[2024-01-24 13:32:12,771] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:12,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:12,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg9669c701-8322-41dd-a3c0-2cb385abd0eb/dqc_reference
[2024-01-24 13:32:14,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:14,044] [INFO] Task started: Prodigal
[2024-01-24 13:32:14,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d663009-689c-45e6-babd-c57c30340296/GCF_003545815.1_ASM354581v1_genomic.fna.gz | prodigal -d GCF_003545815.1_ASM354581v1_genomic.fna/cds.fna -a GCF_003545815.1_ASM354581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:28,019] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:28,020] [INFO] Task started: HMMsearch
[2024-01-24 13:32:28,020] [INFO] Running command: hmmsearch --tblout GCF_003545815.1_ASM354581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9669c701-8322-41dd-a3c0-2cb385abd0eb/dqc_reference/reference_markers.hmm GCF_003545815.1_ASM354581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:28,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:28,313] [INFO] Found 6/6 markers.
[2024-01-24 13:32:28,353] [INFO] Query marker FASTA was written to GCF_003545815.1_ASM354581v1_genomic.fna/markers.fasta
[2024-01-24 13:32:28,354] [INFO] Task started: Blastn
[2024-01-24 13:32:28,354] [INFO] Running command: blastn -query GCF_003545815.1_ASM354581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9669c701-8322-41dd-a3c0-2cb385abd0eb/dqc_reference/reference_markers.fasta -out GCF_003545815.1_ASM354581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:29,361] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:29,365] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:29,365] [INFO] Target genome list was writen to GCF_003545815.1_ASM354581v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:29,370] [INFO] Task started: fastANI
[2024-01-24 13:32:29,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d663009-689c-45e6-babd-c57c30340296/GCF_003545815.1_ASM354581v1_genomic.fna.gz --refList GCF_003545815.1_ASM354581v1_genomic.fna/target_genomes.txt --output GCF_003545815.1_ASM354581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:41,675] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:41,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9669c701-8322-41dd-a3c0-2cb385abd0eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:41,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9669c701-8322-41dd-a3c0-2cb385abd0eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:41,687] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:41,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:41,688] [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 caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	100.0	1466	1467	95	conclusive
Pusillimonas noertemannii	strain=DSM 10065	GCA_003096595.1	305977	305977	type	True	86.7049	1005	1467	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	86.6819	1001	1467	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_013416295.1	305977	305977	type	True	86.6762	1006	1467	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	80.099	528	1467	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	79.7358	485	1467	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	79.6411	458	1467	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.4024	513	1467	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	79.2765	439	1467	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	79.1376	425	1467	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.3947	411	1467	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.2064	266	1467	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.1842	265	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:41,690] [INFO] DFAST Taxonomy check result was written to GCF_003545815.1_ASM354581v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:41,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:41,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:41,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9669c701-8322-41dd-a3c0-2cb385abd0eb/dqc_reference/checkm_data
[2024-01-24 13:32:41,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:41,737] [INFO] Task started: CheckM
[2024-01-24 13:32:41,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003545815.1_ASM354581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003545815.1_ASM354581v1_genomic.fna/checkm_input GCF_003545815.1_ASM354581v1_genomic.fna/checkm_result
[2024-01-24 13:33:25,965] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:25,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,981] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:25,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:25,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003545815.1_ASM354581v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:25,982] [INFO] Task started: Blastn
[2024-01-24 13:33:25,982] [INFO] Running command: blastn -query GCF_003545815.1_ASM354581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9669c701-8322-41dd-a3c0-2cb385abd0eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003545815.1_ASM354581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:28,102] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:28,106] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:28,106] [INFO] Target genome list was writen to GCF_003545815.1_ASM354581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:28,116] [INFO] Task started: fastANI
[2024-01-24 13:33:28,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d663009-689c-45e6-babd-c57c30340296/GCF_003545815.1_ASM354581v1_genomic.fna.gz --refList GCF_003545815.1_ASM354581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003545815.1_ASM354581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:41,324] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:41,340] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:41,341] [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_003545815.1	s__Pusillimonas caeni	100.0	1466	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003096595.1	s__Pusillimonas noertemannii	86.7171	1004	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	99.25	97.76	0.97	0.91	4	-
GCF_017745595.1	s__Bordetella_A petrii_C	80.1864	495	1467	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_013416525.1	s__Parapusillimonas granuli	80.0778	531	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	79.9224	475	1467	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_001270295.1	s__Achromobacter sp001270295	79.7551	406	1467	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	79.7464	484	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	79.6323	458	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679965.1	s__Bordetella_B sp007679965	79.2561	468	1467	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_002188635.1	s__Pigmentiphaga sp002188635	78.88	430	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.65	99.31	0.97	0.93	3	-
GCF_002261265.1	s__Bordetella_A sp002261265	78.8693	367	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.22	99.22	0.95	0.94	3	-
GCF_003854895.1	s__Pigmentiphaga sp003854895	78.2966	419	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441445.1	s__UBA6240 sp002441445	78.1228	305	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA6240	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:41,343] [INFO] GTDB search result was written to GCF_003545815.1_ASM354581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:41,343] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:41,350] [INFO] DFAST_QC result json was written to GCF_003545815.1_ASM354581v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:41,350] [INFO] DFAST_QC completed!
[2024-01-24 13:33:41,350] [INFO] Total running time: 0h1m29s