[2024-01-24 13:31:44,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg134b959d-e014-4551-ba49-30101142bf38/dqc_reference
[2024-01-24 13:31:45,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,673] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg51a7eb7f-c5f7-48f9-8d45-a622d3485ace/GCF_007989365.1_ASM798936v1_genomic.fna.gz | prodigal -d GCF_007989365.1_ASM798936v1_genomic.fna/cds.fna -a GCF_007989365.1_ASM798936v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:55,600] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:55,601] [INFO] Task started: HMMsearch
[2024-01-24 13:31:55,601] [INFO] Running command: hmmsearch --tblout GCF_007989365.1_ASM798936v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg134b959d-e014-4551-ba49-30101142bf38/dqc_reference/reference_markers.hmm GCF_007989365.1_ASM798936v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:55,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:55,846] [INFO] Found 6/6 markers.
[2024-01-24 13:31:55,877] [INFO] Query marker FASTA was written to GCF_007989365.1_ASM798936v1_genomic.fna/markers.fasta
[2024-01-24 13:31:55,878] [INFO] Task started: Blastn
[2024-01-24 13:31:55,878] [INFO] Running command: blastn -query GCF_007989365.1_ASM798936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg134b959d-e014-4551-ba49-30101142bf38/dqc_reference/reference_markers.fasta -out GCF_007989365.1_ASM798936v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:56,745] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:56,883] [INFO] Selected 18 target genomes.
[2024-01-24 13:31:56,883] [INFO] Target genome list was writen to GCF_007989365.1_ASM798936v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:56,900] [INFO] Task started: fastANI
[2024-01-24 13:31:56,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg51a7eb7f-c5f7-48f9-8d45-a622d3485ace/GCF_007989365.1_ASM798936v1_genomic.fna.gz --refList GCF_007989365.1_ASM798936v1_genomic.fna/target_genomes.txt --output GCF_007989365.1_ASM798936v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:06,829] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:06,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg134b959d-e014-4551-ba49-30101142bf38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:06,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg134b959d-e014-4551-ba49-30101142bf38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:06,849] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:06,849] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:06,850] [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
Kozakia baliensis	strain=NBRC 16664	GCA_007989365.1	153496	153496	type	True	100.0	1053	1057	95	conclusive
Kozakia baliensis	strain=DSM 14400	GCA_001787335.1	153496	153496	type	True	99.9619	1044	1057	95	conclusive
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_007991115.1	320497	320497	type	True	78.7138	293	1057	95	below_threshold
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_002005465.1	320497	320497	type	True	78.6562	296	1057	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	78.3187	182	1057	95	below_threshold
Asaia platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	78.1624	223	1057	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	78.1357	221	1057	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	78.1028	210	1057	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	78.0921	139	1057	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	78.0839	156	1057	95	below_threshold
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	78.0306	226	1057	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	77.9611	215	1057	95	below_threshold
Acidomonas methanolica	strain=MB58	GCA_000617865.1	437	437	type	True	77.9135	214	1057	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	77.9117	147	1057	95	below_threshold
Acidomonas methanolica	strain=DSM 5432	GCA_004346035.1	437	437	type	True	77.8901	217	1057	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	77.7036	145	1057	95	below_threshold
Neokomagataea anthophila	strain=TBRC 2177	GCA_018122595.1	2826925	2826925	type	True	77.1334	70	1057	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:06,851] [INFO] DFAST Taxonomy check result was written to GCF_007989365.1_ASM798936v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:06,852] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:06,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:06,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg134b959d-e014-4551-ba49-30101142bf38/dqc_reference/checkm_data
[2024-01-24 13:32:06,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:06,892] [INFO] Task started: CheckM
[2024-01-24 13:32:06,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989365.1_ASM798936v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989365.1_ASM798936v1_genomic.fna/checkm_input GCF_007989365.1_ASM798936v1_genomic.fna/checkm_result
[2024-01-24 13:32:40,579] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:40,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:40,602] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:40,602] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:40,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989365.1_ASM798936v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:40,603] [INFO] Task started: Blastn
[2024-01-24 13:32:40,603] [INFO] Running command: blastn -query GCF_007989365.1_ASM798936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg134b959d-e014-4551-ba49-30101142bf38/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989365.1_ASM798936v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:41,979] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:41,983] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:41,983] [INFO] Target genome list was writen to GCF_007989365.1_ASM798936v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:41,996] [INFO] Task started: fastANI
[2024-01-24 13:32:41,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg51a7eb7f-c5f7-48f9-8d45-a622d3485ace/GCF_007989365.1_ASM798936v1_genomic.fna.gz --refList GCF_007989365.1_ASM798936v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989365.1_ASM798936v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:52,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:52,054] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:52,055] [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_001787335.1	s__Kozakia baliensis	99.9619	1044	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Kozakia	95.0	98.19	97.27	0.93	0.89	4	conclusive
GCF_002005465.1	s__Neoasaia chiangmaiensis	78.6562	296	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neoasaia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900465345.1	s__Asaia bogorensis_A	78.4967	208	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988945.1	s__Swaminathania salitolerans	78.3564	207	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206495.1	s__Komagataeibacter entanii	78.1959	152	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.26	98.23	0.88	0.87	3	-
GCF_000614545.1	s__Asaia platycodi	78.1624	223	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403295.1	s__Komagataeibacter melaceti	78.0921	139	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635085.1	s__Asaia siamensis	78.0306	226	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547995.1	s__Asaia bogorensis	78.0088	208	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_015244675.1	s__Gluconobacter cerevisiae	77.9619	149	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006538885.1	s__Gluconobacter roseus	77.9159	150	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002906255.1	s__Komagataeibacter maltaceti	77.9117	147	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.99	99.99	0.97	0.97	2	-
GCF_004346035.1	s__Acidomonas methanolica	77.8901	217	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
GCF_003994335.1	s__Asaia sp003994335	77.8449	221	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613885.1	s__Asaia prunellae	77.7877	162	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723915.1	s__Gluconobacter albidus	77.5672	171	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCA_015223225.1	s__Roseomonas sp015223225	76.5198	66	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:52,057] [INFO] GTDB search result was written to GCF_007989365.1_ASM798936v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:52,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:52,062] [INFO] DFAST_QC result json was written to GCF_007989365.1_ASM798936v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:52,062] [INFO] DFAST_QC completed!
[2024-01-24 13:32:52,062] [INFO] Total running time: 0h1m8s