[2024-01-24 12:53:37,251] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:37,253] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:37,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cb7a2f2-d6d9-4a22-a6f0-bd8f4ecf387d/dqc_reference
[2024-01-24 12:53:38,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:38,506] [INFO] Task started: Prodigal
[2024-01-24 12:53:38,506] [INFO] Running command: gunzip -c /var/lib/cwl/stga22655f6-70a8-458c-8915-ba6de03a6d14/GCF_030073505.1_ASM3007350v1_genomic.fna.gz | prodigal -d GCF_030073505.1_ASM3007350v1_genomic.fna/cds.fna -a GCF_030073505.1_ASM3007350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:48,471] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:48,472] [INFO] Task started: HMMsearch
[2024-01-24 12:53:48,472] [INFO] Running command: hmmsearch --tblout GCF_030073505.1_ASM3007350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cb7a2f2-d6d9-4a22-a6f0-bd8f4ecf387d/dqc_reference/reference_markers.hmm GCF_030073505.1_ASM3007350v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:48,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:48,716] [INFO] Found 6/6 markers.
[2024-01-24 12:53:48,745] [INFO] Query marker FASTA was written to GCF_030073505.1_ASM3007350v1_genomic.fna/markers.fasta
[2024-01-24 12:53:48,745] [INFO] Task started: Blastn
[2024-01-24 12:53:48,745] [INFO] Running command: blastn -query GCF_030073505.1_ASM3007350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cb7a2f2-d6d9-4a22-a6f0-bd8f4ecf387d/dqc_reference/reference_markers.fasta -out GCF_030073505.1_ASM3007350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:49,763] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:49,767] [INFO] Selected 14 target genomes.
[2024-01-24 12:53:49,768] [INFO] Target genome list was writen to GCF_030073505.1_ASM3007350v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:49,779] [INFO] Task started: fastANI
[2024-01-24 12:53:49,779] [INFO] Running command: fastANI --query /var/lib/cwl/stga22655f6-70a8-458c-8915-ba6de03a6d14/GCF_030073505.1_ASM3007350v1_genomic.fna.gz --refList GCF_030073505.1_ASM3007350v1_genomic.fna/target_genomes.txt --output GCF_030073505.1_ASM3007350v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:58,336] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:58,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cb7a2f2-d6d9-4a22-a6f0-bd8f4ecf387d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:58,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cb7a2f2-d6d9-4a22-a6f0-bd8f4ecf387d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:58,360] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:53:58,361] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:58,361] [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
Gulosibacter molinativorax	strain=ON4	GCA_003010915.2	256821	256821	type	True	99.9988	1097	1098	95	conclusive
Gulosibacter molinativorax	strain=DSM 13485	GCA_000425685.1	256821	256821	type	True	99.9892	1073	1098	95	conclusive
Gulosibacter chungangensis	strain=KCTC 13959	GCA_008831155.1	979746	979746	type	True	81.1585	515	1098	95	below_threshold
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	79.6017	390	1098	95	below_threshold
Gulosibacter macacae	strain=YIM 102482-1	GCA_003865375.1	2488791	2488791	type	True	78.848	291	1098	95	below_threshold
Gulosibacter bifidus	strain=NBRC 103089	GCA_001570925.1	272239	272239	type	True	78.4973	198	1098	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.4878	237	1098	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.3919	191	1098	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	77.3313	237	1098	95	below_threshold
Agromyces intestinalis	strain=KACC 19306	GCA_008365295.1	2592652	2592652	type	True	77.3284	214	1098	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	77.2106	183	1098	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	77.0843	201	1098	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	76.4737	136	1098	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.4264	149	1098	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:58,362] [INFO] DFAST Taxonomy check result was written to GCF_030073505.1_ASM3007350v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:58,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:58,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:58,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cb7a2f2-d6d9-4a22-a6f0-bd8f4ecf387d/dqc_reference/checkm_data
[2024-01-24 12:53:58,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:58,397] [INFO] Task started: CheckM
[2024-01-24 12:53:58,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030073505.1_ASM3007350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030073505.1_ASM3007350v1_genomic.fna/checkm_input GCF_030073505.1_ASM3007350v1_genomic.fna/checkm_result
[2024-01-24 12:54:30,678] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:30,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:30,704] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:30,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:30,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030073505.1_ASM3007350v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:30,705] [INFO] Task started: Blastn
[2024-01-24 12:54:30,705] [INFO] Running command: blastn -query GCF_030073505.1_ASM3007350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cb7a2f2-d6d9-4a22-a6f0-bd8f4ecf387d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030073505.1_ASM3007350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:32,169] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:32,173] [INFO] Selected 13 target genomes.
[2024-01-24 12:54:32,173] [INFO] Target genome list was writen to GCF_030073505.1_ASM3007350v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:32,190] [INFO] Task started: fastANI
[2024-01-24 12:54:32,190] [INFO] Running command: fastANI --query /var/lib/cwl/stga22655f6-70a8-458c-8915-ba6de03a6d14/GCF_030073505.1_ASM3007350v1_genomic.fna.gz --refList GCF_030073505.1_ASM3007350v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030073505.1_ASM3007350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:40,068] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:40,084] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:40,085] [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_000425685.1	s__Gulosibacter molinativorax	99.9892	1073	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_008831155.1	s__Gulosibacter chungangensis	81.1584	515	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163695.1	s__Gulosibacter sp900163695	80.1862	467	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626105.1	s__Gulosibacter sp900626105	79.6652	383	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	98.80	98.80	0.92	0.92	2	-
GCF_000381765.1	s__Gulosibacter faecalis	79.5944	391	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719255.1	s__Gulosibacter sp012719255	79.2388	330	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002931055.1	s__Pseudoclavibacter sp002931055	77.887	225	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	97.65	95.42	0.90	0.86	11	-
GCF_018308945.1	s__Agrococcus sp018308945	77.6013	252	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135055.1	s__Agromyces binzhouensis	77.4398	177	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907355.1	s__Agromyces aurantiacus	77.3074	239	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674665.1	s__Agromyces kandeliae	77.1473	221	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634985.1	s__Agromyces sp003634985	77.0711	218	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538725.1	s__Cellulomonas gelida	76.7164	138	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.61	99.23	0.96	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:40,087] [INFO] GTDB search result was written to GCF_030073505.1_ASM3007350v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:40,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:40,091] [INFO] DFAST_QC result json was written to GCF_030073505.1_ASM3007350v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:40,092] [INFO] DFAST_QC completed!
[2024-01-24 12:54:40,092] [INFO] Total running time: 0h1m3s