[2024-01-24 13:32:41,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg82b60872-b80b-4cde-ad91-7c108392d26e/dqc_reference
[2024-01-24 13:32:43,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,302] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg6856d2f0-f562-4a87-b9ea-624fbb6b81d1/GCF_008801975.1_ASM880197v1_genomic.fna.gz | prodigal -d GCF_008801975.1_ASM880197v1_genomic.fna/cds.fna -a GCF_008801975.1_ASM880197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:53,526] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:53,527] [INFO] Task started: HMMsearch
[2024-01-24 13:32:53,527] [INFO] Running command: hmmsearch --tblout GCF_008801975.1_ASM880197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82b60872-b80b-4cde-ad91-7c108392d26e/dqc_reference/reference_markers.hmm GCF_008801975.1_ASM880197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:53,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:53,818] [INFO] Found 6/6 markers.
[2024-01-24 13:32:53,864] [INFO] Query marker FASTA was written to GCF_008801975.1_ASM880197v1_genomic.fna/markers.fasta
[2024-01-24 13:32:53,864] [INFO] Task started: Blastn
[2024-01-24 13:32:53,865] [INFO] Running command: blastn -query GCF_008801975.1_ASM880197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82b60872-b80b-4cde-ad91-7c108392d26e/dqc_reference/reference_markers.fasta -out GCF_008801975.1_ASM880197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:55,054] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:55,061] [INFO] Selected 21 target genomes.
[2024-01-24 13:32:55,061] [INFO] Target genome list was writen to GCF_008801975.1_ASM880197v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:55,076] [INFO] Task started: fastANI
[2024-01-24 13:32:55,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg6856d2f0-f562-4a87-b9ea-624fbb6b81d1/GCF_008801975.1_ASM880197v1_genomic.fna.gz --refList GCF_008801975.1_ASM880197v1_genomic.fna/target_genomes.txt --output GCF_008801975.1_ASM880197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:15,198] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:15,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82b60872-b80b-4cde-ad91-7c108392d26e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:15,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82b60872-b80b-4cde-ad91-7c108392d26e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:15,218] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:15,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:15,219] [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=CCUG 39790	GCA_008801975.1	75697	75697	type	True	100.0	1159	1169	95	conclusive
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	99.9919	1158	1169	95	conclusive
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	80.2942	494	1169	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	80.1894	462	1169	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	80.1626	501	1169	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	80.1142	514	1169	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	79.8056	538	1169	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	79.7845	465	1169	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	79.7481	478	1169	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.7349	609	1169	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	79.7154	480	1169	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	79.7098	611	1169	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	79.6786	485	1169	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	79.6593	480	1169	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	79.6005	517	1169	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	79.4266	571	1169	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	79.2775	549	1169	95	below_threshold
Bordetella bronchialis	strain=AU3182	GCA_001676705.1	463025	463025	type	True	79.0275	459	1169	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.8655	455	1169	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.8621	367	1169	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.842	373	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:15,230] [INFO] DFAST Taxonomy check result was written to GCF_008801975.1_ASM880197v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:15,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:15,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:15,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82b60872-b80b-4cde-ad91-7c108392d26e/dqc_reference/checkm_data
[2024-01-24 13:33:15,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:15,290] [INFO] Task started: CheckM
[2024-01-24 13:33:15,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008801975.1_ASM880197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008801975.1_ASM880197v1_genomic.fna/checkm_input GCF_008801975.1_ASM880197v1_genomic.fna/checkm_result
[2024-01-24 13:33:53,016] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:53,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:53,039] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:53,040] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:53,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008801975.1_ASM880197v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:53,041] [INFO] Task started: Blastn
[2024-01-24 13:33:53,041] [INFO] Running command: blastn -query GCF_008801975.1_ASM880197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82b60872-b80b-4cde-ad91-7c108392d26e/dqc_reference/reference_markers_gtdb.fasta -out GCF_008801975.1_ASM880197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:55,477] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:55,481] [INFO] Selected 17 target genomes.
[2024-01-24 13:33:55,481] [INFO] Target genome list was writen to GCF_008801975.1_ASM880197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:55,502] [INFO] Task started: fastANI
[2024-01-24 13:33:55,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg6856d2f0-f562-4a87-b9ea-624fbb6b81d1/GCF_008801975.1_ASM880197v1_genomic.fna.gz --refList GCF_008801975.1_ASM880197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008801975.1_ASM880197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:12,645] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:12,659] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:12,659] [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	99.9919	1158	1169	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	88.8324	597	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019104865.1	s__Castellaniella sp019104865	83.0967	605	1169	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	82.8894	619	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.69	99.69	0.95	0.95	2	-
GCA_004321985.1	s__Castellaniella sp004321985	80.5752	460	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270295.1	s__Achromobacter sp001270295	80.532	462	1169	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	80.3182	492	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	80.3002	606	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_019166065.1	s__Candidimonas humi	80.2072	460	1169	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	80.1376	530	1169	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_013416525.1	s__Parapusillimonas granuli	80.1279	504	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007679965.1	s__Bordetella_B sp007679965	80.0385	530	1169	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_900089455.2	s__Orrella dioscoreae	79.8607	462	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Orrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306945.1	s__Bordetella pertussis	79.7261	479	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_017745595.1	s__Bordetella_A petrii_C	79.7075	503	1169	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_002188635.1	s__Pigmentiphaga sp002188635	79.5412	453	1169	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	78.4706	342	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:12,661] [INFO] GTDB search result was written to GCF_008801975.1_ASM880197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:12,661] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:12,666] [INFO] DFAST_QC result json was written to GCF_008801975.1_ASM880197v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:12,666] [INFO] DFAST_QC completed!
[2024-01-24 13:34:12,666] [INFO] Total running time: 0h1m31s