[2024-01-24 13:12:37,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:37,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:37,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg330b857c-ae29-43f9-a206-ccf2a1cdad73/dqc_reference
[2024-01-24 13:12:38,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:38,856] [INFO] Task started: Prodigal
[2024-01-24 13:12:38,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e775c05-643f-45f1-a513-dfc4458bb9ed/GCF_001746855.1_ASM174685v1_genomic.fna.gz | prodigal -d GCF_001746855.1_ASM174685v1_genomic.fna/cds.fna -a GCF_001746855.1_ASM174685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:45,223] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:45,223] [INFO] Task started: HMMsearch
[2024-01-24 13:12:45,223] [INFO] Running command: hmmsearch --tblout GCF_001746855.1_ASM174685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg330b857c-ae29-43f9-a206-ccf2a1cdad73/dqc_reference/reference_markers.hmm GCF_001746855.1_ASM174685v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:45,464] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:45,465] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5e775c05-643f-45f1-a513-dfc4458bb9ed/GCF_001746855.1_ASM174685v1_genomic.fna.gz]
[2024-01-24 13:12:45,490] [INFO] Query marker FASTA was written to GCF_001746855.1_ASM174685v1_genomic.fna/markers.fasta
[2024-01-24 13:12:45,490] [INFO] Task started: Blastn
[2024-01-24 13:12:45,490] [INFO] Running command: blastn -query GCF_001746855.1_ASM174685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg330b857c-ae29-43f9-a206-ccf2a1cdad73/dqc_reference/reference_markers.fasta -out GCF_001746855.1_ASM174685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:46,682] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:46,687] [INFO] Selected 18 target genomes.
[2024-01-24 13:12:46,687] [INFO] Target genome list was writen to GCF_001746855.1_ASM174685v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:46,699] [INFO] Task started: fastANI
[2024-01-24 13:12:46,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e775c05-643f-45f1-a513-dfc4458bb9ed/GCF_001746855.1_ASM174685v1_genomic.fna.gz --refList GCF_001746855.1_ASM174685v1_genomic.fna/target_genomes.txt --output GCF_001746855.1_ASM174685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:56,357] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:56,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg330b857c-ae29-43f9-a206-ccf2a1cdad73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:56,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg330b857c-ae29-43f9-a206-ccf2a1cdad73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:56,372] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:12:56,372] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:12:56,372] [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	81.423	283	713	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	81.3528	275	713	95	below_threshold
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	79.4758	260	713	95	below_threshold
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	79.272	212	713	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	79.0739	232	713	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	78.9483	182	713	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	78.2146	229	713	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	78.1347	228	713	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	77.9464	169	713	95	below_threshold
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	77.9404	154	713	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.4181	177	713	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	77.3703	177	713	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.7801	151	713	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	76.6892	134	713	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	76.55	99	713	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.5065	161	713	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.3585	151	713	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	76.1847	149	713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:12:56,374] [INFO] DFAST Taxonomy check result was written to GCF_001746855.1_ASM174685v1_genomic.fna/tc_result.tsv
[2024-01-24 13:12:56,375] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:56,375] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:56,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg330b857c-ae29-43f9-a206-ccf2a1cdad73/dqc_reference/checkm_data
[2024-01-24 13:12:56,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:56,399] [INFO] Task started: CheckM
[2024-01-24 13:12:56,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001746855.1_ASM174685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001746855.1_ASM174685v1_genomic.fna/checkm_input GCF_001746855.1_ASM174685v1_genomic.fna/checkm_result
[2024-01-24 13:13:18,670] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:18,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:18,692] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:18,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:18,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001746855.1_ASM174685v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:18,693] [INFO] Task started: Blastn
[2024-01-24 13:13:18,693] [INFO] Running command: blastn -query GCF_001746855.1_ASM174685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg330b857c-ae29-43f9-a206-ccf2a1cdad73/dqc_reference/reference_markers_gtdb.fasta -out GCF_001746855.1_ASM174685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:20,452] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:20,455] [INFO] Selected 12 target genomes.
[2024-01-24 13:13:20,456] [INFO] Target genome list was writen to GCF_001746855.1_ASM174685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:20,468] [INFO] Task started: fastANI
[2024-01-24 13:13:20,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e775c05-643f-45f1-a513-dfc4458bb9ed/GCF_001746855.1_ASM174685v1_genomic.fna.gz --refList GCF_001746855.1_ASM174685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001746855.1_ASM174685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:26,629] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:26,641] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:26,641] [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_001746855.1	s__Pauljensenia hongkongensis	99.9996	711	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	98.51	97.69	0.81	0.72	5	conclusive
GCF_000429245.1	s__Pauljensenia georgiae	93.8647	599	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.90	96.98	0.94	0.93	3	-
GCF_000185285.1	s__Pauljensenia sp000185285	81.1653	335	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.02	95.63	0.93	0.91	5	-
GCA_001072465.1	s__Pauljensenia sp001072465	81.121	315	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_001064145.1	s__Pauljensenia sp001064145	81.0041	304	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018382595.1	s__Pauljensenia sp018382595	80.9846	282	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466265.1	s__Pauljensenia sp000466265	80.8758	319	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.80	96.80	0.90	0.90	2	-
GCF_005696695.1	s__Pauljensenia odontolytica_C	80.8523	331	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.76	95.52	0.95	0.90	3	-
GCF_000411415.1	s__Pauljensenia sp000411415	80.718	308	713	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	80.5327	278	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.43	97.43	0.84	0.84	2	-
GCF_900499005.1	s__Pauljensenia culturomici	79.952	305	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208035.1	s__Pauljensenia hyovaginalis	79.4308	263	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.48	95.48	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:26,644] [INFO] GTDB search result was written to GCF_001746855.1_ASM174685v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:26,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:26,649] [INFO] DFAST_QC result json was written to GCF_001746855.1_ASM174685v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:26,649] [INFO] DFAST_QC completed!
[2024-01-24 13:13:26,650] [INFO] Total running time: 0h0m49s