[2023-06-05 18:17:13,287] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:17:13,289] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:17:13,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f42def2-ac3a-4ab1-a92f-c5b520cdd634/dqc_reference
[2023-06-05 18:17:14,621] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:17:14,621] [INFO] Task started: Prodigal
[2023-06-05 18:17:14,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ec15744-944b-4742-a8c3-49aa9ecfbd9a/GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna.gz | prodigal -d GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/cds.fna -a GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:17:17,128] [INFO] Task succeeded: Prodigal
[2023-06-05 18:17:17,128] [INFO] Task started: HMMsearch
[2023-06-05 18:17:17,128] [INFO] Running command: hmmsearch --tblout GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f42def2-ac3a-4ab1-a92f-c5b520cdd634/dqc_reference/reference_markers.hmm GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:17:17,253] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:17:17,255] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0ec15744-944b-4742-a8c3-49aa9ecfbd9a/GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna.gz]
[2023-06-05 18:17:17,269] [INFO] Query marker FASTA was written to GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/markers.fasta
[2023-06-05 18:17:17,269] [INFO] Task started: Blastn
[2023-06-05 18:17:17,269] [INFO] Running command: blastn -query GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f42def2-ac3a-4ab1-a92f-c5b520cdd634/dqc_reference/reference_markers.fasta -out GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:17:17,847] [INFO] Task succeeded: Blastn
[2023-06-05 18:17:17,853] [INFO] Selected 20 target genomes.
[2023-06-05 18:17:17,853] [INFO] Target genome list was writen to GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/target_genomes.txt
[2023-06-05 18:17:17,867] [INFO] Task started: fastANI
[2023-06-05 18:17:17,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ec15744-944b-4742-a8c3-49aa9ecfbd9a/GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna.gz --refList GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/target_genomes.txt --output GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:17:29,819] [INFO] Task succeeded: fastANI
[2023-06-05 18:17:29,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f42def2-ac3a-4ab1-a92f-c5b520cdd634/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:17:29,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f42def2-ac3a-4ab1-a92f-c5b520cdd634/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:17:29,825] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:17:29,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:17:29,825] [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
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	79.7729	69	133	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	79.7531	69	133	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:17:29,827] [INFO] DFAST Taxonomy check result was written to GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/tc_result.tsv
[2023-06-05 18:17:29,827] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:17:29,827] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:17:29,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f42def2-ac3a-4ab1-a92f-c5b520cdd634/dqc_reference/checkm_data
[2023-06-05 18:17:29,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:17:29,846] [INFO] Task started: CheckM
[2023-06-05 18:17:29,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/checkm_input GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/checkm_result
[2023-06-05 18:17:45,533] [INFO] Task succeeded: CheckM
[2023-06-05 18:17:45,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:17:45,565] [INFO] ===== Completeness check finished =====
[2023-06-05 18:17:45,565] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:17:45,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/markers.fasta)
[2023-06-05 18:17:45,566] [INFO] Task started: Blastn
[2023-06-05 18:17:45,566] [INFO] Running command: blastn -query GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f42def2-ac3a-4ab1-a92f-c5b520cdd634/dqc_reference/reference_markers_gtdb.fasta -out GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:17:46,437] [INFO] Task succeeded: Blastn
[2023-06-05 18:17:46,441] [INFO] Selected 13 target genomes.
[2023-06-05 18:17:46,441] [INFO] Target genome list was writen to GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:17:46,467] [INFO] Task started: fastANI
[2023-06-05 18:17:46,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ec15744-944b-4742-a8c3-49aa9ecfbd9a/GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna.gz --refList GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/target_genomes_gtdb.txt --output GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:17:53,275] [INFO] Task succeeded: fastANI
[2023-06-05 18:17:53,284] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:17:53,284] [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_900128465.1	s__Pauljensenia bouchesdurhonensis	97.5562	126	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000466265.1	s__Pauljensenia sp000466265	85.034	110	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.80	96.80	0.90	0.90	2	-
GCF_000278725.1	s__Pauljensenia sp000278725	83.1122	103	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.30	95.28	0.90	0.88	4	-
GCA_018382595.1	s__Pauljensenia sp018382595	83.0985	82	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001838165.1	s__Pauljensenia sp001838165	83.0301	88	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	95.77	0.94	0.90	5	-
GCF_001064145.1	s__Pauljensenia sp001064145	82.6749	97	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005696695.1	s__Pauljensenia odontolytica_C	82.5465	93	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.76	95.52	0.95	0.90	3	-
GCA_018375675.1	s__Pauljensenia sp018375675	82.4719	91	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847525.1	s__Pauljensenia odontolytica_B	82.4638	93	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	96.22	0.94	0.92	3	-
GCF_000411415.1	s__Pauljensenia sp000411415	82.3372	99	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.95	97.15	0.96	0.94	6	-
GCA_902373545.1	s__Pauljensenia sp902373545	82.3334	107	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.43	97.43	0.84	0.84	2	-
GCA_001072465.1	s__Pauljensenia sp001072465	82.187	100	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_009730335.1	s__Pauljensenia odontolytica_A	81.5688	96	133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.93	96.74	0.95	0.91	4	-
--------------------------------------------------------------------------------
[2023-06-05 18:17:53,285] [INFO] GTDB search result was written to GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/result_gtdb.tsv
[2023-06-05 18:17:53,286] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:17:53,289] [INFO] DFAST_QC result json was written to GCA_902406145.1_UHGG_MGYG-HGUT-04268_genomic.fna/dqc_result.json
[2023-06-05 18:17:53,289] [INFO] DFAST_QC completed!
[2023-06-05 18:17:53,289] [INFO] Total running time: 0h0m40s