[2024-01-25 17:42:50,481] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:50,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:50,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgd780a86a-a14f-476c-9b76-4eeae5e9930b/dqc_reference
[2024-01-25 17:42:51,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:51,655] [INFO] Task started: Prodigal
[2024-01-25 17:42:51,655] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5cc3c63-da83-4c67-9a38-49e1c92e417e/GCF_025994315.1_ASM2599431v1_genomic.fna.gz | prodigal -d GCF_025994315.1_ASM2599431v1_genomic.fna/cds.fna -a GCF_025994315.1_ASM2599431v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:59,245] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:59,246] [INFO] Task started: HMMsearch
[2024-01-25 17:42:59,246] [INFO] Running command: hmmsearch --tblout GCF_025994315.1_ASM2599431v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd780a86a-a14f-476c-9b76-4eeae5e9930b/dqc_reference/reference_markers.hmm GCF_025994315.1_ASM2599431v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:59,459] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:59,460] [INFO] Found 6/6 markers.
[2024-01-25 17:42:59,488] [INFO] Query marker FASTA was written to GCF_025994315.1_ASM2599431v1_genomic.fna/markers.fasta
[2024-01-25 17:42:59,488] [INFO] Task started: Blastn
[2024-01-25 17:42:59,488] [INFO] Running command: blastn -query GCF_025994315.1_ASM2599431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd780a86a-a14f-476c-9b76-4eeae5e9930b/dqc_reference/reference_markers.fasta -out GCF_025994315.1_ASM2599431v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:00,242] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:00,245] [INFO] Selected 16 target genomes.
[2024-01-25 17:43:00,245] [INFO] Target genome list was writen to GCF_025994315.1_ASM2599431v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:00,269] [INFO] Task started: fastANI
[2024-01-25 17:43:00,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5cc3c63-da83-4c67-9a38-49e1c92e417e/GCF_025994315.1_ASM2599431v1_genomic.fna.gz --refList GCF_025994315.1_ASM2599431v1_genomic.fna/target_genomes.txt --output GCF_025994315.1_ASM2599431v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:10,768] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:10,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd780a86a-a14f-476c-9b76-4eeae5e9930b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:10,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd780a86a-a14f-476c-9b76-4eeae5e9930b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:10,777] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:43:10,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:43:10,778] [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 lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	80.5273	505	965	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	80.3702	476	965	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	80.3523	493	965	95	below_threshold
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	80.2653	490	965	95	below_threshold
Asaia platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	79.9545	483	965	95	below_threshold
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	79.7088	361	965	95	below_threshold
Asaia astilbis	strain=JCM 15831	GCA_000613845.1	610244	610244	type	True	79.2834	405	965	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.6911	177	965	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	77.3552	114	965	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	77.108	146	965	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.2125	84	965	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	75.9656	64	965	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	75.8972	61	965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:10,779] [INFO] DFAST Taxonomy check result was written to GCF_025994315.1_ASM2599431v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:10,780] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:10,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:10,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd780a86a-a14f-476c-9b76-4eeae5e9930b/dqc_reference/checkm_data
[2024-01-25 17:43:10,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:10,811] [INFO] Task started: CheckM
[2024-01-25 17:43:10,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994315.1_ASM2599431v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994315.1_ASM2599431v1_genomic.fna/checkm_input GCF_025994315.1_ASM2599431v1_genomic.fna/checkm_result
[2024-01-25 17:43:36,556] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:36,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:36,578] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:36,578] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:36,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994315.1_ASM2599431v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:36,579] [INFO] Task started: Blastn
[2024-01-25 17:43:36,579] [INFO] Running command: blastn -query GCF_025994315.1_ASM2599431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd780a86a-a14f-476c-9b76-4eeae5e9930b/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994315.1_ASM2599431v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:37,992] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:37,995] [INFO] Selected 12 target genomes.
[2024-01-25 17:43:37,995] [INFO] Target genome list was writen to GCF_025994315.1_ASM2599431v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:38,007] [INFO] Task started: fastANI
[2024-01-25 17:43:38,007] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5cc3c63-da83-4c67-9a38-49e1c92e417e/GCF_025994315.1_ASM2599431v1_genomic.fna.gz --refList GCF_025994315.1_ASM2599431v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994315.1_ASM2599431v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:45,637] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:45,645] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:45,645] [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_007988945.1	s__Swaminathania salitolerans	99.9989	959	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003994335.1	s__Asaia sp003994335	80.7196	494	965	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	80.3498	491	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_014635085.1	s__Asaia siamensis	80.2653	490	965	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	80.2532	476	965	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	79.9545	483	965	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	79.694	362	965	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	79.2834	405	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538885.1	s__Gluconobacter roseus	77.9626	163	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004346035.1	s__Acidomonas methanolica	77.9573	267	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
GCA_903643085.1	s__BOG-908 sp903643085	76.1881	52	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-908	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133265.1	s__PALSA-911 sp003133265	76.0183	82	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:45,647] [INFO] GTDB search result was written to GCF_025994315.1_ASM2599431v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:45,647] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:45,650] [INFO] DFAST_QC result json was written to GCF_025994315.1_ASM2599431v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:45,650] [INFO] DFAST_QC completed!
[2024-01-25 17:43:45,650] [INFO] Total running time: 0h0m55s