[2024-01-25 18:48:20,902] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:20,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:20,903] [INFO] DQC Reference Directory: /var/lib/cwl/stga469049a-0c0d-4ce7-b41f-b517e5ce038c/dqc_reference
[2024-01-25 18:48:22,032] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:22,032] [INFO] Task started: Prodigal
[2024-01-25 18:48:22,032] [INFO] Running command: gunzip -c /var/lib/cwl/stg76c36422-76c5-4fba-bb5d-3d761bfd22dd/GCF_014203015.1_ASM1420301v1_genomic.fna.gz | prodigal -d GCF_014203015.1_ASM1420301v1_genomic.fna/cds.fna -a GCF_014203015.1_ASM1420301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:31,843] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:31,844] [INFO] Task started: HMMsearch
[2024-01-25 18:48:31,844] [INFO] Running command: hmmsearch --tblout GCF_014203015.1_ASM1420301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga469049a-0c0d-4ce7-b41f-b517e5ce038c/dqc_reference/reference_markers.hmm GCF_014203015.1_ASM1420301v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:32,056] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:32,057] [INFO] Found 6/6 markers.
[2024-01-25 18:48:32,087] [INFO] Query marker FASTA was written to GCF_014203015.1_ASM1420301v1_genomic.fna/markers.fasta
[2024-01-25 18:48:32,087] [INFO] Task started: Blastn
[2024-01-25 18:48:32,087] [INFO] Running command: blastn -query GCF_014203015.1_ASM1420301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga469049a-0c0d-4ce7-b41f-b517e5ce038c/dqc_reference/reference_markers.fasta -out GCF_014203015.1_ASM1420301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:33,122] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:33,124] [INFO] Selected 21 target genomes.
[2024-01-25 18:48:33,124] [INFO] Target genome list was writen to GCF_014203015.1_ASM1420301v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:33,132] [INFO] Task started: fastANI
[2024-01-25 18:48:33,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg76c36422-76c5-4fba-bb5d-3d761bfd22dd/GCF_014203015.1_ASM1420301v1_genomic.fna.gz --refList GCF_014203015.1_ASM1420301v1_genomic.fna/target_genomes.txt --output GCF_014203015.1_ASM1420301v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:53,221] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:53,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga469049a-0c0d-4ce7-b41f-b517e5ce038c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:53,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga469049a-0c0d-4ce7-b41f-b517e5ce038c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:53,234] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:48:53,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:53,234] [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
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	100.0	1288	1292	95	conclusive
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	99.865	1144	1292	95	conclusive
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	80.1339	526	1292	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	79.868	567	1292	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.8534	560	1292	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	79.8155	517	1292	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	79.6937	505	1292	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	79.6492	665	1292	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	79.6465	584	1292	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.6411	655	1292	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	79.5705	524	1292	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	79.491	517	1292	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	79.4266	524	1292	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	79.3539	564	1292	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	79.3522	613	1292	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	79.2903	542	1292	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	79.1974	603	1292	95	below_threshold
Bordetella bronchialis	strain=AU3182	GCA_001676705.1	463025	463025	type	True	78.7353	507	1292	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.6185	503	1292	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.8283	390	1292	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.7888	386	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:53,236] [INFO] DFAST Taxonomy check result was written to GCF_014203015.1_ASM1420301v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:53,236] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:53,236] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:53,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga469049a-0c0d-4ce7-b41f-b517e5ce038c/dqc_reference/checkm_data
[2024-01-25 18:48:53,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:53,277] [INFO] Task started: CheckM
[2024-01-25 18:48:53,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203015.1_ASM1420301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203015.1_ASM1420301v1_genomic.fna/checkm_input GCF_014203015.1_ASM1420301v1_genomic.fna/checkm_result
[2024-01-25 18:49:29,979] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:29,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:29,998] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:29,998] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:29,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203015.1_ASM1420301v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:29,999] [INFO] Task started: Blastn
[2024-01-25 18:49:29,999] [INFO] Running command: blastn -query GCF_014203015.1_ASM1420301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga469049a-0c0d-4ce7-b41f-b517e5ce038c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203015.1_ASM1420301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:32,187] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:32,190] [INFO] Selected 17 target genomes.
[2024-01-25 18:49:32,190] [INFO] Target genome list was writen to GCF_014203015.1_ASM1420301v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:32,203] [INFO] Task started: fastANI
[2024-01-25 18:49:32,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg76c36422-76c5-4fba-bb5d-3d761bfd22dd/GCF_014203015.1_ASM1420301v1_genomic.fna.gz --refList GCF_014203015.1_ASM1420301v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203015.1_ASM1420301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:49,516] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:49,529] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:49,529] [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_014203015.1	s__Castellaniella defragrans	100.0	1288	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.06	98.49	0.94	0.90	4	conclusive
GCA_002421865.1	s__Castellaniella sp002421865	88.8403	652	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592225.1	s__Castellaniella caeni	82.9285	684	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.69	99.69	0.95	0.95	2	-
GCA_019104865.1	s__Castellaniella sp019104865	82.8114	679	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004321985.1	s__Castellaniella sp004321985	80.4068	512	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	80.1957	655	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_001270295.1	s__Achromobacter sp001270295	80.1926	493	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209565.1	s__Candidimonas nitroreducens	80.1449	525	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416525.1	s__Parapusillimonas granuli	79.8246	563	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_019166065.1	s__Candidimonas humi	79.8102	517	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261345.1	s__Bordetella_A sp002261345	79.8074	606	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCF_007679965.1	s__Bordetella_B sp007679965	79.7423	592	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017745595.1	s__Bordetella_A petrii_C	79.6722	543	1292	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_000306945.1	s__Bordetella pertussis	79.6463	511	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_900089455.2	s__Orrella dioscoreae	79.4885	525	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Orrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002188635.1	s__Pigmentiphaga sp002188635	79.2974	490	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.65	99.31	0.97	0.93	3	-
GCA_002894305.1	s__Comamonas_C sp002894305	78.1271	377	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:49,530] [INFO] GTDB search result was written to GCF_014203015.1_ASM1420301v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:49,530] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:49,533] [INFO] DFAST_QC result json was written to GCF_014203015.1_ASM1420301v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:49,534] [INFO] DFAST_QC completed!
[2024-01-25 18:49:49,534] [INFO] Total running time: 0h1m29s