[2024-01-24 13:31:33,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a6e7be0-75de-4f27-be29-412833529c04/dqc_reference
[2024-01-24 13:31:35,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:35,040] [INFO] Task started: Prodigal
[2024-01-24 13:31:35,040] [INFO] Running command: gunzip -c /var/lib/cwl/stg21b81959-e02f-49a1-bc4d-4e4287976367/GCF_013267395.1_ASM1326739v1_genomic.fna.gz | prodigal -d GCF_013267395.1_ASM1326739v1_genomic.fna/cds.fna -a GCF_013267395.1_ASM1326739v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:57,534] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:57,534] [INFO] Task started: HMMsearch
[2024-01-24 13:31:57,534] [INFO] Running command: hmmsearch --tblout GCF_013267395.1_ASM1326739v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a6e7be0-75de-4f27-be29-412833529c04/dqc_reference/reference_markers.hmm GCF_013267395.1_ASM1326739v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:58,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:58,015] [INFO] Found 6/6 markers.
[2024-01-24 13:31:58,084] [INFO] Query marker FASTA was written to GCF_013267395.1_ASM1326739v1_genomic.fna/markers.fasta
[2024-01-24 13:31:58,085] [INFO] Task started: Blastn
[2024-01-24 13:31:58,085] [INFO] Running command: blastn -query GCF_013267395.1_ASM1326739v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a6e7be0-75de-4f27-be29-412833529c04/dqc_reference/reference_markers.fasta -out GCF_013267395.1_ASM1326739v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:59,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:59,144] [INFO] Selected 18 target genomes.
[2024-01-24 13:31:59,145] [INFO] Target genome list was writen to GCF_013267395.1_ASM1326739v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:59,154] [INFO] Task started: fastANI
[2024-01-24 13:31:59,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg21b81959-e02f-49a1-bc4d-4e4287976367/GCF_013267395.1_ASM1326739v1_genomic.fna.gz --refList GCF_013267395.1_ASM1326739v1_genomic.fna/target_genomes.txt --output GCF_013267395.1_ASM1326739v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:26,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:26,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a6e7be0-75de-4f27-be29-412833529c04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:26,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a6e7be0-75de-4f27-be29-412833529c04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:26,380] [INFO] Found 18 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:32:26,380] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:26,381] [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 denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	100.0	2245	2245	95	conclusive
Achromobacter denitrificans	strain=NCTC8582	GCA_900444675.1	32002	32002	type	True	99.9981	2185	2245	95	conclusive
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	99.9812	2167	2245	95	conclusive
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	99.9543	2161	2245	95	conclusive
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	91.1884	1738	2245	95	below_threshold
Achromobacter agilis	strain=LMG 3411	GCA_900496965.1	1353888	1353888	type	True	90.3649	1762	2245	95	below_threshold
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	88.3793	1631	2245	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	86.9885	1624	2245	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	86.3372	1493	2245	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	86.297	1497	2245	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	82.5306	950	2245	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.7957	480	2245	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.4689	533	2245	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.8093	298	2245	95	below_threshold
Adlercreutzia hattorii	strain=8CFCBH1	GCA_011405655.1	2707299	2707299	type	True	75.2118	67	2245	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_016865385.1	394340	446660	type	True	75.2007	60	2245	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	74.6639	54	2245	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	74.6564	55	2245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:26,382] [INFO] DFAST Taxonomy check result was written to GCF_013267395.1_ASM1326739v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:26,382] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:26,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:26,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a6e7be0-75de-4f27-be29-412833529c04/dqc_reference/checkm_data
[2024-01-24 13:32:26,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:26,450] [INFO] Task started: CheckM
[2024-01-24 13:32:26,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013267395.1_ASM1326739v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013267395.1_ASM1326739v1_genomic.fna/checkm_input GCF_013267395.1_ASM1326739v1_genomic.fna/checkm_result
[2024-01-24 13:33:38,894] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:38,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:38,916] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:38,917] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:38,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013267395.1_ASM1326739v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:38,918] [INFO] Task started: Blastn
[2024-01-24 13:33:38,918] [INFO] Running command: blastn -query GCF_013267395.1_ASM1326739v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a6e7be0-75de-4f27-be29-412833529c04/dqc_reference/reference_markers_gtdb.fasta -out GCF_013267395.1_ASM1326739v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:40,795] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:40,802] [INFO] Selected 16 target genomes.
[2024-01-24 13:33:40,803] [INFO] Target genome list was writen to GCF_013267395.1_ASM1326739v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:40,828] [INFO] Task started: fastANI
[2024-01-24 13:33:40,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg21b81959-e02f-49a1-bc4d-4e4287976367/GCF_013267395.1_ASM1326739v1_genomic.fna.gz --refList GCF_013267395.1_ASM1326739v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013267395.1_ASM1326739v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:07,668] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:07,686] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:07,687] [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_001571365.1	s__Achromobacter denitrificans	99.9812	2167	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	conclusive
GCF_900496975.1	s__Achromobacter veterisilvae	91.199	1737	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900496965.1	s__Achromobacter agilis	90.3559	1763	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757485.1	s__Achromobacter sp000757485	89.9926	1775	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	88.8663	1510	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_903652925.1	s__Achromobacter anxifer	88.357	1635	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.16	99.16	0.95	0.95	2	-
GCF_000165835.1	s__Achromobacter xylosoxidans_B	87.9997	1698	2245	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	87.9164	1659	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	-
GCF_902859645.1	s__Achromobacter insuavis	86.7439	1430	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_016127315.1	s__Achromobacter insuavis_A	86.6639	1504	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_902859695.1	s__Achromobacter ruhlandii	86.5017	1428	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_001457475.1	s__Achromobacter xylosoxidans	86.3197	1495	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	-
GCA_000955795.1	s__Ralstonia sp000955795	77.4928	345	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425265.1	s__Pseudoduganella sp001425265	77.0452	579	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425045.1	s__Pseudoduganella sp001425045	77.0263	575	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361735.1	s__Azoarcus indigens	76.7333	437	2245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:07,689] [INFO] GTDB search result was written to GCF_013267395.1_ASM1326739v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:07,689] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:07,693] [INFO] DFAST_QC result json was written to GCF_013267395.1_ASM1326739v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:07,693] [INFO] DFAST_QC completed!
[2024-01-24 13:34:07,693] [INFO] Total running time: 0h2m34s