[2024-01-24 12:29:21,778] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:21,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:21,781] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fad754f-b206-499e-8710-aa4532b94fb2/dqc_reference
[2024-01-24 12:29:23,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:23,022] [INFO] Task started: Prodigal
[2024-01-24 12:29:23,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg03c2912a-4c37-4e61-8447-81b71e89a382/GCF_009371975.2_ASM937197v2_genomic.fna.gz | prodigal -d GCF_009371975.2_ASM937197v2_genomic.fna/cds.fna -a GCF_009371975.2_ASM937197v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:30,706] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:30,707] [INFO] Task started: HMMsearch
[2024-01-24 12:29:30,707] [INFO] Running command: hmmsearch --tblout GCF_009371975.2_ASM937197v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fad754f-b206-499e-8710-aa4532b94fb2/dqc_reference/reference_markers.hmm GCF_009371975.2_ASM937197v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:30,947] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:30,949] [INFO] Found 6/6 markers.
[2024-01-24 12:29:30,978] [INFO] Query marker FASTA was written to GCF_009371975.2_ASM937197v2_genomic.fna/markers.fasta
[2024-01-24 12:29:30,978] [INFO] Task started: Blastn
[2024-01-24 12:29:30,978] [INFO] Running command: blastn -query GCF_009371975.2_ASM937197v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fad754f-b206-499e-8710-aa4532b94fb2/dqc_reference/reference_markers.fasta -out GCF_009371975.2_ASM937197v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:32,274] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:32,283] [INFO] Selected 17 target genomes.
[2024-01-24 12:29:32,284] [INFO] Target genome list was writen to GCF_009371975.2_ASM937197v2_genomic.fna/target_genomes.txt
[2024-01-24 12:29:32,292] [INFO] Task started: fastANI
[2024-01-24 12:29:32,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg03c2912a-4c37-4e61-8447-81b71e89a382/GCF_009371975.2_ASM937197v2_genomic.fna.gz --refList GCF_009371975.2_ASM937197v2_genomic.fna/target_genomes.txt --output GCF_009371975.2_ASM937197v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:42,149] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:42,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fad754f-b206-499e-8710-aa4532b94fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:42,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fad754f-b206-499e-8710-aa4532b94fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:42,166] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:29:42,166] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:29:42,166] [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
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	82.4744	544	875	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	82.4064	536	875	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	80.9657	475	875	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	80.8494	471	875	95	below_threshold
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	80.6754	467	875	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.8174	406	875	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.5344	359	875	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.2141	336	875	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.112	412	875	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.1024	340	875	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.0994	376	875	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.9109	377	875	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	78.769	356	875	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	78.7476	345	875	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	78.6364	326	875	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.6203	330	875	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	78.5281	335	875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:42,168] [INFO] DFAST Taxonomy check result was written to GCF_009371975.2_ASM937197v2_genomic.fna/tc_result.tsv
[2024-01-24 12:29:42,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:42,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:42,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fad754f-b206-499e-8710-aa4532b94fb2/dqc_reference/checkm_data
[2024-01-24 12:29:42,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:42,202] [INFO] Task started: CheckM
[2024-01-24 12:29:42,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009371975.2_ASM937197v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009371975.2_ASM937197v2_genomic.fna/checkm_input GCF_009371975.2_ASM937197v2_genomic.fna/checkm_result
[2024-01-24 12:30:11,082] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:11,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:11,110] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:11,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:11,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009371975.2_ASM937197v2_genomic.fna/markers.fasta)
[2024-01-24 12:30:11,111] [INFO] Task started: Blastn
[2024-01-24 12:30:11,111] [INFO] Running command: blastn -query GCF_009371975.2_ASM937197v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fad754f-b206-499e-8710-aa4532b94fb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009371975.2_ASM937197v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:13,155] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:13,159] [INFO] Selected 9 target genomes.
[2024-01-24 12:30:13,159] [INFO] Target genome list was writen to GCF_009371975.2_ASM937197v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:13,166] [INFO] Task started: fastANI
[2024-01-24 12:30:13,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg03c2912a-4c37-4e61-8447-81b71e89a382/GCF_009371975.2_ASM937197v2_genomic.fna.gz --refList GCF_009371975.2_ASM937197v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009371975.2_ASM937197v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:18,425] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:18,440] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:18,440] [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_009371975.2	s__Marinisubtilis pacificus	100.0	873	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	97.81	97.81	0.83	0.83	2	conclusive
GCF_013414345.1	s__Marinisubtilis indicus	93.8232	721	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
GCF_002813345.1	s__Marinisubtilis sp002813345	85.2271	594	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280615.1	s__Chryseoglobus sp002280615	83.6715	336	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464255.1	s__Chryseoglobus sp001464255	83.5032	398	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	82.7652	531	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425665.1	s__Yonghaparkia sp001425665	82.6667	521	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	99.25	99.25	0.97	0.97	2	-
GCA_012530535.1	s__Yonghaparkia sp012530535	82.6501	550	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502445.1	s__Yonghaparkia sp005502445	82.4754	476	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:18,442] [INFO] GTDB search result was written to GCF_009371975.2_ASM937197v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:18,443] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:18,446] [INFO] DFAST_QC result json was written to GCF_009371975.2_ASM937197v2_genomic.fna/dqc_result.json
[2024-01-24 12:30:18,446] [INFO] DFAST_QC completed!
[2024-01-24 12:30:18,446] [INFO] Total running time: 0h0m57s