[2023-06-04 18:00:17,378] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:00:17,380] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:00:17,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg21507584-4688-482b-a5b9-d29b3c888414/dqc_reference
[2023-06-04 18:00:18,672] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:00:18,673] [INFO] Task started: Prodigal
[2023-06-04 18:00:18,673] [INFO] Running command: gunzip -c /var/lib/cwl/stg481752e9-50de-42bb-bef6-b0134eb2a618/GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna.gz | prodigal -d GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/cds.fna -a GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:00:27,896] [INFO] Task succeeded: Prodigal
[2023-06-04 18:00:27,897] [INFO] Task started: HMMsearch
[2023-06-04 18:00:27,897] [INFO] Running command: hmmsearch --tblout GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21507584-4688-482b-a5b9-d29b3c888414/dqc_reference/reference_markers.hmm GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:00:28,149] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:00:28,150] [INFO] Found 6/6 markers.
[2023-06-04 18:00:28,173] [INFO] Query marker FASTA was written to GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/markers.fasta
[2023-06-04 18:00:28,174] [INFO] Task started: Blastn
[2023-06-04 18:00:28,174] [INFO] Running command: blastn -query GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/markers.fasta -db /var/lib/cwl/stg21507584-4688-482b-a5b9-d29b3c888414/dqc_reference/reference_markers.fasta -out GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:28,767] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:28,772] [INFO] Selected 11 target genomes.
[2023-06-04 18:00:28,773] [INFO] Target genome list was writen to GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/target_genomes.txt
[2023-06-04 18:00:28,802] [INFO] Task started: fastANI
[2023-06-04 18:00:28,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg481752e9-50de-42bb-bef6-b0134eb2a618/GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna.gz --refList GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/target_genomes.txt --output GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:00:34,593] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:34,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21507584-4688-482b-a5b9-d29b3c888414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:00:34,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21507584-4688-482b-a5b9-d29b3c888414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:00:34,600] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-04 18:00:34,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-04 18:00:34,600] [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	98.1479	610	657	95	conclusive
Porphyromonas uenonis	strain=DSM 23387	GCA_000482365.1	281920	281920	type	True	88.8419	523	657	95	below_threshold
Porphyromonas uenonis	strain=JCM 13868	GCA_000613705.1	281920	281920	type	True	88.7777	506	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:00:34,602] [INFO] DFAST Taxonomy check result was written to GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/tc_result.tsv
[2023-06-04 18:00:34,603] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:00:34,603] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:00:34,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21507584-4688-482b-a5b9-d29b3c888414/dqc_reference/checkm_data
[2023-06-04 18:00:34,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:00:34,642] [INFO] Task started: CheckM
[2023-06-04 18:00:34,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/checkm_input GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/checkm_result
[2023-06-04 18:01:06,731] [INFO] Task succeeded: CheckM
[2023-06-04 18:01:06,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:01:06,751] [INFO] ===== Completeness check finished =====
[2023-06-04 18:01:06,751] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:01:06,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/markers.fasta)
[2023-06-04 18:01:06,752] [INFO] Task started: Blastn
[2023-06-04 18:01:06,752] [INFO] Running command: blastn -query GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/markers.fasta -db /var/lib/cwl/stg21507584-4688-482b-a5b9-d29b3c888414/dqc_reference/reference_markers_gtdb.fasta -out GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:01:07,488] [INFO] Task succeeded: Blastn
[2023-06-04 18:01:07,492] [INFO] Selected 8 target genomes.
[2023-06-04 18:01:07,493] [INFO] Target genome list was writen to GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:01:07,596] [INFO] Task started: fastANI
[2023-06-04 18:01:07,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg481752e9-50de-42bb-bef6-b0134eb2a618/GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna.gz --refList GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/target_genomes_gtdb.txt --output GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:01:13,597] [INFO] Task succeeded: fastANI
[2023-06-04 18:01:13,610] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:01:13,611] [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	98.1835	609	657	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	91.649	543	657	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	91.288	460	657	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	91.1539	324	657	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	90.7326	512	657	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	88.8543	523	657	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	88.1209	518	657	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	87.5687	490	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	96.94	96.91	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-04 18:01:13,613] [INFO] GTDB search result was written to GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/result_gtdb.tsv
[2023-06-04 18:01:13,614] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:01:13,617] [INFO] DFAST_QC result json was written to GCA_902406175.1_UHGG_MGYG-HGUT-04267_genomic.fna/dqc_result.json
[2023-06-04 18:01:13,617] [INFO] DFAST_QC completed!
[2023-06-04 18:01:13,618] [INFO] Total running time: 0h0m56s