[2024-01-24 14:14:31,437] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:31,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:31,440] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd63800e-d928-4b22-8b6a-be5c2aedf3d1/dqc_reference
[2024-01-24 14:14:32,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:32,672] [INFO] Task started: Prodigal
[2024-01-24 14:14:32,672] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cd216f4-34d2-49d7-b1a6-f5dc3383e608/GCF_030165005.1_ASM3016500v1_genomic.fna.gz | prodigal -d GCF_030165005.1_ASM3016500v1_genomic.fna/cds.fna -a GCF_030165005.1_ASM3016500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:44,405] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:44,406] [INFO] Task started: HMMsearch
[2024-01-24 14:14:44,406] [INFO] Running command: hmmsearch --tblout GCF_030165005.1_ASM3016500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd63800e-d928-4b22-8b6a-be5c2aedf3d1/dqc_reference/reference_markers.hmm GCF_030165005.1_ASM3016500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:44,714] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:44,715] [INFO] Found 6/6 markers.
[2024-01-24 14:14:44,761] [INFO] Query marker FASTA was written to GCF_030165005.1_ASM3016500v1_genomic.fna/markers.fasta
[2024-01-24 14:14:44,761] [INFO] Task started: Blastn
[2024-01-24 14:14:44,762] [INFO] Running command: blastn -query GCF_030165005.1_ASM3016500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd63800e-d928-4b22-8b6a-be5c2aedf3d1/dqc_reference/reference_markers.fasta -out GCF_030165005.1_ASM3016500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:45,967] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:45,970] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:45,971] [INFO] Target genome list was writen to GCF_030165005.1_ASM3016500v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:45,985] [INFO] Task started: fastANI
[2024-01-24 14:14:45,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cd216f4-34d2-49d7-b1a6-f5dc3383e608/GCF_030165005.1_ASM3016500v1_genomic.fna.gz --refList GCF_030165005.1_ASM3016500v1_genomic.fna/target_genomes.txt --output GCF_030165005.1_ASM3016500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:03,179] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:03,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd63800e-d928-4b22-8b6a-be5c2aedf3d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:03,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd63800e-d928-4b22-8b6a-be5c2aedf3d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:03,197] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:03,198] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:03,198] [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
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	86.2167	1020	1438	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	85.2388	959	1438	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	85.2027	989	1438	95	below_threshold
Blastococcus atacamensis	strain=P6	GCA_002938425.1	2070508	2070508	type	True	84.5167	863	1438	95	below_threshold
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	83.8554	975	1438	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	83.2234	865	1438	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	83.2223	890	1438	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	82.7599	861	1438	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	82.699	869	1438	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	82.557	860	1438	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	82.503	887	1438	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	82.4474	883	1438	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	82.4366	894	1438	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	82.4323	870	1438	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	81.7176	785	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:03,199] [INFO] DFAST Taxonomy check result was written to GCF_030165005.1_ASM3016500v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:03,200] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:03,200] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:03,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd63800e-d928-4b22-8b6a-be5c2aedf3d1/dqc_reference/checkm_data
[2024-01-24 14:15:03,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:03,261] [INFO] Task started: CheckM
[2024-01-24 14:15:03,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030165005.1_ASM3016500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030165005.1_ASM3016500v1_genomic.fna/checkm_input GCF_030165005.1_ASM3016500v1_genomic.fna/checkm_result
[2024-01-24 14:16:02,818] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:02,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:02,842] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:02,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:02,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030165005.1_ASM3016500v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:02,843] [INFO] Task started: Blastn
[2024-01-24 14:16:02,843] [INFO] Running command: blastn -query GCF_030165005.1_ASM3016500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd63800e-d928-4b22-8b6a-be5c2aedf3d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_030165005.1_ASM3016500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:04,671] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:04,675] [INFO] Selected 22 target genomes.
[2024-01-24 14:16:04,675] [INFO] Target genome list was writen to GCF_030165005.1_ASM3016500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:04,693] [INFO] Task started: fastANI
[2024-01-24 14:16:04,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cd216f4-34d2-49d7-b1a6-f5dc3383e608/GCF_030165005.1_ASM3016500v1_genomic.fna.gz --refList GCF_030165005.1_ASM3016500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030165005.1_ASM3016500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:31,121] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:31,145] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:16:31,145] [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_000284015.1	s__Blastococcus saxobsidens_A	91.4742	1118	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124835.1	s__Blastococcus xanthinilyticus	86.2344	1019	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109665.1	s__Blastococcus sp900109665	85.8384	1033	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010682065.1	s__Blastococcus saxobsidens_B	85.2028	886	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571075.1	s__Blastococcus sp004571075	84.804	896	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002938425.1	s__Blastococcus atacamensis	84.5081	863	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319175.1	s__Blastococcus sp003319175	84.3476	875	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570425.1	s__Blastococcus sp004570425	83.6233	846	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410015.1	s__Blastococcus sp013410015	83.3514	914	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112815.1	s__Blastococcus sp900112815	83.2515	934	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222955.1	s__Blastococcus sp005222955	83.0929	773	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188025.1	s__Blastococcus sp900188025	82.9675	898	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230285.1	s__Blastococcus sp900230285	82.9619	898	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111455.1	s__Geodermatophilus poikilotrophus	82.7388	863	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188375.1	s__Geodermatophilus pulveris	82.5484	860	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620185.1	s__Blastococcus sp000620185	82.4271	864	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215145.1	s__Geodermatophilus sabuli	82.3637	878	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003428645.1	s__Geodermatophilus sp003428645	82.2249	872	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319115.1	s__Geodermatophilus sp003319115	82.2056	828	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306785.1	s__Modestobacter marinus_A	81.8499	847	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930475.1	s__Modestobacter altitudinis	81.7102	787	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620205.1	s__Modestobacter sp000620205	81.6143	829	1438	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:31,147] [INFO] GTDB search result was written to GCF_030165005.1_ASM3016500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:31,147] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:31,152] [INFO] DFAST_QC result json was written to GCF_030165005.1_ASM3016500v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:31,152] [INFO] DFAST_QC completed!
[2024-01-24 14:16:31,152] [INFO] Total running time: 0h1m60s