[2024-01-24 12:53:37,025] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:37,027] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:37,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg251d1445-0521-47b2-a2c8-5add08232af4/dqc_reference
[2024-01-24 12:53:38,265] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:38,266] [INFO] Task started: Prodigal
[2024-01-24 12:53:38,266] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bca4e67-056c-4967-8a34-58b9b59bbce1/GCF_007970665.1_ASM797066v1_genomic.fna.gz | prodigal -d GCF_007970665.1_ASM797066v1_genomic.fna/cds.fna -a GCF_007970665.1_ASM797066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:51,957] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:51,958] [INFO] Task started: HMMsearch
[2024-01-24 12:53:51,958] [INFO] Running command: hmmsearch --tblout GCF_007970665.1_ASM797066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg251d1445-0521-47b2-a2c8-5add08232af4/dqc_reference/reference_markers.hmm GCF_007970665.1_ASM797066v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:52,244] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:52,245] [INFO] Found 6/6 markers.
[2024-01-24 12:53:52,300] [INFO] Query marker FASTA was written to GCF_007970665.1_ASM797066v1_genomic.fna/markers.fasta
[2024-01-24 12:53:52,300] [INFO] Task started: Blastn
[2024-01-24 12:53:52,300] [INFO] Running command: blastn -query GCF_007970665.1_ASM797066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg251d1445-0521-47b2-a2c8-5add08232af4/dqc_reference/reference_markers.fasta -out GCF_007970665.1_ASM797066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:53,045] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:53,048] [INFO] Selected 9 target genomes.
[2024-01-24 12:53:53,048] [INFO] Target genome list was writen to GCF_007970665.1_ASM797066v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:53,053] [INFO] Task started: fastANI
[2024-01-24 12:53:53,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bca4e67-056c-4967-8a34-58b9b59bbce1/GCF_007970665.1_ASM797066v1_genomic.fna.gz --refList GCF_007970665.1_ASM797066v1_genomic.fna/target_genomes.txt --output GCF_007970665.1_ASM797066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:05,776] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:05,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg251d1445-0521-47b2-a2c8-5add08232af4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:05,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg251d1445-0521-47b2-a2c8-5add08232af4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:05,792] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:05,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:05,792] [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
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	100.0	1737	1737	95	conclusive
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	78.544	809	1737	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	78.2607	712	1737	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.4802	764	1737	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	77.1906	769	1737	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	77.1414	761	1737	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	77.1024	610	1737	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	76.9902	583	1737	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	76.6871	628	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:05,794] [INFO] DFAST Taxonomy check result was written to GCF_007970665.1_ASM797066v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:05,794] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:05,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:05,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg251d1445-0521-47b2-a2c8-5add08232af4/dqc_reference/checkm_data
[2024-01-24 12:54:05,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:05,850] [INFO] Task started: CheckM
[2024-01-24 12:54:05,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007970665.1_ASM797066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007970665.1_ASM797066v1_genomic.fna/checkm_input GCF_007970665.1_ASM797066v1_genomic.fna/checkm_result
[2024-01-24 12:55:18,139] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:18,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:18,161] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:18,161] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:18,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007970665.1_ASM797066v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:18,162] [INFO] Task started: Blastn
[2024-01-24 12:55:18,162] [INFO] Running command: blastn -query GCF_007970665.1_ASM797066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg251d1445-0521-47b2-a2c8-5add08232af4/dqc_reference/reference_markers_gtdb.fasta -out GCF_007970665.1_ASM797066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:19,283] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:19,287] [INFO] Selected 9 target genomes.
[2024-01-24 12:55:19,287] [INFO] Target genome list was writen to GCF_007970665.1_ASM797066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:19,299] [INFO] Task started: fastANI
[2024-01-24 12:55:19,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bca4e67-056c-4967-8a34-58b9b59bbce1/GCF_007970665.1_ASM797066v1_genomic.fna.gz --refList GCF_007970665.1_ASM797066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007970665.1_ASM797066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:31,085] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:31,095] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:31,096] [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_007970665.1	s__Baekduia soli	100.0	1737	1737	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000688095.1	s__Baekduia sp000688095	81.598	1019	1737	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424625.1	s__Baekduia woesei_A	80.8835	982	1737	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215085.1	s__Baekduia sp016215085	80.7067	662	1737	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017084525.1	s__Baekduia sp017084525	79.3278	780	1737	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888335.1	s__VAWY01 sp005888335	78.2543	761	1737	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__VAWY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044185.1	s__SEOHO-28 sp003044185	78.2307	718	1737	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	98.17	98.17	0.92	0.92	2	-
GCA_018268595.1	s__Conexibacter sp018268595	77.7943	590	1737	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788585.1	s__SYBY01 sp005788585	76.9022	456	1737	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:31,098] [INFO] GTDB search result was written to GCF_007970665.1_ASM797066v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:31,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:31,101] [INFO] DFAST_QC result json was written to GCF_007970665.1_ASM797066v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:31,101] [INFO] DFAST_QC completed!
[2024-01-24 12:55:31,102] [INFO] Total running time: 0h1m54s