] DFAST Taxonomy check result was written to GCF_002209555.1_ASM220955v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:48,534] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:48,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:48,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg918bab33-f333-4280-b976-272661e2a23d/dqc_reference/checkm_data
[2024-01-24 12:44:48,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:48,601] [INFO] Task started: CheckM
[2024-01-24 12:44:48,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002209555.1_ASM220955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002209555.1_ASM220955v1_genomic.fna/checkm_input GCF_002209555.1_ASM220955v1_genomic.fna/checkm_result
[2024-01-24 12:45:48,298] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:48,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:48,328] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:48,329] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:48,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002209555.1_ASM220955v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:48,330] [INFO] Task started: Blastn
[2024-01-24 12:45:48,330] [INFO] Running command: blastn -query GCF_002209555.1_ASM220955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg918bab33-f333-4280-b976-272661e2a23d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002209555.1_ASM220955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:50,271] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:50,281] [INFO] Selected 7 target genomes.
[2024-01-24 12:45:50,281] [INFO] Target genome list was writen to GCF_002209555.1_ASM220955v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:50,291] [INFO] Task started: fastANI
[2024-01-24 12:45:50,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd3fe0c-bb4b-4d45-b71a-04f9872437b6/GCF_002209555.1_ASM220955v1_genomic.fna.gz --refList GCF_002209555.1_ASM220955v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002209555.1_ASM220955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:03,021] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:03,033] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:03,033] [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_002209555.1	s__Achromobacter insolitus	100.0	2133	2136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.13	98.86	0.96	0.89	17	conclusive
GCF_002192695.1	s__Achromobacter xylosoxidans_C	90.018	1824	2136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.40	98.40	0.91	0.91	2	-
GCF_014490035.1	s__Achromobacter bronchisepticus_A	89.9432	1831	2136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.75	98.99	0.98	0.93	5	-
GCF_902859735.1	s__Achromobacter aegrifaciens	89.8691	1834	2136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	-
GCF_000165835.1	s__Achromobacter xylosoxidans_B	89.8121	1865	2136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.34	96.34	0.92	0.92	2	-
GCF_903652925.1	s__Achromobacter anxifer	89.3906	1778	2136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.16	99.16	0.95	0.95	2	-
GCF_002885955.2	s__Achromobacter pulmonis_A	86.3544	1462	2136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:03,034] [INFO] GTDB search result was written to GCF_002209555.1_ASM220955v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:03,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:03,038] [INFO] DFAST_QC result json was written to GCF_002209555.1_ASM220955v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:03,038] [INFO] DFAST_QC completed!
[2024-01-24 12:46:03,038] [INFO] Total running time: 0h1m52s