[2024-01-24 13:31:41,510] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:41,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:41,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bb34104-d977-4d86-b549-60bcaf816e06/dqc_reference
[2024-01-24 13:31:42,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:42,709] [INFO] Task started: Prodigal
[2024-01-24 13:31:42,709] [INFO] Running command: gunzip -c /var/lib/cwl/stge5bfc517-bd64-4000-bfdc-cca64622dc73/GCF_003044185.1_ASM304418v1_genomic.fna.gz | prodigal -d GCF_003044185.1_ASM304418v1_genomic.fna/cds.fna -a GCF_003044185.1_ASM304418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:54,172] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:54,173] [INFO] Task started: HMMsearch
[2024-01-24 13:31:54,173] [INFO] Running command: hmmsearch --tblout GCF_003044185.1_ASM304418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bb34104-d977-4d86-b549-60bcaf816e06/dqc_reference/reference_markers.hmm GCF_003044185.1_ASM304418v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:54,473] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:54,474] [INFO] Found 6/6 markers.
[2024-01-24 13:31:54,520] [INFO] Query marker FASTA was written to GCF_003044185.1_ASM304418v1_genomic.fna/markers.fasta
[2024-01-24 13:31:54,522] [INFO] Task started: Blastn
[2024-01-24 13:31:54,523] [INFO] Running command: blastn -query GCF_003044185.1_ASM304418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb34104-d977-4d86-b549-60bcaf816e06/dqc_reference/reference_markers.fasta -out GCF_003044185.1_ASM304418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:55,244] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:55,247] [INFO] Selected 10 target genomes.
[2024-01-24 13:31:55,248] [INFO] Target genome list was writen to GCF_003044185.1_ASM304418v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:55,288] [INFO] Task started: fastANI
[2024-01-24 13:31:55,288] [INFO] Running command: fastANI --query /var/lib/cwl/stge5bfc517-bd64-4000-bfdc-cca64622dc73/GCF_003044185.1_ASM304418v1_genomic.fna.gz --refList GCF_003044185.1_ASM304418v1_genomic.fna/target_genomes.txt --output GCF_003044185.1_ASM304418v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:07,202] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:07,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bb34104-d977-4d86-b549-60bcaf816e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:07,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bb34104-d977-4d86-b549-60bcaf816e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:07,213] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:07,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:07,213] [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
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	100.0	1576	1576	95	conclusive
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	78.2804	716	1576	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	77.9635	699	1576	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.9003	736	1576	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	77.6187	626	1576	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	77.5337	768	1576	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	77.2888	685	1576	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	77.0855	583	1576	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	75.1697	163	1576	95	below_threshold
Microbacterium nanhaiense	strain=CGMCC 4.7181	GCA_014646015.1	1301026	1301026	type	True	74.9265	201	1576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:07,218] [INFO] DFAST Taxonomy check result was written to GCF_003044185.1_ASM304418v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:07,218] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:07,218] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:07,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bb34104-d977-4d86-b549-60bcaf816e06/dqc_reference/checkm_data
[2024-01-24 13:32:07,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:07,280] [INFO] Task started: CheckM
[2024-01-24 13:32:07,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003044185.1_ASM304418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003044185.1_ASM304418v1_genomic.fna/checkm_input GCF_003044185.1_ASM304418v1_genomic.fna/checkm_result
[2024-01-24 13:33:01,567] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:01,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:01,588] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:01,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:01,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003044185.1_ASM304418v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:01,589] [INFO] Task started: Blastn
[2024-01-24 13:33:01,590] [INFO] Running command: blastn -query GCF_003044185.1_ASM304418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb34104-d977-4d86-b549-60bcaf816e06/dqc_reference/reference_markers_gtdb.fasta -out GCF_003044185.1_ASM304418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:02,704] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:02,707] [INFO] Selected 17 target genomes.
[2024-01-24 13:33:02,707] [INFO] Target genome list was writen to GCF_003044185.1_ASM304418v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:02,847] [INFO] Task started: fastANI
[2024-01-24 13:33:02,848] [INFO] Running command: fastANI --query /var/lib/cwl/stge5bfc517-bd64-4000-bfdc-cca64622dc73/GCF_003044185.1_ASM304418v1_genomic.fna.gz --refList GCF_003044185.1_ASM304418v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003044185.1_ASM304418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:20,230] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:20,249] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:20,249] [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_003044185.1	s__SEOHO-28 sp003044185	100.0	1576	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	98.17	98.17	0.92	0.92	2	conclusive
GCA_013695395.1	s__SEOHO-28 sp013695395	79.0256	408	1576	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_017084525.1	s__Baekduia sp017084525	78.9897	784	1576	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	78.8415	543	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813955.1	s__CADCVQ01 sp013813955	78.6524	290	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806205.1	s__SEOHO-28 sp902806205	78.4472	514	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882425.1	s__F1-60-MAGs163 sp017882425	78.369	430	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970665.1	s__Baekduia soli	78.23	727	1576	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	78.1969	756	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806175.1	s__CADCVQ01 sp902806175	78.1123	548	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688095.1	s__Baekduia sp000688095	78.0435	753	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268595.1	s__Conexibacter sp018268595	78.0421	611	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199525.1	s__Conexibacter arvalis	77.9272	729	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882375.1	s__Palsa-744 sp017882375	77.7538	394	1576	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_902806215.1	s__CADCVT01 sp902806215	77.453	530	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478825.1	s__Patulibacter sp015478825	77.3642	406	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420025.1	s__Patulibacter americanus	77.1126	576	1576	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:20,251] [INFO] GTDB search result was written to GCF_003044185.1_ASM304418v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:20,251] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:20,255] [INFO] DFAST_QC result json was written to GCF_003044185.1_ASM304418v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:20,255] [INFO] DFAST_QC completed!
[2024-01-24 13:33:20,255] [INFO] Total running time: 0h1m39s