[2024-01-24 13:40:43,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,317] [INFO] DQC Reference Directory: /var/lib/cwl/stgeff66d23-f8a0-4e9b-ac66-37e71f12c9a8/dqc_reference
[2024-01-24 13:40:44,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,725] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgac2b1b99-8615-4218-bd8c-a6a5ddf8d640/GCF_900637265.1_50432_C01_genomic.fna.gz | prodigal -d GCF_900637265.1_50432_C01_genomic.fna/cds.fna -a GCF_900637265.1_50432_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:06,598] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:06,598] [INFO] Task started: HMMsearch
[2024-01-24 13:41:06,598] [INFO] Running command: hmmsearch --tblout GCF_900637265.1_50432_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeff66d23-f8a0-4e9b-ac66-37e71f12c9a8/dqc_reference/reference_markers.hmm GCF_900637265.1_50432_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:06,958] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:06,960] [INFO] Found 6/6 markers.
[2024-01-24 13:41:07,013] [INFO] Query marker FASTA was written to GCF_900637265.1_50432_C01_genomic.fna/markers.fasta
[2024-01-24 13:41:07,013] [INFO] Task started: Blastn
[2024-01-24 13:41:07,014] [INFO] Running command: blastn -query GCF_900637265.1_50432_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff66d23-f8a0-4e9b-ac66-37e71f12c9a8/dqc_reference/reference_markers.fasta -out GCF_900637265.1_50432_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:08,062] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:08,064] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:08,065] [INFO] Target genome list was writen to GCF_900637265.1_50432_C01_genomic.fna/target_genomes.txt
[2024-01-24 13:41:08,068] [INFO] Task started: fastANI
[2024-01-24 13:41:08,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgac2b1b99-8615-4218-bd8c-a6a5ddf8d640/GCF_900637265.1_50432_C01_genomic.fna.gz --refList GCF_900637265.1_50432_C01_genomic.fna/target_genomes.txt --output GCF_900637265.1_50432_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:21,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:21,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeff66d23-f8a0-4e9b-ac66-37e71f12c9a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:21,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeff66d23-f8a0-4e9b-ac66-37e71f12c9a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:21,658] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:41:21,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:21,658] [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=NCTC13520	GCA_900637265.1	217204	217204	type	True	100.0	2157	2157	95	conclusive
Achromobacter insolitus	strain=LMG 6003	GCA_902859615.1	217204	217204	type	True	99.9926	2122	2157	95	conclusive
Achromobacter insolitus	strain=LMG 6003	GCA_002209555.1	217204	217204	type	True	99.9917	2133	2157	95	conclusive
Achromobacter insolitus	strain=DSM 23807	GCA_001971645.1	217204	217204	type	True	99.9886	2156	2157	95	conclusive
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	98.9962	2057	2157	95	conclusive
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.1712	1454	2157	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.8026	867	2157	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.7073	313	2157	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.081	272	2157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:21,664] [INFO] DFAST Taxonomy check result was written to GCF_900637265.1_50432_C01_genomic.fna/tc_result.tsv
[2024-01-24 13:41:21,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:21,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:21,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeff66d23-f8a0-4e9b-ac66-37e71f12c9a8/dqc_reference/checkm_data
[2024-01-24 13:41:21,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:21,731] [INFO] Task started: CheckM
[2024-01-24 13:41:21,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637265.1_50432_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637265.1_50432_C01_genomic.fna/checkm_input GCF_900637265.1_50432_C01_genomic.fna/checkm_result
[2024-01-24 13:42:25,285] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:25,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:25,308] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:25,309] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:25,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637265.1_50432_C01_genomic.fna/markers.fasta)
[2024-01-24 13:42:25,310] [INFO] Task started: Blastn
[2024-01-24 13:42:25,310] [INFO] Running command: blastn -query GCF_900637265.1_50432_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff66d23-f8a0-4e9b-ac66-37e71f12c9a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637265.1_50432_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:27,506] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:27,513] [INFO] Selected 7 target genomes.
[2024-01-24 13:42:27,513] [INFO] Target genome list was writen to GCF_900637265.1_50432_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:27,555] [INFO] Task started: fastANI
[2024-01-24 13:42:27,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgac2b1b99-8615-4218-bd8c-a6a5ddf8d640/GCF_900637265.1_50432_C01_genomic.fna.gz --refList GCF_900637265.1_50432_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900637265.1_50432_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:41,019] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:41,029] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:41,029] [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	99.9917	2133	2157	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	90.1068	1818	2157	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	90.044	1821	2157	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	89.8813	1848	2157	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	89.851	1864	2157	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	89.3287	1784	2157	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	86.2332	1491	2157	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 13:42:41,031] [INFO] GTDB search result was written to GCF_900637265.1_50432_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:41,032] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:41,035] [INFO] DFAST_QC result json was written to GCF_900637265.1_50432_C01_genomic.fna/dqc_result.json
[2024-01-24 13:42:41,036] [INFO] DFAST_QC completed!
[2024-01-24 13:42:41,036] [INFO] Total running time: 0h1m58s