[2024-01-24 13:09:49,464] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg66ac1763-602f-4f56-a458-227c3cb44610/dqc_reference
[2024-01-24 13:09:50,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,802] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg882c9391-04e2-4831-b932-ff40685ffb0c/GCF_024168865.1_ASM2416886v1_genomic.fna.gz | prodigal -d GCF_024168865.1_ASM2416886v1_genomic.fna/cds.fna -a GCF_024168865.1_ASM2416886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:12,494] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:12,495] [INFO] Task started: HMMsearch
[2024-01-24 13:10:12,495] [INFO] Running command: hmmsearch --tblout GCF_024168865.1_ASM2416886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66ac1763-602f-4f56-a458-227c3cb44610/dqc_reference/reference_markers.hmm GCF_024168865.1_ASM2416886v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:12,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:12,859] [INFO] Found 6/6 markers.
[2024-01-24 13:10:12,912] [INFO] Query marker FASTA was written to GCF_024168865.1_ASM2416886v1_genomic.fna/markers.fasta
[2024-01-24 13:10:12,912] [INFO] Task started: Blastn
[2024-01-24 13:10:12,913] [INFO] Running command: blastn -query GCF_024168865.1_ASM2416886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66ac1763-602f-4f56-a458-227c3cb44610/dqc_reference/reference_markers.fasta -out GCF_024168865.1_ASM2416886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:13,933] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:13,936] [INFO] Selected 9 target genomes.
[2024-01-24 13:10:13,937] [INFO] Target genome list was writen to GCF_024168865.1_ASM2416886v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:13,941] [INFO] Task started: fastANI
[2024-01-24 13:10:13,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg882c9391-04e2-4831-b932-ff40685ffb0c/GCF_024168865.1_ASM2416886v1_genomic.fna.gz --refList GCF_024168865.1_ASM2416886v1_genomic.fna/target_genomes.txt --output GCF_024168865.1_ASM2416886v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:27,769] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:27,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66ac1763-602f-4f56-a458-227c3cb44610/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:27,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66ac1763-602f-4f56-a458-227c3cb44610/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:27,778] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:10:27,779] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:27,779] [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=NCTC 13520	GCA_024168865.1	217204	217204	type	True	100.0	2158	2159	95	conclusive
Achromobacter insolitus	strain=LMG 6003	GCA_902859615.1	217204	217204	type	True	98.9878	2035	2159	95	conclusive
Achromobacter insolitus	strain=DSM 23807	GCA_001971645.1	217204	217204	type	True	98.9828	2058	2159	95	conclusive
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	98.9793	2059	2159	95	conclusive
Achromobacter insolitus	strain=LMG 6003	GCA_002209555.1	217204	217204	type	True	98.962	2048	2159	95	conclusive
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.0986	1464	2159	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.891	856	2159	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.7357	303	2159	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.2873	443	2159	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:27,780] [INFO] DFAST Taxonomy check result was written to GCF_024168865.1_ASM2416886v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:27,781] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:27,781] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:27,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66ac1763-602f-4f56-a458-227c3cb44610/dqc_reference/checkm_data
[2024-01-24 13:10:27,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:27,841] [INFO] Task started: CheckM
[2024-01-24 13:10:27,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024168865.1_ASM2416886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024168865.1_ASM2416886v1_genomic.fna/checkm_input GCF_024168865.1_ASM2416886v1_genomic.fna/checkm_result
[2024-01-24 13:11:27,364] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:27,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:27,389] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:27,389] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:27,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024168865.1_ASM2416886v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:27,390] [INFO] Task started: Blastn
[2024-01-24 13:11:27,390] [INFO] Running command: blastn -query GCF_024168865.1_ASM2416886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66ac1763-602f-4f56-a458-227c3cb44610/dqc_reference/reference_markers_gtdb.fasta -out GCF_024168865.1_ASM2416886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:29,383] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:29,388] [INFO] Selected 8 target genomes.
[2024-01-24 13:11:29,388] [INFO] Target genome list was writen to GCF_024168865.1_ASM2416886v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:29,495] [INFO] Task started: fastANI
[2024-01-24 13:11:29,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg882c9391-04e2-4831-b932-ff40685ffb0c/GCF_024168865.1_ASM2416886v1_genomic.fna.gz --refList GCF_024168865.1_ASM2416886v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024168865.1_ASM2416886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:43,678] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:43,687] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:43,687] [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	98.962	2048	2159	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	90.1139	1816	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.40	98.40	0.91	0.91	2	-
GCF_013267355.1	s__Achromobacter pestifer_A	90.075	1840	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490035.1	s__Achromobacter bronchisepticus_A	89.9524	1833	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.75	98.99	0.98	0.93	5	-
GCF_000165835.1	s__Achromobacter xylosoxidans_B	89.8488	1890	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.34	96.34	0.92	0.92	2	-
GCF_902859735.1	s__Achromobacter aegrifaciens	89.8381	1828	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	-
GCF_903652925.1	s__Achromobacter anxifer	89.2643	1790	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.16	99.16	0.95	0.95	2	-
GCF_902859645.1	s__Achromobacter insuavis	85.3419	1398	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:43,689] [INFO] GTDB search result was written to GCF_024168865.1_ASM2416886v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:43,689] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:43,692] [INFO] DFAST_QC result json was written to GCF_024168865.1_ASM2416886v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:43,692] [INFO] DFAST_QC completed!
[2024-01-24 13:11:43,692] [INFO] Total running time: 0h1m54s