[2024-01-24 13:36:32,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,154] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,155] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbb1c7f3-b950-4133-8a7b-efa7e80e038b/dqc_reference
[2024-01-24 13:36:33,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,467] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cec96f2-7cf5-485f-b31a-961f909539a2/GCF_014636455.1_ASM1463645v1_genomic.fna.gz | prodigal -d GCF_014636455.1_ASM1463645v1_genomic.fna/cds.fna -a GCF_014636455.1_ASM1463645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:43,514] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:43,514] [INFO] Task started: HMMsearch
[2024-01-24 13:36:43,514] [INFO] Running command: hmmsearch --tblout GCF_014636455.1_ASM1463645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbb1c7f3-b950-4133-8a7b-efa7e80e038b/dqc_reference/reference_markers.hmm GCF_014636455.1_ASM1463645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:43,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:43,783] [INFO] Found 6/6 markers.
[2024-01-24 13:36:43,815] [INFO] Query marker FASTA was written to GCF_014636455.1_ASM1463645v1_genomic.fna/markers.fasta
[2024-01-24 13:36:43,815] [INFO] Task started: Blastn
[2024-01-24 13:36:43,815] [INFO] Running command: blastn -query GCF_014636455.1_ASM1463645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbb1c7f3-b950-4133-8a7b-efa7e80e038b/dqc_reference/reference_markers.fasta -out GCF_014636455.1_ASM1463645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:44,784] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:44,788] [INFO] Selected 13 target genomes.
[2024-01-24 13:36:44,789] [INFO] Target genome list was writen to GCF_014636455.1_ASM1463645v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:44,796] [INFO] Task started: fastANI
[2024-01-24 13:36:44,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cec96f2-7cf5-485f-b31a-961f909539a2/GCF_014636455.1_ASM1463645v1_genomic.fna.gz --refList GCF_014636455.1_ASM1463645v1_genomic.fna/target_genomes.txt --output GCF_014636455.1_ASM1463645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:53,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:53,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbb1c7f3-b950-4133-8a7b-efa7e80e038b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:53,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbb1c7f3-b950-4133-8a7b-efa7e80e038b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:53,363] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:36:53,364] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:53,364] [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
Mycetocola zhadangensis	strain=CGMCC 1.12042	GCA_014636455.1	1164595	1164595	type	True	100.0	1080	1081	95	conclusive
Mycetocola zhadangensis	strain=ZD1-4	GCA_003668565.1	1164595	1164595	type	True	99.9981	1079	1081	95	conclusive
Mycetocola zhujimingii	strain=449 = CGMCC 1.16372	GCA_003065425.1	2079792	2079792	type	True	81.7957	636	1081	95	below_threshold
Mycetocola manganoxydans	strain=KCTC 19753	GCA_014651755.1	699879	699879	type	True	80.2401	506	1081	95	below_threshold
Mycetocola manganoxydans	strain=CCTCC AB209002	GCA_003667545.1	699879	699879	type	True	80.2215	502	1081	95	below_threshold
Mycetocola miduiensis	strain=CGMCC 1.11101	GCA_900115155.1	995034	995034	type	True	80.0656	469	1081	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	78.3453	287	1081	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.9504	256	1081	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	77.8478	290	1081	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.8254	280	1081	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	77.5735	219	1081	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.4197	244	1081	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	77.3279	201	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:53,366] [INFO] DFAST Taxonomy check result was written to GCF_014636455.1_ASM1463645v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:53,366] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:53,366] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:53,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbb1c7f3-b950-4133-8a7b-efa7e80e038b/dqc_reference/checkm_data
[2024-01-24 13:36:53,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:53,400] [INFO] Task started: CheckM
[2024-01-24 13:36:53,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636455.1_ASM1463645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636455.1_ASM1463645v1_genomic.fna/checkm_input GCF_014636455.1_ASM1463645v1_genomic.fna/checkm_result
[2024-01-24 13:37:27,767] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:27,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:27,819] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:27,819] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:27,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636455.1_ASM1463645v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:27,820] [INFO] Task started: Blastn
[2024-01-24 13:37:27,820] [INFO] Running command: blastn -query GCF_014636455.1_ASM1463645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbb1c7f3-b950-4133-8a7b-efa7e80e038b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636455.1_ASM1463645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:29,466] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:29,470] [INFO] Selected 8 target genomes.
[2024-01-24 13:37:29,470] [INFO] Target genome list was writen to GCF_014636455.1_ASM1463645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:29,498] [INFO] Task started: fastANI
[2024-01-24 13:37:29,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cec96f2-7cf5-485f-b31a-961f909539a2/GCF_014636455.1_ASM1463645v1_genomic.fna.gz --refList GCF_014636455.1_ASM1463645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636455.1_ASM1463645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:35,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,356] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:35,357] [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_003668565.1	s__Mycetocola_A zhadangensis	99.9981	1079	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003065425.1	s__Mycetocola_A zhujimingii	81.7957	636	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	98.22	98.22	0.95	0.95	2	-
GCF_003667545.1	s__Mycetocola_A manganoxydans	80.2181	503	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015752285.1	s__Mycetocola_A sp015752285	80.1564	505	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115155.1	s__Mycetocola_A miduiensis	80.0656	469	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167575.1	s__Okibacterium fritillariae	78.6303	294	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217495.1	s__Microterricola gilva	78.3331	288	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570845.1	s__Leifsonia_A flava	78.1091	292	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	95.29	95.29	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,358] [INFO] GTDB search result was written to GCF_014636455.1_ASM1463645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:35,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:35,363] [INFO] DFAST_QC result json was written to GCF_014636455.1_ASM1463645v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:35,363] [INFO] DFAST_QC completed!
[2024-01-24 13:37:35,363] [INFO] Total running time: 0h1m3s