[2024-01-24 13:49:27,471] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,473] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg94d28d81-b4dc-45cc-b4fe-674f8d409655/dqc_reference
[2024-01-24 13:49:28,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,830] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,831] [INFO] Running command: gunzip -c /var/lib/cwl/stge87d32e5-4267-46bb-a464-55516a19743d/GCF_900445025.1_51670_G01_genomic.fna.gz | prodigal -d GCF_900445025.1_51670_G01_genomic.fna/cds.fna -a GCF_900445025.1_51670_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:36,162] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:36,163] [INFO] Task started: HMMsearch
[2024-01-24 13:49:36,163] [INFO] Running command: hmmsearch --tblout GCF_900445025.1_51670_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94d28d81-b4dc-45cc-b4fe-674f8d409655/dqc_reference/reference_markers.hmm GCF_900445025.1_51670_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:36,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:36,430] [INFO] Found 6/6 markers.
[2024-01-24 13:49:36,459] [INFO] Query marker FASTA was written to GCF_900445025.1_51670_G01_genomic.fna/markers.fasta
[2024-01-24 13:49:36,459] [INFO] Task started: Blastn
[2024-01-24 13:49:36,459] [INFO] Running command: blastn -query GCF_900445025.1_51670_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg94d28d81-b4dc-45cc-b4fe-674f8d409655/dqc_reference/reference_markers.fasta -out GCF_900445025.1_51670_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:37,476] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:37,484] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:37,484] [INFO] Target genome list was writen to GCF_900445025.1_51670_G01_genomic.fna/target_genomes.txt
[2024-01-24 13:49:37,506] [INFO] Task started: fastANI
[2024-01-24 13:49:37,506] [INFO] Running command: fastANI --query /var/lib/cwl/stge87d32e5-4267-46bb-a464-55516a19743d/GCF_900445025.1_51670_G01_genomic.fna.gz --refList GCF_900445025.1_51670_G01_genomic.fna/target_genomes.txt --output GCF_900445025.1_51670_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:48,082] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:48,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94d28d81-b4dc-45cc-b4fe-674f8d409655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:48,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94d28d81-b4dc-45cc-b4fe-674f8d409655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:48,099] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:48,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:48,099] [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=DSM 20733	GCA_900105015.1	52773	52773	type	True	81.8744	481	805	95	below_threshold
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	81.8654	497	805	95	below_threshold
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	79.3116	264	805	95	below_threshold
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	78.5887	140	805	95	below_threshold
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	78.396	172	805	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	78.3855	200	805	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	78.1328	189	805	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	78.1056	159	805	95	below_threshold
Actinomyces naeslundii	strain=Howell 279	GCA_000285995.1	1655	1655	type	True	78.0422	149	805	95	below_threshold
Actinomyces oris	strain=CCUG 34288	GCA_006546825.1	544580	544580	suspected-type	True	77.9558	157	805	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	77.9483	167	805	95	below_threshold
Actinomyces naeslundii	strain=NCTC 10301	GCA_001956585.1	1655	1655	type	True	77.8236	150	805	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	77.6198	135	805	95	below_threshold
Actinomyces johnsonii	strain=CCUG 34287	GCA_006546835.1	544581	544581	type	True	77.6148	148	805	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	76.8405	79	805	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	76.6975	79	805	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	76.6882	61	805	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	76.5728	92	805	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.5035	111	805	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	76.3636	86	805	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	76.329	92	805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:48,101] [INFO] DFAST Taxonomy check result was written to GCF_900445025.1_51670_G01_genomic.fna/tc_result.tsv
[2024-01-24 13:49:48,102] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:48,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:48,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94d28d81-b4dc-45cc-b4fe-674f8d409655/dqc_reference/checkm_data
[2024-01-24 13:49:48,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:48,129] [INFO] Task started: CheckM
[2024-01-24 13:49:48,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445025.1_51670_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445025.1_51670_G01_genomic.fna/checkm_input GCF_900445025.1_51670_G01_genomic.fna/checkm_result
[2024-01-24 13:50:15,376] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:15,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:15,404] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:15,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:15,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445025.1_51670_G01_genomic.fna/markers.fasta)
[2024-01-24 13:50:15,405] [INFO] Task started: Blastn
[2024-01-24 13:50:15,406] [INFO] Running command: blastn -query GCF_900445025.1_51670_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg94d28d81-b4dc-45cc-b4fe-674f8d409655/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445025.1_51670_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:17,022] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:17,028] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:17,028] [INFO] Target genome list was writen to GCF_900445025.1_51670_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:17,047] [INFO] Task started: fastANI
[2024-01-24 13:50:17,047] [INFO] Running command: fastANI --query /var/lib/cwl/stge87d32e5-4267-46bb-a464-55516a19743d/GCF_900445025.1_51670_G01_genomic.fna.gz --refList GCF_900445025.1_51670_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445025.1_51670_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:22,097] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:22,110] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:22,110] [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_900445025.1	s__Pauljensenia odontolytica	100.0	803	805	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_009730335.1	s__Pauljensenia odontolytica_A	88.5175	667	805	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	88.0872	659	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	96.22	0.94	0.92	3	-
GCA_018382595.1	s__Pauljensenia sp018382595	87.7357	542	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018375675.1	s__Pauljensenia sp018375675	87.7148	607	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001072465.1	s__Pauljensenia sp001072465	87.6924	635	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_005696695.1	s__Pauljensenia odontolytica_C	87.6078	638	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.76	95.52	0.95	0.90	3	-
GCF_001064145.1	s__Pauljensenia sp001064145	87.2573	629	805	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	86.8705	512	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.35	95.27	0.85	0.81	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:22,111] [INFO] GTDB search result was written to GCF_900445025.1_51670_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:22,112] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:22,119] [INFO] DFAST_QC result json was written to GCF_900445025.1_51670_G01_genomic.fna/dqc_result.json
[2024-01-24 13:50:22,119] [INFO] DFAST_QC completed!
[2024-01-24 13:50:22,119] [INFO] Total running time: 0h0m55s