[2024-01-24 11:51:23,862] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,872] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b20cfc3-4ace-4d58-8bf4-13b32cf00433/dqc_reference
[2024-01-24 11:51:25,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,241] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,241] [INFO] Running command: gunzip -c /var/lib/cwl/stga17b8c07-d0b8-4be7-b822-35ce65701a85/GCF_014137945.1_ASM1413794v1_genomic.fna.gz | prodigal -d GCF_014137945.1_ASM1413794v1_genomic.fna/cds.fna -a GCF_014137945.1_ASM1413794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:32,589] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:32,590] [INFO] Task started: HMMsearch
[2024-01-24 11:51:32,590] [INFO] Running command: hmmsearch --tblout GCF_014137945.1_ASM1413794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b20cfc3-4ace-4d58-8bf4-13b32cf00433/dqc_reference/reference_markers.hmm GCF_014137945.1_ASM1413794v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:32,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:32,834] [INFO] Found 6/6 markers.
[2024-01-24 11:51:32,862] [INFO] Query marker FASTA was written to GCF_014137945.1_ASM1413794v1_genomic.fna/markers.fasta
[2024-01-24 11:51:32,862] [INFO] Task started: Blastn
[2024-01-24 11:51:32,862] [INFO] Running command: blastn -query GCF_014137945.1_ASM1413794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b20cfc3-4ace-4d58-8bf4-13b32cf00433/dqc_reference/reference_markers.fasta -out GCF_014137945.1_ASM1413794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:34,169] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:34,172] [INFO] Selected 20 target genomes.
[2024-01-24 11:51:34,173] [INFO] Target genome list was writen to GCF_014137945.1_ASM1413794v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:34,187] [INFO] Task started: fastANI
[2024-01-24 11:51:34,187] [INFO] Running command: fastANI --query /var/lib/cwl/stga17b8c07-d0b8-4be7-b822-35ce65701a85/GCF_014137945.1_ASM1413794v1_genomic.fna.gz --refList GCF_014137945.1_ASM1413794v1_genomic.fna/target_genomes.txt --output GCF_014137945.1_ASM1413794v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:46,159] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:46,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b20cfc3-4ace-4d58-8bf4-13b32cf00433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:46,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b20cfc3-4ace-4d58-8bf4-13b32cf00433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:46,177] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:46,177] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:46,177] [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	82.5729	552	908	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	82.5197	545	908	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	81.3116	502	908	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	81.2346	503	908	95	below_threshold
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	80.8868	501	908	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.8793	434	908	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.8252	365	908	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.5487	420	908	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	79.3577	391	908	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.3393	309	908	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.3325	400	908	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.3131	377	908	95	below_threshold
Agromyces protaetiae	strain=FW100M-8	GCA_004135405.1	2509455	2509455	type	True	79.3096	414	908	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.2858	396	908	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.2309	395	908	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	79.0539	439	908	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.0137	431	908	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	79.0119	374	908	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.9703	355	908	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	78.8174	384	908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:46,179] [INFO] DFAST Taxonomy check result was written to GCF_014137945.1_ASM1413794v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:46,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:46,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:46,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b20cfc3-4ace-4d58-8bf4-13b32cf00433/dqc_reference/checkm_data
[2024-01-24 11:51:46,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:46,209] [INFO] Task started: CheckM
[2024-01-24 11:51:46,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014137945.1_ASM1413794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014137945.1_ASM1413794v1_genomic.fna/checkm_input GCF_014137945.1_ASM1413794v1_genomic.fna/checkm_result
[2024-01-24 11:52:13,616] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:13,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:13,643] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:13,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:13,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014137945.1_ASM1413794v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:13,644] [INFO] Task started: Blastn
[2024-01-24 11:52:13,644] [INFO] Running command: blastn -query GCF_014137945.1_ASM1413794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b20cfc3-4ace-4d58-8bf4-13b32cf00433/dqc_reference/reference_markers_gtdb.fasta -out GCF_014137945.1_ASM1413794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:16,128] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:16,132] [INFO] Selected 7 target genomes.
[2024-01-24 11:52:16,132] [INFO] Target genome list was writen to GCF_014137945.1_ASM1413794v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:16,138] [INFO] Task started: fastANI
[2024-01-24 11:52:16,138] [INFO] Running command: fastANI --query /var/lib/cwl/stga17b8c07-d0b8-4be7-b822-35ce65701a85/GCF_014137945.1_ASM1413794v1_genomic.fna.gz --refList GCF_014137945.1_ASM1413794v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014137945.1_ASM1413794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:21,385] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:21,398] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:21,399] [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_014137945.1	s__Yonghaparkia alkaliphila	100.0	906	908	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001425665.1	s__Yonghaparkia sp001425665	89.8492	701	908	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	99.25	99.25	0.97	0.97	2	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	87.1578	675	908	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_005502445.1	s__Yonghaparkia sp005502445	85.6531	581	908	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012530535.1	s__Yonghaparkia sp012530535	84.1639	617	908	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200395.1	s__Chryseoglobus frigidaquae	82.5046	556	908	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013414345.1	s__Marinisubtilis indicus	81.8253	533	908	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:21,400] [INFO] GTDB search result was written to GCF_014137945.1_ASM1413794v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:21,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:21,405] [INFO] DFAST_QC result json was written to GCF_014137945.1_ASM1413794v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:21,405] [INFO] DFAST_QC completed!
[2024-01-24 11:52:21,405] [INFO] Total running time: 0h0m58s