[2024-01-24 12:13:43,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:43,015] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:43,016] [INFO] DQC Reference Directory: /var/lib/cwl/stga42878e6-24be-4063-ba4b-180fb83c7ae2/dqc_reference
[2024-01-24 12:13:44,408] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:44,409] [INFO] Task started: Prodigal
[2024-01-24 12:13:44,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ed9de32-3817-49c2-ae4e-0000ebf8c72e/GCF_000025265.1_ASM2526v1_genomic.fna.gz | prodigal -d GCF_000025265.1_ASM2526v1_genomic.fna/cds.fna -a GCF_000025265.1_ASM2526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:59,629] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:59,629] [INFO] Task started: HMMsearch
[2024-01-24 12:13:59,629] [INFO] Running command: hmmsearch --tblout GCF_000025265.1_ASM2526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga42878e6-24be-4063-ba4b-180fb83c7ae2/dqc_reference/reference_markers.hmm GCF_000025265.1_ASM2526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:00,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:00,087] [INFO] Found 6/6 markers.
[2024-01-24 12:14:00,159] [INFO] Query marker FASTA was written to GCF_000025265.1_ASM2526v1_genomic.fna/markers.fasta
[2024-01-24 12:14:00,160] [INFO] Task started: Blastn
[2024-01-24 12:14:00,160] [INFO] Running command: blastn -query GCF_000025265.1_ASM2526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42878e6-24be-4063-ba4b-180fb83c7ae2/dqc_reference/reference_markers.fasta -out GCF_000025265.1_ASM2526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:00,982] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:00,986] [INFO] Selected 11 target genomes.
[2024-01-24 12:14:00,986] [INFO] Target genome list was writen to GCF_000025265.1_ASM2526v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:00,991] [INFO] Task started: fastANI
[2024-01-24 12:14:00,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed9de32-3817-49c2-ae4e-0000ebf8c72e/GCF_000025265.1_ASM2526v1_genomic.fna.gz --refList GCF_000025265.1_ASM2526v1_genomic.fna/target_genomes.txt --output GCF_000025265.1_ASM2526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:20,592] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:20,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga42878e6-24be-4063-ba4b-180fb83c7ae2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:20,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga42878e6-24be-4063-ba4b-180fb83c7ae2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:20,603] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:20,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:20,604] [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
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	100.0	2119	2119	95	conclusive
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	84.2949	1219	2119	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	77.5955	843	2119	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	77.456	796	2119	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	77.3904	732	2119	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	77.1725	891	2119	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	77.1118	776	2119	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	76.6388	701	2119	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	76.6071	660	2119	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	75.063	385	2119	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	75.0556	456	2119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:20,605] [INFO] DFAST Taxonomy check result was written to GCF_000025265.1_ASM2526v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:20,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:20,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:20,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga42878e6-24be-4063-ba4b-180fb83c7ae2/dqc_reference/checkm_data
[2024-01-24 12:14:20,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:20,671] [INFO] Task started: CheckM
[2024-01-24 12:14:20,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000025265.1_ASM2526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000025265.1_ASM2526v1_genomic.fna/checkm_input GCF_000025265.1_ASM2526v1_genomic.fna/checkm_result
[2024-01-24 12:15:35,998] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:35,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:36,027] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:36,028] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:36,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000025265.1_ASM2526v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:36,029] [INFO] Task started: Blastn
[2024-01-24 12:15:36,029] [INFO] Running command: blastn -query GCF_000025265.1_ASM2526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42878e6-24be-4063-ba4b-180fb83c7ae2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000025265.1_ASM2526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:37,219] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:37,222] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:37,222] [INFO] Target genome list was writen to GCF_000025265.1_ASM2526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:37,279] [INFO] Task started: fastANI
[2024-01-24 12:15:37,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed9de32-3817-49c2-ae4e-0000ebf8c72e/GCF_000025265.1_ASM2526v1_genomic.fna.gz --refList GCF_000025265.1_ASM2526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000025265.1_ASM2526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:58,594] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:58,608] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:58,609] [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_000025265.1	s__Conexibacter woesei	100.0	2119	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014199525.1	s__Conexibacter arvalis	84.296	1219	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268595.1	s__Conexibacter sp018268595	81.6234	851	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655225.1	s__Conexibacter sp015655225	80.3669	620	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695395.1	s__SEOHO-28 sp013695395	77.7367	340	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425945.1	s__Solirubrobacter sp000425945	77.7033	896	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806175.1	s__CADCVQ01 sp902806175	77.6275	630	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424625.1	s__Baekduia woesei_A	77.5089	896	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882445.1	s__Palsa-744 sp017882445	77.4064	380	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688095.1	s__Baekduia sp000688095	77.3716	910	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240115.1	s__Palsa-465 sp019240115	77.1744	601	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806215.1	s__CADCVT01 sp902806215	77.0483	547	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344625.1	s__Solirubrobacter sp003344625	76.9803	899	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423665.1	s__Solirubrobacter soli	76.975	1005	2119	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:58,611] [INFO] GTDB search result was written to GCF_000025265.1_ASM2526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:58,611] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:58,615] [INFO] DFAST_QC result json was written to GCF_000025265.1_ASM2526v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:58,615] [INFO] DFAST_QC completed!
[2024-01-24 12:15:58,615] [INFO] Total running time: 0h2m16s