[2024-01-24 14:55:08,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fc48264-3241-4900-ac07-1d7ca82be010/dqc_reference
[2024-01-24 14:55:09,987] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,988] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,988] [INFO] Running command: gunzip -c /var/lib/cwl/stg114d7a56-d382-41ee-96fe-4a909189ed08/GCF_003096595.1_ASM309659v1_genomic.fna.gz | prodigal -d GCF_003096595.1_ASM309659v1_genomic.fna/cds.fna -a GCF_003096595.1_ASM309659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:23,659] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:23,660] [INFO] Task started: HMMsearch
[2024-01-24 14:55:23,660] [INFO] Running command: hmmsearch --tblout GCF_003096595.1_ASM309659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fc48264-3241-4900-ac07-1d7ca82be010/dqc_reference/reference_markers.hmm GCF_003096595.1_ASM309659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:23,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:23,953] [INFO] Found 6/6 markers.
[2024-01-24 14:55:24,002] [INFO] Query marker FASTA was written to GCF_003096595.1_ASM309659v1_genomic.fna/markers.fasta
[2024-01-24 14:55:24,002] [INFO] Task started: Blastn
[2024-01-24 14:55:24,002] [INFO] Running command: blastn -query GCF_003096595.1_ASM309659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fc48264-3241-4900-ac07-1d7ca82be010/dqc_reference/reference_markers.fasta -out GCF_003096595.1_ASM309659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:24,914] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:24,918] [INFO] Selected 18 target genomes.
[2024-01-24 14:55:24,918] [INFO] Target genome list was writen to GCF_003096595.1_ASM309659v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:24,928] [INFO] Task started: fastANI
[2024-01-24 14:55:24,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg114d7a56-d382-41ee-96fe-4a909189ed08/GCF_003096595.1_ASM309659v1_genomic.fna.gz --refList GCF_003096595.1_ASM309659v1_genomic.fna/target_genomes.txt --output GCF_003096595.1_ASM309659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:41,470] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:41,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fc48264-3241-4900-ac07-1d7ca82be010/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:41,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fc48264-3241-4900-ac07-1d7ca82be010/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:41,484] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:55:41,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:41,484] [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_003096595.1	305977	305977	type	True	100.0	1390	1393	95	conclusive
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	99.9996	1393	1393	95	conclusive
Pusillimonas noertemannii	strain=DSM 10065	GCA_013416295.1	305977	305977	type	True	99.9979	1388	1393	95	conclusive
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	86.6811	1018	1393	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.8268	468	1393	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	79.7888	484	1393	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	79.6449	451	1393	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	79.2284	507	1393	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	79.1641	409	1393	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	79.0446	424	1393	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.0241	451	1393	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	78.8908	410	1393	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.5219	379	1393	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.1887	232	1393	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	76.6646	159	1393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:41,486] [INFO] DFAST Taxonomy check result was written to GCF_003096595.1_ASM309659v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:41,487] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:41,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:41,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fc48264-3241-4900-ac07-1d7ca82be010/dqc_reference/checkm_data
[2024-01-24 14:55:41,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:41,532] [INFO] Task started: CheckM
[2024-01-24 14:55:41,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003096595.1_ASM309659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003096595.1_ASM309659v1_genomic.fna/checkm_input GCF_003096595.1_ASM309659v1_genomic.fna/checkm_result
[2024-01-24 14:56:23,064] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:23,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:23,083] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:23,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:23,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003096595.1_ASM309659v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:23,084] [INFO] Task started: Blastn
[2024-01-24 14:56:23,085] [INFO] Running command: blastn -query GCF_003096595.1_ASM309659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fc48264-3241-4900-ac07-1d7ca82be010/dqc_reference/reference_markers_gtdb.fasta -out GCF_003096595.1_ASM309659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:24,774] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:24,778] [INFO] Selected 18 target genomes.
[2024-01-24 14:56:24,779] [INFO] Target genome list was writen to GCF_003096595.1_ASM309659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:24,824] [INFO] Task started: fastANI
[2024-01-24 14:56:24,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg114d7a56-d382-41ee-96fe-4a909189ed08/GCF_003096595.1_ASM309659v1_genomic.fna.gz --refList GCF_003096595.1_ASM309659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003096595.1_ASM309659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:41,065] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:41,090] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:41,091] [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	100.0	1390	1393	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	86.6575	1020	1393	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	79.8499	466	1393	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	79.7889	484	1393	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	79.6675	450	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356245.1	s__Bordetella_A petrii_D	79.4117	457	1393	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	79.408	469	1393	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_002261345.1	s__Bordetella_A sp002261345	79.325	437	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCA_013416435.1	s__Parapusillimonas sp013416435	79.3138	399	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270295.1	s__Achromobacter sp001270295	79.1924	387	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	79.1032	455	1393	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_002261225.1	s__Bordetella_C sp002261225	78.767	416	1393	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_002261265.1	s__Bordetella_A sp002261265	78.7383	382	1393	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_002188635.1	s__Pigmentiphaga sp002188635	78.0527	396	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.65	99.31	0.97	0.93	3	-
GCA_001577345.1	s__Gallionella acididurans	76.8062	57	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001051995.2	s__Thauera humireducens	76.6524	160	1393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:41,092] [INFO] GTDB search result was written to GCF_003096595.1_ASM309659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:41,093] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:41,096] [INFO] DFAST_QC result json was written to GCF_003096595.1_ASM309659v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:41,096] [INFO] DFAST_QC completed!
[2024-01-24 14:56:41,097] [INFO] Total running time: 0h1m33s