[2024-01-24 11:12:39,528] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,533] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3648edc-8b77-49fd-b88a-bc00059785e1/dqc_reference
[2024-01-24 11:12:40,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:40,964] [INFO] Task started: Prodigal
[2024-01-24 11:12:40,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d75eb1c-7628-4c9d-b6b0-a3436466988d/GCF_003350095.1_ASM335009v1_genomic.fna.gz | prodigal -d GCF_003350095.1_ASM335009v1_genomic.fna/cds.fna -a GCF_003350095.1_ASM335009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:52,480] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:52,480] [INFO] Task started: HMMsearch
[2024-01-24 11:12:52,480] [INFO] Running command: hmmsearch --tblout GCF_003350095.1_ASM335009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3648edc-8b77-49fd-b88a-bc00059785e1/dqc_reference/reference_markers.hmm GCF_003350095.1_ASM335009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:52,753] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:52,754] [INFO] Found 6/6 markers.
[2024-01-24 11:12:52,795] [INFO] Query marker FASTA was written to GCF_003350095.1_ASM335009v1_genomic.fna/markers.fasta
[2024-01-24 11:12:52,795] [INFO] Task started: Blastn
[2024-01-24 11:12:52,795] [INFO] Running command: blastn -query GCF_003350095.1_ASM335009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3648edc-8b77-49fd-b88a-bc00059785e1/dqc_reference/reference_markers.fasta -out GCF_003350095.1_ASM335009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:53,721] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:53,724] [INFO] Selected 18 target genomes.
[2024-01-24 11:12:53,724] [INFO] Target genome list was writen to GCF_003350095.1_ASM335009v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:53,732] [INFO] Task started: fastANI
[2024-01-24 11:12:53,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d75eb1c-7628-4c9d-b6b0-a3436466988d/GCF_003350095.1_ASM335009v1_genomic.fna.gz --refList GCF_003350095.1_ASM335009v1_genomic.fna/target_genomes.txt --output GCF_003350095.1_ASM335009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:09,468] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:09,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3648edc-8b77-49fd-b88a-bc00059785e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:09,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3648edc-8b77-49fd-b88a-bc00059785e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:09,483] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:13:09,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:09,483] [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
Bordetella avium	strain=HAMBI_2160	GCA_003350095.1	521	521	type	True	100.0	1206	1208	95	conclusive
Bordetella avium	strain=NCTC12033	GCA_900445835.1	521	521	type	True	99.9956	1207	1208	95	conclusive
Bordetella avium	strain=ATCC 35086	GCA_003581385.1	521	521	type	True	99.9899	1204	1208	95	conclusive
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	82.4479	775	1208	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	82.2721	803	1208	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	82.2572	799	1208	95	below_threshold
Bordetella holmesii	strain=NCTC12912	GCA_900445775.1	35814	35814	type	True	80.9827	609	1208	95	below_threshold
Bordetella holmesii	strain=FDAARGOS_1539	GCA_020735985.1	35814	35814	type	True	80.9423	605	1208	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.6968	584	1208	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	79.683	542	1208	95	below_threshold
Achromobacter animicus	strain=LMG 26690	GCA_902859585.1	1389935	1389935	type	True	79.6262	521	1208	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.2403	165	1208	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.1183	166	1208	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	77.0468	130	1208	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	76.8919	157	1208	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	76.6189	150	1208	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	76.5105	112	1208	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	76.495	143	1208	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:09,485] [INFO] DFAST Taxonomy check result was written to GCF_003350095.1_ASM335009v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:09,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:09,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:09,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3648edc-8b77-49fd-b88a-bc00059785e1/dqc_reference/checkm_data
[2024-01-24 11:13:09,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:09,525] [INFO] Task started: CheckM
[2024-01-24 11:13:09,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003350095.1_ASM335009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003350095.1_ASM335009v1_genomic.fna/checkm_input GCF_003350095.1_ASM335009v1_genomic.fna/checkm_result
[2024-01-24 11:13:45,610] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:45,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:45,637] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:45,637] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:45,638] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003350095.1_ASM335009v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:45,638] [INFO] Task started: Blastn
[2024-01-24 11:13:45,638] [INFO] Running command: blastn -query GCF_003350095.1_ASM335009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3648edc-8b77-49fd-b88a-bc00059785e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003350095.1_ASM335009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:47,181] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:47,185] [INFO] Selected 12 target genomes.
[2024-01-24 11:13:47,186] [INFO] Target genome list was writen to GCF_003350095.1_ASM335009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:47,196] [INFO] Task started: fastANI
[2024-01-24 11:13:47,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d75eb1c-7628-4c9d-b6b0-a3436466988d/GCF_003350095.1_ASM335009v1_genomic.fna.gz --refList GCF_003350095.1_ASM335009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003350095.1_ASM335009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:57,881] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:57,891] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:57,891] [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_900445835.1	s__Bordetella avium	99.9956	1207	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.81	99.47	0.98	0.95	26	conclusive
GCF_000657795.2	s__Bordetella pseudohinzii	82.4914	770	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.97	99.86	0.99	0.98	8	-
GCF_001548475.1	s__Bordetella hinzii	82.2698	796	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.54	99.31	0.93	0.91	26	-
GCF_002261355.1	s__Bordetella sp002261355	81.7649	706	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000612485.1	s__Bordetella holmesii	80.9651	611	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.96	99.94	1.00	0.99	92	-
GCF_900078335.1	s__Bordetella trematum	80.5814	646	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.15	97.27	0.96	0.93	14	-
GCF_002261475.1	s__Bordetella sp002261475	80.2135	570	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.06	99.06	0.95	0.95	2	-
GCF_017356245.1	s__Bordetella_A petrii_D	79.6887	516	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218885.1	s__Bordetella_A sp019218885	79.406	484	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912175.1	s__Comamonas_F wautersii_A	77.1126	146	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901827185.1	s__Variovorax sp901827185	76.6694	132	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.21	98.21	0.91	0.91	2	-
GCA_013697775.1	s__Ramlibacter sp013697775	76.5093	129	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:57,895] [INFO] GTDB search result was written to GCF_003350095.1_ASM335009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:57,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:57,901] [INFO] DFAST_QC result json was written to GCF_003350095.1_ASM335009v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:57,901] [INFO] DFAST_QC completed!
[2024-01-24 11:13:57,901] [INFO] Total running time: 0h1m18s