[2023-06-08 20:04:28,236] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:04:28,239] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:04:28,240] [INFO] DQC Reference Directory: /var/lib/cwl/stgf738221c-7b80-4bd9-9cb8-430e3abdbaaa/dqc_reference
[2023-06-08 20:04:29,474] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:04:29,475] [INFO] Task started: Prodigal
[2023-06-08 20:04:29,475] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c0f68fd-ccd8-4b3f-b2ea-6ea9085a83a3/GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna.gz | prodigal -d GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/cds.fna -a GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:04:34,053] [INFO] Task succeeded: Prodigal
[2023-06-08 20:04:34,054] [INFO] Task started: HMMsearch
[2023-06-08 20:04:34,054] [INFO] Running command: hmmsearch --tblout GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf738221c-7b80-4bd9-9cb8-430e3abdbaaa/dqc_reference/reference_markers.hmm GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:04:34,266] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:04:34,267] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2c0f68fd-ccd8-4b3f-b2ea-6ea9085a83a3/GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna.gz]
[2023-06-08 20:04:34,289] [INFO] Query marker FASTA was written to GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/markers.fasta
[2023-06-08 20:04:34,289] [INFO] Task started: Blastn
[2023-06-08 20:04:34,290] [INFO] Running command: blastn -query GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/markers.fasta -db /var/lib/cwl/stgf738221c-7b80-4bd9-9cb8-430e3abdbaaa/dqc_reference/reference_markers.fasta -out GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:04:35,252] [INFO] Task succeeded: Blastn
[2023-06-08 20:04:35,257] [INFO] Selected 18 target genomes.
[2023-06-08 20:04:35,258] [INFO] Target genome list was writen to GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/target_genomes.txt
[2023-06-08 20:04:35,282] [INFO] Task started: fastANI
[2023-06-08 20:04:35,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c0f68fd-ccd8-4b3f-b2ea-6ea9085a83a3/GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna.gz --refList GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/target_genomes.txt --output GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:04:42,912] [INFO] Task succeeded: fastANI
[2023-06-08 20:04:42,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf738221c-7b80-4bd9-9cb8-430e3abdbaaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:04:42,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf738221c-7b80-4bd9-9cb8-430e3abdbaaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:04:42,926] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:04:42,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:04:42,926] [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	82.0044	260	401	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	81.8871	255	401	95	below_threshold
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	79.1839	140	401	95	below_threshold
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	79.1069	61	401	95	below_threshold
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	78.8412	99	401	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	78.6706	100	401	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	78.5766	111	401	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	78.187	86	401	95	below_threshold
Actinomyces naeslundii	strain=NCTC 10301	GCA_001956585.1	1655	1655	type	True	78.011	78	401	95	below_threshold
Actinomyces naeslundii	strain=Howell 279	GCA_000285995.1	1655	1655	type	True	77.9887	73	401	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	77.7509	81	401	95	below_threshold
Actinomyces johnsonii	strain=CCUG 34287T	GCA_008693165.1	544581	544581	type	True	77.5365	88	401	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	77.5017	90	401	95	below_threshold
Actinomyces johnsonii	strain=CCUG 34287	GCA_006546835.1	544581	544581	type	True	77.4638	88	401	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.7696	77	401	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	76.1603	61	401	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	76.0402	52	401	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:04:42,929] [INFO] DFAST Taxonomy check result was written to GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/tc_result.tsv
[2023-06-08 20:04:42,929] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:04:42,930] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:04:42,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf738221c-7b80-4bd9-9cb8-430e3abdbaaa/dqc_reference/checkm_data
[2023-06-08 20:04:42,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:04:42,958] [INFO] Task started: CheckM
[2023-06-08 20:04:42,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/checkm_input GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/checkm_result
[2023-06-08 20:05:03,147] [INFO] Task succeeded: CheckM
[2023-06-08 20:05:03,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 20:05:03,170] [INFO] ===== Completeness check finished =====
[2023-06-08 20:05:03,171] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:05:03,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/markers.fasta)
[2023-06-08 20:05:03,172] [INFO] Task started: Blastn
[2023-06-08 20:05:03,172] [INFO] Running command: blastn -query GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/markers.fasta -db /var/lib/cwl/stgf738221c-7b80-4bd9-9cb8-430e3abdbaaa/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:05:04,654] [INFO] Task succeeded: Blastn
[2023-06-08 20:05:04,659] [INFO] Selected 9 target genomes.
[2023-06-08 20:05:04,659] [INFO] Target genome list was writen to GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:05:04,665] [INFO] Task started: fastANI
[2023-06-08 20:05:04,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c0f68fd-ccd8-4b3f-b2ea-6ea9085a83a3/GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna.gz --refList GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/target_genomes_gtdb.txt --output GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:05:08,640] [INFO] Task succeeded: fastANI
[2023-06-08 20:05:08,653] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:05:08,653] [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_001064145.1	s__Pauljensenia sp001064145	98.3578	379	401	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_001838165.1	s__Pauljensenia sp001838165	92.5652	368	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	95.77	0.94	0.90	5	-
GCA_018375675.1	s__Pauljensenia sp018375675	92.0744	359	401	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	91.4892	360	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.76	95.52	0.95	0.90	3	-
GCA_001072465.1	s__Pauljensenia sp001072465	91.3355	369	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCA_018382595.1	s__Pauljensenia sp018382595	91.0863	343	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373435.1	s__Pauljensenia sp902373435	90.7829	314	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.35	95.27	0.85	0.81	3	-
GCF_009730335.1	s__Pauljensenia odontolytica_A	90.3926	367	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.93	96.74	0.95	0.91	4	-
GCF_002847525.1	s__Pauljensenia odontolytica_B	89.9216	355	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	96.22	0.94	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-08 20:05:08,655] [INFO] GTDB search result was written to GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/result_gtdb.tsv
[2023-06-08 20:05:08,656] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:05:08,660] [INFO] DFAST_QC result json was written to GCA_902461205.1_UHGG-TPA_MGYG-HGUT-00308_genomic.fna/dqc_result.json
[2023-06-08 20:05:08,660] [INFO] DFAST_QC completed!
[2023-06-08 20:05:08,660] [INFO] Total running time: 0h0m40s