[2024-01-24 13:16:56,158] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:56,159] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:56,160] [INFO] DQC Reference Directory: /var/lib/cwl/stg201238c2-a647-4af0-9d0b-0b198d9307d9/dqc_reference
[2024-01-24 13:16:57,351] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:16:57,352] [INFO] Task started: Prodigal
[2024-01-24 13:16:57,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a6a18f4-ad5e-43f6-8949-9ddfb1560b15/GCF_007989265.1_ASM798926v1_genomic.fna.gz | prodigal -d GCF_007989265.1_ASM798926v1_genomic.fna/cds.fna -a GCF_007989265.1_ASM798926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:07,337] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:07,337] [INFO] Task started: HMMsearch
[2024-01-24 13:17:07,337] [INFO] Running command: hmmsearch --tblout GCF_007989265.1_ASM798926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg201238c2-a647-4af0-9d0b-0b198d9307d9/dqc_reference/reference_markers.hmm GCF_007989265.1_ASM798926v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:07,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:07,604] [INFO] Found 6/6 markers.
[2024-01-24 13:17:07,636] [INFO] Query marker FASTA was written to GCF_007989265.1_ASM798926v1_genomic.fna/markers.fasta
[2024-01-24 13:17:07,637] [INFO] Task started: Blastn
[2024-01-24 13:17:07,637] [INFO] Running command: blastn -query GCF_007989265.1_ASM798926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg201238c2-a647-4af0-9d0b-0b198d9307d9/dqc_reference/reference_markers.fasta -out GCF_007989265.1_ASM798926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:08,365] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:08,368] [INFO] Selected 13 target genomes.
[2024-01-24 13:17:08,369] [INFO] Target genome list was writen to GCF_007989265.1_ASM798926v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:08,387] [INFO] Task started: fastANI
[2024-01-24 13:17:08,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a6a18f4-ad5e-43f6-8949-9ddfb1560b15/GCF_007989265.1_ASM798926v1_genomic.fna.gz --refList GCF_007989265.1_ASM798926v1_genomic.fna/target_genomes.txt --output GCF_007989265.1_ASM798926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:18,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:18,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg201238c2-a647-4af0-9d0b-0b198d9307d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:18,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg201238c2-a647-4af0-9d0b-0b198d9307d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:18,723] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:18,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:18,724] [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 bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	100.0	1090	1091	95	conclusive
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	99.9998	1046	1091	95	conclusive
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	83.0886	723	1091	95	below_threshold
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	82.0011	641	1091	95	below_threshold
Asaia platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	81.6133	630	1091	95	below_threshold
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	80.7843	518	1091	95	below_threshold
Asaia astilbis	strain=JCM 15831	GCA_000613845.1	610244	610244	type	True	80.5261	503	1091	95	below_threshold
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	77.5911	186	1091	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:18,728] [INFO] DFAST Taxonomy check result was written to GCF_007989265.1_ASM798926v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:18,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:18,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:18,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg201238c2-a647-4af0-9d0b-0b198d9307d9/dqc_reference/checkm_data
[2024-01-24 13:17:18,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:18,762] [INFO] Task started: CheckM
[2024-01-24 13:17:18,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989265.1_ASM798926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989265.1_ASM798926v1_genomic.fna/checkm_input GCF_007989265.1_ASM798926v1_genomic.fna/checkm_result
[2024-01-24 13:17:53,183] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:53,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:53,209] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:53,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:53,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989265.1_ASM798926v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:53,211] [INFO] Task started: Blastn
[2024-01-24 13:17:53,211] [INFO] Running command: blastn -query GCF_007989265.1_ASM798926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg201238c2-a647-4af0-9d0b-0b198d9307d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989265.1_ASM798926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:54,366] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:54,369] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:54,369] [INFO] Target genome list was writen to GCF_007989265.1_ASM798926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:54,376] [INFO] Task started: fastANI
[2024-01-24 13:17:54,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a6a18f4-ad5e-43f6-8949-9ddfb1560b15/GCF_007989265.1_ASM798926v1_genomic.fna.gz --refList GCF_007989265.1_ASM798926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989265.1_ASM798926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:01,287] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:01,299] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:01,300] [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_001547995.1	s__Asaia bogorensis	99.9998	1046	1091	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	conclusive
GCF_900465345.1	s__Asaia bogorensis_A	94.4773	897	1091	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	82.7138	691	1091	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	82.017	639	1091	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614545.1	s__Asaia platycodi	81.6133	630	1091	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	80.7843	518	1091	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	80.3938	486	1091	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538885.1	s__Gluconobacter roseus	77.5911	186	1091	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:01,302] [INFO] GTDB search result was written to GCF_007989265.1_ASM798926v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:01,302] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:01,305] [INFO] DFAST_QC result json was written to GCF_007989265.1_ASM798926v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:01,306] [INFO] DFAST_QC completed!
[2024-01-24 13:18:01,306] [INFO] Total running time: 0h1m5s