[2024-01-25 17:47:20,425] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:20,427] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:20,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg12767346-7930-44e5-9673-563650d1d8fb/dqc_reference
[2024-01-25 17:47:21,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:21,576] [INFO] Task started: Prodigal
[2024-01-25 17:47:21,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg11de47b3-f1a7-4ad5-b4c7-5ad202ae7f29/GCF_000614545.1_ASM61454v1_genomic.fna.gz | prodigal -d GCF_000614545.1_ASM61454v1_genomic.fna/cds.fna -a GCF_000614545.1_ASM61454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:29,630] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:29,630] [INFO] Task started: HMMsearch
[2024-01-25 17:47:29,630] [INFO] Running command: hmmsearch --tblout GCF_000614545.1_ASM61454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12767346-7930-44e5-9673-563650d1d8fb/dqc_reference/reference_markers.hmm GCF_000614545.1_ASM61454v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:29,828] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:29,829] [INFO] Found 6/6 markers.
[2024-01-25 17:47:29,855] [INFO] Query marker FASTA was written to GCF_000614545.1_ASM61454v1_genomic.fna/markers.fasta
[2024-01-25 17:47:29,856] [INFO] Task started: Blastn
[2024-01-25 17:47:29,856] [INFO] Running command: blastn -query GCF_000614545.1_ASM61454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12767346-7930-44e5-9673-563650d1d8fb/dqc_reference/reference_markers.fasta -out GCF_000614545.1_ASM61454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:30,554] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:30,556] [INFO] Selected 13 target genomes.
[2024-01-25 17:47:30,557] [INFO] Target genome list was writen to GCF_000614545.1_ASM61454v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:30,567] [INFO] Task started: fastANI
[2024-01-25 17:47:30,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg11de47b3-f1a7-4ad5-b4c7-5ad202ae7f29/GCF_000614545.1_ASM61454v1_genomic.fna.gz --refList GCF_000614545.1_ASM61454v1_genomic.fna/target_genomes.txt --output GCF_000614545.1_ASM61454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:39,627] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:39,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12767346-7930-44e5-9673-563650d1d8fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:39,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12767346-7930-44e5-9673-563650d1d8fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:39,636] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:47:39,636] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:39,636] [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 platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	100.0	1029	1031	95	conclusive
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	85.6047	848	1031	95	below_threshold
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	82.3494	644	1031	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	81.693	638	1031	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	81.6048	633	1031	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	81.5177	653	1031	95	below_threshold
Asaia astilbis	strain=JCM 15831	GCA_000613845.1	610244	610244	type	True	81.206	607	1031	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	77.5428	178	1031	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	77.5416	182	1031	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.2524	121	1031	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.7361	100	1031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:39,637] [INFO] DFAST Taxonomy check result was written to GCF_000614545.1_ASM61454v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:39,638] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:39,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:39,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12767346-7930-44e5-9673-563650d1d8fb/dqc_reference/checkm_data
[2024-01-25 17:47:39,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:39,671] [INFO] Task started: CheckM
[2024-01-25 17:47:39,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000614545.1_ASM61454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000614545.1_ASM61454v1_genomic.fna/checkm_input GCF_000614545.1_ASM61454v1_genomic.fna/checkm_result
[2024-01-25 17:48:06,777] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:06,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:06,810] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:06,811] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:06,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000614545.1_ASM61454v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:06,812] [INFO] Task started: Blastn
[2024-01-25 17:48:06,812] [INFO] Running command: blastn -query GCF_000614545.1_ASM61454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12767346-7930-44e5-9673-563650d1d8fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000614545.1_ASM61454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:08,036] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:08,040] [INFO] Selected 8 target genomes.
[2024-01-25 17:48:08,040] [INFO] Target genome list was writen to GCF_000614545.1_ASM61454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:08,052] [INFO] Task started: fastANI
[2024-01-25 17:48:08,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg11de47b3-f1a7-4ad5-b4c7-5ad202ae7f29/GCF_000614545.1_ASM61454v1_genomic.fna.gz --refList GCF_000614545.1_ASM61454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000614545.1_ASM61454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:13,740] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:13,745] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:13,746] [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_000614545.1	s__Asaia platycodi	100.0	1029	1031	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_014635085.1	s__Asaia siamensis	85.6047	848	1031	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	82.3494	644	1031	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	81.7674	662	1031	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	81.5177	653	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_900465345.1	s__Asaia bogorensis_A	81.4489	615	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613845.1	s__Asaia astilbis	81.206	607	1031	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	80.1639	477	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:13,747] [INFO] GTDB search result was written to GCF_000614545.1_ASM61454v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:13,747] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:13,750] [INFO] DFAST_QC result json was written to GCF_000614545.1_ASM61454v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:13,750] [INFO] DFAST_QC completed!
[2024-01-25 17:48:13,750] [INFO] Total running time: 0h0m53s