[2024-01-25 18:16:05,352] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:05,353] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:05,353] [INFO] DQC Reference Directory: /var/lib/cwl/stgac78aaf5-c473-4dfc-add6-61aad25d2646/dqc_reference
[2024-01-25 18:16:06,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:06,612] [INFO] Task started: Prodigal
[2024-01-25 18:16:06,612] [INFO] Running command: gunzip -c /var/lib/cwl/stgacd5fff7-ebaf-497b-a161-fe9a292103ad/GCF_000212375.1_ASM21237v1_genomic.fna.gz | prodigal -d GCF_000212375.1_ASM21237v1_genomic.fna/cds.fna -a GCF_000212375.1_ASM21237v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:14,940] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:14,940] [INFO] Task started: HMMsearch
[2024-01-25 18:16:14,940] [INFO] Running command: hmmsearch --tblout GCF_000212375.1_ASM21237v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac78aaf5-c473-4dfc-add6-61aad25d2646/dqc_reference/reference_markers.hmm GCF_000212375.1_ASM21237v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:15,171] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:15,172] [INFO] Found 6/6 markers.
[2024-01-25 18:16:15,193] [INFO] Query marker FASTA was written to GCF_000212375.1_ASM21237v1_genomic.fna/markers.fasta
[2024-01-25 18:16:15,194] [INFO] Task started: Blastn
[2024-01-25 18:16:15,194] [INFO] Running command: blastn -query GCF_000212375.1_ASM21237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac78aaf5-c473-4dfc-add6-61aad25d2646/dqc_reference/reference_markers.fasta -out GCF_000212375.1_ASM21237v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:15,728] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:15,731] [INFO] Selected 12 target genomes.
[2024-01-25 18:16:15,732] [INFO] Target genome list was writen to GCF_000212375.1_ASM21237v1_genomic.fna/target_genomes.txt
[2024-01-25 18:16:15,740] [INFO] Task started: fastANI
[2024-01-25 18:16:15,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgacd5fff7-ebaf-497b-a161-fe9a292103ad/GCF_000212375.1_ASM21237v1_genomic.fna.gz --refList GCF_000212375.1_ASM21237v1_genomic.fna/target_genomes.txt --output GCF_000212375.1_ASM21237v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:23,081] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:23,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac78aaf5-c473-4dfc-add6-61aad25d2646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:23,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac78aaf5-c473-4dfc-add6-61aad25d2646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:23,087] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:23,087] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:23,087] [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
Porphyromonas asaccharolytica	strain=DSM 20707	GCA_000212375.1	28123	28123	type	True	100.0	727	728	95	conclusive
Porphyromonas uenonis	strain=DSM 23387	GCA_000482365.1	281920	281920	type	True	88.7343	567	728	95	below_threshold
Porphyromonas uenonis	strain=JCM 13868	GCA_000613705.1	281920	281920	type	True	88.6616	545	728	95	below_threshold
Porphyromonas bobii	strain=EMRHCC_6C	GCA_943169685.1	2811780	2811780	type	True	75.9884	50	728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:23,089] [INFO] DFAST Taxonomy check result was written to GCF_000212375.1_ASM21237v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:23,089] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:23,089] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:23,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac78aaf5-c473-4dfc-add6-61aad25d2646/dqc_reference/checkm_data
[2024-01-25 18:16:23,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:23,116] [INFO] Task started: CheckM
[2024-01-25 18:16:23,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000212375.1_ASM21237v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000212375.1_ASM21237v1_genomic.fna/checkm_input GCF_000212375.1_ASM21237v1_genomic.fna/checkm_result
[2024-01-25 18:16:51,777] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:51,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:51,803] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:51,803] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:51,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000212375.1_ASM21237v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:51,804] [INFO] Task started: Blastn
[2024-01-25 18:16:51,804] [INFO] Running command: blastn -query GCF_000212375.1_ASM21237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac78aaf5-c473-4dfc-add6-61aad25d2646/dqc_reference/reference_markers_gtdb.fasta -out GCF_000212375.1_ASM21237v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:52,586] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:52,588] [INFO] Selected 8 target genomes.
[2024-01-25 18:16:52,588] [INFO] Target genome list was writen to GCF_000212375.1_ASM21237v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:52,604] [INFO] Task started: fastANI
[2024-01-25 18:16:52,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgacd5fff7-ebaf-497b-a161-fe9a292103ad/GCF_000212375.1_ASM21237v1_genomic.fna.gz --refList GCF_000212375.1_ASM21237v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000212375.1_ASM21237v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:59,741] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:59,747] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:59,747] [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_000212375.1	s__Porphyromonas asaccharolytica	100.0	727	728	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.28	98.18	0.93	0.93	3	conclusive
GCA_900539765.1	s__Porphyromonas sp900539765	91.6174	563	728	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.35	98.07	0.90	0.87	3	-
GCA_900546675.1	s__Porphyromonas sp900546675	91.152	493	728	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	97.06	96.88	0.79	0.75	4	-
GCA_900548415.1	s__Porphyromonas sp900548415	91.1356	328	728	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	96.69	96.69	0.92	0.92	2	-
GCA_900538385.1	s__Porphyromonas sp900538385	90.8172	541	728	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	97.10	96.55	0.91	0.91	3	-
GCF_000482365.1	s__Porphyromonas uenonis	88.7685	565	728	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.34	96.78	0.97	0.96	3	-
GCF_000174775.1	s__Porphyromonas uenonis_A	88.1625	551	728	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539155.1	s__Porphyromonas sp900539155	88.0325	517	728	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	96.94	96.91	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:59,748] [INFO] GTDB search result was written to GCF_000212375.1_ASM21237v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:59,749] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:59,751] [INFO] DFAST_QC result json was written to GCF_000212375.1_ASM21237v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:59,751] [INFO] DFAST_QC completed!
[2024-01-25 18:16:59,752] [INFO] Total running time: 0h0m54s