[2024-01-24 11:44:23,036] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,038] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,038] [INFO] DQC Reference Directory: /var/lib/cwl/stg66a483d1-ca11-4695-a16e-b2aad544a84a/dqc_reference
[2024-01-24 11:44:26,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,344] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg438d4cba-712f-467d-ab71-dfbe02914a6b/GCF_013416335.1_ASM1341633v1_genomic.fna.gz | prodigal -d GCF_013416335.1_ASM1341633v1_genomic.fna/cds.fna -a GCF_013416335.1_ASM1341633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:40,565] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:40,566] [INFO] Task started: HMMsearch
[2024-01-24 11:44:40,566] [INFO] Running command: hmmsearch --tblout GCF_013416335.1_ASM1341633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66a483d1-ca11-4695-a16e-b2aad544a84a/dqc_reference/reference_markers.hmm GCF_013416335.1_ASM1341633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:40,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:40,859] [INFO] Found 6/6 markers.
[2024-01-24 11:44:40,900] [INFO] Query marker FASTA was written to GCF_013416335.1_ASM1341633v1_genomic.fna/markers.fasta
[2024-01-24 11:44:40,900] [INFO] Task started: Blastn
[2024-01-24 11:44:40,900] [INFO] Running command: blastn -query GCF_013416335.1_ASM1341633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66a483d1-ca11-4695-a16e-b2aad544a84a/dqc_reference/reference_markers.fasta -out GCF_013416335.1_ASM1341633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:41,740] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:41,743] [INFO] Selected 19 target genomes.
[2024-01-24 11:44:41,743] [INFO] Target genome list was writen to GCF_013416335.1_ASM1341633v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:41,751] [INFO] Task started: fastANI
[2024-01-24 11:44:41,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg438d4cba-712f-467d-ab71-dfbe02914a6b/GCF_013416335.1_ASM1341633v1_genomic.fna.gz --refList GCF_013416335.1_ASM1341633v1_genomic.fna/target_genomes.txt --output GCF_013416335.1_ASM1341633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:54,783] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:54,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66a483d1-ca11-4695-a16e-b2aad544a84a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:54,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66a483d1-ca11-4695-a16e-b2aad544a84a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:54,797] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:54,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:54,798] [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
Pusillimonas soli	strain=DSM 25264	GCA_013416335.1	659016	659016	type	True	100.0	1369	1373	95	conclusive
Pusillimonas soli	strain=KCTC 22455	GCA_004153445.1	659016	659016	type	True	99.9997	1369	1373	95	conclusive
Pusillimonas ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	79.0286	420	1373	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	78.4868	388	1373	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	78.447	382	1373	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	78.2422	385	1373	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	78.0351	362	1373	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003096595.1	305977	305977	type	True	77.9719	301	1373	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	77.9132	300	1373	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.766	289	1373	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	77.728	302	1373	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.4364	68	1373	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	76.2465	61	1373	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	76.1916	63	1373	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	76.0026	78	1373	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	75.5999	87	1373	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	75.4951	83	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:54,800] [INFO] DFAST Taxonomy check result was written to GCF_013416335.1_ASM1341633v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:54,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:54,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:54,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66a483d1-ca11-4695-a16e-b2aad544a84a/dqc_reference/checkm_data
[2024-01-24 11:44:54,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:54,847] [INFO] Task started: CheckM
[2024-01-24 11:44:54,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013416335.1_ASM1341633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013416335.1_ASM1341633v1_genomic.fna/checkm_input GCF_013416335.1_ASM1341633v1_genomic.fna/checkm_result
[2024-01-24 11:45:37,622] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:37,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:37,646] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:37,646] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:37,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013416335.1_ASM1341633v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:37,647] [INFO] Task started: Blastn
[2024-01-24 11:45:37,647] [INFO] Running command: blastn -query GCF_013416335.1_ASM1341633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66a483d1-ca11-4695-a16e-b2aad544a84a/dqc_reference/reference_markers_gtdb.fasta -out GCF_013416335.1_ASM1341633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:39,176] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:39,180] [INFO] Selected 18 target genomes.
[2024-01-24 11:45:39,181] [INFO] Target genome list was writen to GCF_013416335.1_ASM1341633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:39,194] [INFO] Task started: fastANI
[2024-01-24 11:45:39,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg438d4cba-712f-467d-ab71-dfbe02914a6b/GCF_013416335.1_ASM1341633v1_genomic.fna.gz --refList GCF_013416335.1_ASM1341633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013416335.1_ASM1341633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:55,687] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:55,705] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:55,706] [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_004153445.1	s__Pusillimonas_B soli	99.9997	1369	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004153455.1	s__Pusillimonas_B ginsengisoli	79.0563	418	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000209655.1	s__Pusillimonas_C sp000209655	78.8676	295	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416525.1	s__Parapusillimonas granuli	78.4684	379	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009857885.1	s__Pusillimonas_B sp009857885	78.2544	370	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209565.1	s__Candidimonas nitroreducens	78.2422	385	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416435.1	s__Parapusillimonas sp013416435	78.2088	346	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	78.0898	390	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	78.0547	360	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096595.1	s__Pusillimonas noertemannii	77.9719	301	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	99.25	97.76	0.97	0.91	4	-
GCF_004022565.1	s__Pusillimonas_D thiosulfatoxidans	77.8854	310	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_D	95.0	97.98	97.65	0.84	0.81	3	-
GCF_000306945.1	s__Bordetella pertussis	77.7767	288	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_002261345.1	s__Bordetella_A sp002261345	77.6658	326	1373	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_002261225.1	s__Bordetella_C sp002261225	77.345	294	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	77.259	335	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCA_019104865.1	s__Castellaniella sp019104865	77.1313	198	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009763255.1	s__Bordetella_A sp009763255	77.0196	163	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	97.90	97.90	0.93	0.93	2	-
GCF_014170335.1	s__Achromobacter sp014170335	77.0045	283	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:55,708] [INFO] GTDB search result was written to GCF_013416335.1_ASM1341633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:55,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:55,712] [INFO] DFAST_QC result json was written to GCF_013416335.1_ASM1341633v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:55,712] [INFO] DFAST_QC completed!
[2024-01-24 11:45:55,712] [INFO] Total running time: 0h1m33s