[2024-01-24 13:40:44,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,160] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg9725091a-ec43-4161-b8ab-fde7b8b43af2/dqc_reference
[2024-01-24 13:40:45,652] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,653] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,654] [INFO] Running command: gunzip -c /var/lib/cwl/stg7831d41f-ce8b-4c3e-8e6d-4bcb5d3afce3/GCF_003545825.1_ASM354582v1_genomic.fna.gz | prodigal -d GCF_003545825.1_ASM354582v1_genomic.fna/cds.fna -a GCF_003545825.1_ASM354582v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:00,469] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:00,469] [INFO] Task started: HMMsearch
[2024-01-24 13:41:00,469] [INFO] Running command: hmmsearch --tblout GCF_003545825.1_ASM354582v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9725091a-ec43-4161-b8ab-fde7b8b43af2/dqc_reference/reference_markers.hmm GCF_003545825.1_ASM354582v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,794] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,831] [INFO] Query marker FASTA was written to GCF_003545825.1_ASM354582v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,831] [INFO] Task started: Blastn
[2024-01-24 13:41:00,831] [INFO] Running command: blastn -query GCF_003545825.1_ASM354582v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9725091a-ec43-4161-b8ab-fde7b8b43af2/dqc_reference/reference_markers.fasta -out GCF_003545825.1_ASM354582v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,806] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,810] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:01,810] [INFO] Target genome list was writen to GCF_003545825.1_ASM354582v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,819] [INFO] Task started: fastANI
[2024-01-24 13:41:01,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg7831d41f-ce8b-4c3e-8e6d-4bcb5d3afce3/GCF_003545825.1_ASM354582v1_genomic.fna.gz --refList GCF_003545825.1_ASM354582v1_genomic.fna/target_genomes.txt --output GCF_003545825.1_ASM354582v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:18,744] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:18,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9725091a-ec43-4161-b8ab-fde7b8b43af2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:18,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9725091a-ec43-4161-b8ab-fde7b8b43af2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:18,757] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:18,757] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:18,757] [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 noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	100.0	1397	1397	95	conclusive
Pusillimonas noertemannii	strain=DSM 10065	GCA_013416295.1	305977	305977	type	True	99.9981	1393	1397	95	conclusive
Pusillimonas noertemannii	strain=DSM 10065	GCA_003096595.1	305977	305977	type	True	99.9981	1388	1397	95	conclusive
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	86.6507	1006	1397	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.7983	472	1397	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	79.7615	485	1397	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	79.5713	450	1397	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	79.0739	522	1397	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	79.0685	423	1397	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	78.9957	429	1397	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	78.8404	464	1397	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	78.7416	416	1397	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.5332	382	1397	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.1551	236	1397	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	76.7569	164	1397	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:18,759] [INFO] DFAST Taxonomy check result was written to GCF_003545825.1_ASM354582v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:18,760] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:18,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:18,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9725091a-ec43-4161-b8ab-fde7b8b43af2/dqc_reference/checkm_data
[2024-01-24 13:41:18,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:18,803] [INFO] Task started: CheckM
[2024-01-24 13:41:18,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003545825.1_ASM354582v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003545825.1_ASM354582v1_genomic.fna/checkm_input GCF_003545825.1_ASM354582v1_genomic.fna/checkm_result
[2024-01-24 13:42:01,393] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:01,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:01,418] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:01,418] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:01,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003545825.1_ASM354582v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:01,419] [INFO] Task started: Blastn
[2024-01-24 13:42:01,419] [INFO] Running command: blastn -query GCF_003545825.1_ASM354582v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9725091a-ec43-4161-b8ab-fde7b8b43af2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003545825.1_ASM354582v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:03,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:03,252] [INFO] Selected 18 target genomes.
[2024-01-24 13:42:03,252] [INFO] Target genome list was writen to GCF_003545825.1_ASM354582v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:03,268] [INFO] Task started: fastANI
[2024-01-24 13:42:03,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg7831d41f-ce8b-4c3e-8e6d-4bcb5d3afce3/GCF_003545825.1_ASM354582v1_genomic.fna.gz --refList GCF_003545825.1_ASM354582v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003545825.1_ASM354582v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:18,752] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:18,772] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:18,772] [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_003096595.1	s__Pusillimonas noertemannii	99.9981	1388	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	99.25	97.76	0.97	0.91	4	conclusive
GCF_003545815.1	s__Pusillimonas caeni	86.6629	1005	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416525.1	s__Parapusillimonas granuli	79.8208	470	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002209565.1	s__Candidimonas nitroreducens	79.7582	484	1397	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	79.5803	450	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270295.1	s__Achromobacter sp001270295	79.372	374	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356245.1	s__Bordetella_A petrii_D	79.3319	467	1397	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_017745595.1	s__Bordetella_A petrii_C	79.2836	482	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416435.1	s__Parapusillimonas sp013416435	79.2136	397	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261345.1	s__Bordetella_A sp002261345	79.2029	453	1397	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_900129885.1	s__Candidimonas_A bauzanensis	79.1336	451	1397	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_002261265.1	s__Bordetella_A sp002261265	78.7905	382	1397	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_002261225.1	s__Bordetella_C sp002261225	78.6827	431	1397	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_002188635.1	s__Pigmentiphaga sp002188635	77.9506	400	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.65	99.31	0.97	0.93	3	-
GCF_001051995.2	s__Thauera humireducens	76.7318	167	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
GCA_001577345.1	s__Gallionella acididurans	76.5853	57	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003702045.1	s__Pseudomonas_E viridiflava_C	75.7442	55	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.39	99.39	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:18,774] [INFO] GTDB search result was written to GCF_003545825.1_ASM354582v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:18,775] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:18,778] [INFO] DFAST_QC result json was written to GCF_003545825.1_ASM354582v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:18,778] [INFO] DFAST_QC completed!
[2024-01-24 13:42:18,779] [INFO] Total running time: 0h1m35s