[2024-01-24 11:26:10,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:10,882] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:10,882] [INFO] DQC Reference Directory: /var/lib/cwl/stg320c9a3c-a971-44a4-ab1d-b51eed2ffe42/dqc_reference
[2024-01-24 11:26:12,191] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:12,192] [INFO] Task started: Prodigal
[2024-01-24 11:26:12,192] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4fa7269-767d-4a34-bea8-940a5a836809/GCF_030161875.1_ASM3016187v1_genomic.fna.gz | prodigal -d GCF_030161875.1_ASM3016187v1_genomic.fna/cds.fna -a GCF_030161875.1_ASM3016187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:22,322] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:22,322] [INFO] Task started: HMMsearch
[2024-01-24 11:26:22,322] [INFO] Running command: hmmsearch --tblout GCF_030161875.1_ASM3016187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg320c9a3c-a971-44a4-ab1d-b51eed2ffe42/dqc_reference/reference_markers.hmm GCF_030161875.1_ASM3016187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:22,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:22,610] [INFO] Found 6/6 markers.
[2024-01-24 11:26:22,658] [INFO] Query marker FASTA was written to GCF_030161875.1_ASM3016187v1_genomic.fna/markers.fasta
[2024-01-24 11:26:22,659] [INFO] Task started: Blastn
[2024-01-24 11:26:22,659] [INFO] Running command: blastn -query GCF_030161875.1_ASM3016187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg320c9a3c-a971-44a4-ab1d-b51eed2ffe42/dqc_reference/reference_markers.fasta -out GCF_030161875.1_ASM3016187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:24,024] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:24,030] [INFO] Selected 23 target genomes.
[2024-01-24 11:26:24,030] [INFO] Target genome list was writen to GCF_030161875.1_ASM3016187v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:24,039] [INFO] Task started: fastANI
[2024-01-24 11:26:24,039] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4fa7269-767d-4a34-bea8-940a5a836809/GCF_030161875.1_ASM3016187v1_genomic.fna.gz --refList GCF_030161875.1_ASM3016187v1_genomic.fna/target_genomes.txt --output GCF_030161875.1_ASM3016187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:39,704] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:39,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg320c9a3c-a971-44a4-ab1d-b51eed2ffe42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:39,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg320c9a3c-a971-44a4-ab1d-b51eed2ffe42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:39,724] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:39,724] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:39,725] [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
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	84.7917	700	1096	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	83.3243	594	1096	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	79.5935	396	1096	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	79.5897	387	1096	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.1505	493	1096	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	79.0632	480	1096	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.0307	425	1096	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	79.0155	469	1096	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.0135	456	1096	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	78.9594	429	1096	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	78.8738	403	1096	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	78.8585	443	1096	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.7672	462	1096	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	78.7417	394	1096	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	78.706	405	1096	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.6653	379	1096	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.6559	394	1096	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	78.6424	390	1096	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	78.6017	399	1096	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.5996	399	1096	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	78.5393	396	1096	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	78.4948	384	1096	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.4756	402	1096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:39,728] [INFO] DFAST Taxonomy check result was written to GCF_030161875.1_ASM3016187v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:39,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:39,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:39,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg320c9a3c-a971-44a4-ab1d-b51eed2ffe42/dqc_reference/checkm_data
[2024-01-24 11:26:39,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:39,771] [INFO] Task started: CheckM
[2024-01-24 11:26:39,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161875.1_ASM3016187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161875.1_ASM3016187v1_genomic.fna/checkm_input GCF_030161875.1_ASM3016187v1_genomic.fna/checkm_result
[2024-01-24 11:27:32,338] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:32,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:32,363] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:32,363] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:32,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161875.1_ASM3016187v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:32,364] [INFO] Task started: Blastn
[2024-01-24 11:27:32,364] [INFO] Running command: blastn -query GCF_030161875.1_ASM3016187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg320c9a3c-a971-44a4-ab1d-b51eed2ffe42/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161875.1_ASM3016187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:34,696] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:34,701] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:34,701] [INFO] Target genome list was writen to GCF_030161875.1_ASM3016187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:34,709] [INFO] Task started: fastANI
[2024-01-24 11:27:34,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4fa7269-767d-4a34-bea8-940a5a836809/GCF_030161875.1_ASM3016187v1_genomic.fna.gz --refList GCF_030161875.1_ASM3016187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161875.1_ASM3016187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:41,012] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:41,028] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:41,028] [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_014483895.1	s__Protaetiibacter sp014483895	85.0855	739	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898835.1	s__Protaetiibacter sp001898835	84.8066	718	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003627075.1	s__Protaetiibacter intestinalis	84.7653	703	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	84.6837	636	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243275.1	s__Protaetiibacter sp003243275	84.1045	668	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365275.1	s__Protaetiibacter larvae	83.3494	591	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216815.1	s__Protaetiibacter sp004216815	83.2007	697	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017545.1	s__Protaetiibacter sp008017545	81.9337	585	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:41,030] [INFO] GTDB search result was written to GCF_030161875.1_ASM3016187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:41,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:41,038] [INFO] DFAST_QC result json was written to GCF_030161875.1_ASM3016187v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:41,038] [INFO] DFAST_QC completed!
[2024-01-24 11:27:41,038] [INFO] Total running time: 0h1m30s