[2024-01-24 13:47:12,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:12,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:12,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg85394400-78de-4bef-a4ca-9effa8f720f7/dqc_reference
[2024-01-24 13:47:13,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:13,502] [INFO] Task started: Prodigal
[2024-01-24 13:47:13,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ecc994d-1b07-4c96-af2e-382afc236461/GCF_000613885.1_ASM61388v1_genomic.fna.gz | prodigal -d GCF_000613885.1_ASM61388v1_genomic.fna/cds.fna -a GCF_000613885.1_ASM61388v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:22,797] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:22,798] [INFO] Task started: HMMsearch
[2024-01-24 13:47:22,798] [INFO] Running command: hmmsearch --tblout GCF_000613885.1_ASM61388v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85394400-78de-4bef-a4ca-9effa8f720f7/dqc_reference/reference_markers.hmm GCF_000613885.1_ASM61388v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:23,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:23,053] [INFO] Found 6/6 markers.
[2024-01-24 13:47:23,084] [INFO] Query marker FASTA was written to GCF_000613885.1_ASM61388v1_genomic.fna/markers.fasta
[2024-01-24 13:47:23,084] [INFO] Task started: Blastn
[2024-01-24 13:47:23,084] [INFO] Running command: blastn -query GCF_000613885.1_ASM61388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85394400-78de-4bef-a4ca-9effa8f720f7/dqc_reference/reference_markers.fasta -out GCF_000613885.1_ASM61388v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:23,807] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:23,811] [INFO] Selected 17 target genomes.
[2024-01-24 13:47:23,812] [INFO] Target genome list was writen to GCF_000613885.1_ASM61388v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:23,819] [INFO] Task started: fastANI
[2024-01-24 13:47:23,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ecc994d-1b07-4c96-af2e-382afc236461/GCF_000613885.1_ASM61388v1_genomic.fna.gz --refList GCF_000613885.1_ASM61388v1_genomic.fna/target_genomes.txt --output GCF_000613885.1_ASM61388v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:33,139] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:33,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85394400-78de-4bef-a4ca-9effa8f720f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:33,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85394400-78de-4bef-a4ca-9effa8f720f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:33,161] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:33,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:33,161] [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
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	100.0	1039	1041	95	conclusive
Asaia platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	82.3537	663	1041	95	below_threshold
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	82.0405	665	1041	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	80.6848	516	1041	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	80.6661	527	1041	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	80.6049	531	1041	95	below_threshold
Asaia astilbis	strain=JCM 15831	GCA_000613845.1	610244	610244	type	True	80.3128	495	1041	95	below_threshold
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	77.6587	130	1041	95	below_threshold
Gluconobacter thailandicus	strain=F149-1	GCA_000964465.1	257438	257438	type	True	77.4632	112	1041	95	below_threshold
Gluconobacter thailandicus	strain=NBRC 100600	GCA_007990185.1	257438	257438	type	True	77.4299	115	1041	95	below_threshold
Gluconobacter frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	77.3817	113	1041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:33,163] [INFO] DFAST Taxonomy check result was written to GCF_000613885.1_ASM61388v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:33,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:33,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:33,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85394400-78de-4bef-a4ca-9effa8f720f7/dqc_reference/checkm_data
[2024-01-24 13:47:33,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:33,211] [INFO] Task started: CheckM
[2024-01-24 13:47:33,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613885.1_ASM61388v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613885.1_ASM61388v1_genomic.fna/checkm_input GCF_000613885.1_ASM61388v1_genomic.fna/checkm_result
[2024-01-24 13:48:05,248] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:05,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:05,266] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:05,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:05,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613885.1_ASM61388v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:05,267] [INFO] Task started: Blastn
[2024-01-24 13:48:05,268] [INFO] Running command: blastn -query GCF_000613885.1_ASM61388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85394400-78de-4bef-a4ca-9effa8f720f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613885.1_ASM61388v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:06,313] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:06,318] [INFO] Selected 20 target genomes.
[2024-01-24 13:48:06,318] [INFO] Target genome list was writen to GCF_000613885.1_ASM61388v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:06,347] [INFO] Task started: fastANI
[2024-01-24 13:48:06,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ecc994d-1b07-4c96-af2e-382afc236461/GCF_000613885.1_ASM61388v1_genomic.fna.gz --refList GCF_000613885.1_ASM61388v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613885.1_ASM61388v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:19,392] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:19,407] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:19,407] [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_000613885.1	s__Asaia prunellae	100.0	1039	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000614545.1	s__Asaia platycodi	82.3537	663	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635085.1	s__Asaia siamensis	82.029	666	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994335.1	s__Asaia sp003994335	80.8332	537	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900465345.1	s__Asaia bogorensis_A	80.6251	511	1041	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	80.5932	532	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_000613845.1	s__Asaia astilbis	80.3128	495	1041	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	79.6871	353	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005465.1	s__Neoasaia chiangmaiensis	78.2402	156	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neoasaia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004346035.1	s__Acidomonas methanolica	77.8811	135	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
GCF_006538885.1	s__Gluconobacter roseus	77.6091	132	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000964465.1	s__Gluconobacter_A thailandicus	77.4621	112	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	98.77	97.43	0.93	0.88	11	-
GCF_002723955.1	s__Gluconobacter_A frateurii	77.3556	114	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.06	97.06	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:19,409] [INFO] GTDB search result was written to GCF_000613885.1_ASM61388v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:19,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:19,413] [INFO] DFAST_QC result json was written to GCF_000613885.1_ASM61388v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:19,413] [INFO] DFAST_QC completed!
[2024-01-24 13:48:19,413] [INFO] Total running time: 0h1m7s