[2024-01-24 14:07:14,837] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:14,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:14,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg6505446d-b9c3-4a58-841a-0e5166c86905/dqc_reference
[2024-01-24 14:07:16,099] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:16,099] [INFO] Task started: Prodigal
[2024-01-24 14:07:16,100] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0b42e0b-99d5-4879-aaca-56d43f361036/GCF_003581425.1_ASM358142v1_genomic.fna.gz | prodigal -d GCF_003581425.1_ASM358142v1_genomic.fna/cds.fna -a GCF_003581425.1_ASM358142v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:24,501] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:24,501] [INFO] Task started: HMMsearch
[2024-01-24 14:07:24,501] [INFO] Running command: hmmsearch --tblout GCF_003581425.1_ASM358142v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6505446d-b9c3-4a58-841a-0e5166c86905/dqc_reference/reference_markers.hmm GCF_003581425.1_ASM358142v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:24,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:24,763] [INFO] Found 6/6 markers.
[2024-01-24 14:07:24,796] [INFO] Query marker FASTA was written to GCF_003581425.1_ASM358142v1_genomic.fna/markers.fasta
[2024-01-24 14:07:24,797] [INFO] Task started: Blastn
[2024-01-24 14:07:24,797] [INFO] Running command: blastn -query GCF_003581425.1_ASM358142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6505446d-b9c3-4a58-841a-0e5166c86905/dqc_reference/reference_markers.fasta -out GCF_003581425.1_ASM358142v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:26,163] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:26,167] [INFO] Selected 24 target genomes.
[2024-01-24 14:07:26,168] [INFO] Target genome list was writen to GCF_003581425.1_ASM358142v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:26,182] [INFO] Task started: fastANI
[2024-01-24 14:07:26,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0b42e0b-99d5-4879-aaca-56d43f361036/GCF_003581425.1_ASM358142v1_genomic.fna.gz --refList GCF_003581425.1_ASM358142v1_genomic.fna/target_genomes.txt --output GCF_003581425.1_ASM358142v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:44,354] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:44,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6505446d-b9c3-4a58-841a-0e5166c86905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:44,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6505446d-b9c3-4a58-841a-0e5166c86905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:44,388] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:44,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:44,388] [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
Amnibacterium setariae	strain=DD4a	GCA_003581425.1	2306585	2306585	type	True	100.0	1158	1158	95	conclusive
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	85.3845	865	1158	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	78.7068	522	1158	95	below_threshold
Gryllotalpicola ginsengisoli	strain=DSM 22003	GCA_000419445.1	444608	444608	type	True	78.6632	403	1158	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	78.5713	448	1158	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3464	485	1158	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	78.3393	499	1158	95	below_threshold
Agromyces terreus	strain=JCM 14581	GCA_009749465.1	424795	424795	type	True	78.3267	447	1158	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	78.2926	490	1158	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	78.16	447	1158	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	78.1561	473	1158	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.1241	412	1158	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	78.1234	470	1158	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	78.0993	470	1158	95	below_threshold
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	78.0969	438	1158	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	78.0614	458	1158	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.0304	427	1158	95	below_threshold
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	77.9881	393	1158	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.9068	361	1158	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.8908	405	1158	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	77.7701	396	1158	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	77.5971	327	1158	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	77.5501	381	1158	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	77.5241	377	1158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:44,395] [INFO] DFAST Taxonomy check result was written to GCF_003581425.1_ASM358142v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:44,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:44,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:44,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6505446d-b9c3-4a58-841a-0e5166c86905/dqc_reference/checkm_data
[2024-01-24 14:07:44,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:44,437] [INFO] Task started: CheckM
[2024-01-24 14:07:44,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003581425.1_ASM358142v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003581425.1_ASM358142v1_genomic.fna/checkm_input GCF_003581425.1_ASM358142v1_genomic.fna/checkm_result
[2024-01-24 14:08:26,182] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:26,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:26,201] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:26,202] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:26,202] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003581425.1_ASM358142v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:26,203] [INFO] Task started: Blastn
[2024-01-24 14:08:26,203] [INFO] Running command: blastn -query GCF_003581425.1_ASM358142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6505446d-b9c3-4a58-841a-0e5166c86905/dqc_reference/reference_markers_gtdb.fasta -out GCF_003581425.1_ASM358142v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:28,900] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:28,904] [INFO] Selected 22 target genomes.
[2024-01-24 14:08:28,904] [INFO] Target genome list was writen to GCF_003581425.1_ASM358142v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:28,945] [INFO] Task started: fastANI
[2024-01-24 14:08:28,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0b42e0b-99d5-4879-aaca-56d43f361036/GCF_003581425.1_ASM358142v1_genomic.fna.gz --refList GCF_003581425.1_ASM358142v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003581425.1_ASM358142v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:48,566] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:48,585] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:48,586] [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_003581425.1	s__Amnibacterium setariae	100.0	1158	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004364555.1	s__Amnibacterium kyonggiense	85.3513	867	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916505.1	s__Naasia sp017916505	79.1932	494	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916515.1	s__Naasia sp017916515	78.9076	440	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419445.1	s__Gryllotalpicola ginsengisoli	78.6852	401	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355965.1	s__JAFIQW01 sp017355965	78.6665	475	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAFIQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866585.1	s__Rathayibacter sp002930885	78.5777	482	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.23	95.98	0.89	0.85	55	-
GCF_001425665.1	s__Yonghaparkia sp001425665	78.5684	412	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	99.25	99.25	0.97	0.97	2	-
GCF_017833035.1	s__Frigoribacterium sp017833035	78.521	447	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	78.5173	436	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205025.1	s__Rathayibacter sp013205025	78.4704	529	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751785.1	s__Frigoribacterium sp003751785	78.4638	466	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749465.1	s__Agromyces terreus	78.3454	445	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954365.1	s__Frigoribacterium sp007954365	78.1987	445	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	78.1716	449	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009780695.1	s__Gryllotalpicola sp009780695	78.1651	393	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	99.84	99.84	0.94	0.94	2	-
GCF_009749405.1	s__Agromyces lapidis	78.1335	453	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752465.1	s__Agrococcus jenensis	78.116	452	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001806325.1	s__Curtobacterium sp001806325	78.1081	444	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.12	98.02	0.92	0.92	4	-
GCF_007923295.1	s__Agrococcus sediminis	77.9867	452	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.99	97.99	0.92	0.92	2	-
GCF_900099705.1	s__Agrococcus jejuensis	77.783	472	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759705.1	s__Microbacterium ulmi	77.5589	380	1158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:48,588] [INFO] GTDB search result was written to GCF_003581425.1_ASM358142v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:48,589] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:48,594] [INFO] DFAST_QC result json was written to GCF_003581425.1_ASM358142v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:48,595] [INFO] DFAST_QC completed!
[2024-01-24 14:08:48,595] [INFO] Total running time: 0h1m34s