[2024-01-25 20:15:35,849] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:35,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:35,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d7574fd-da6d-46d5-af11-f74dbe4a6f04/dqc_reference
[2024-01-25 20:15:36,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:36,983] [INFO] Task started: Prodigal
[2024-01-25 20:15:36,983] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf6ab96c-8b64-4868-a8b0-54f983053af6/GCF_016735675.1_ASM1673567v1_genomic.fna.gz | prodigal -d GCF_016735675.1_ASM1673567v1_genomic.fna/cds.fna -a GCF_016735675.1_ASM1673567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:47,535] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:47,535] [INFO] Task started: HMMsearch
[2024-01-25 20:15:47,535] [INFO] Running command: hmmsearch --tblout GCF_016735675.1_ASM1673567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d7574fd-da6d-46d5-af11-f74dbe4a6f04/dqc_reference/reference_markers.hmm GCF_016735675.1_ASM1673567v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:47,751] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:47,752] [INFO] Found 6/6 markers.
[2024-01-25 20:15:47,788] [INFO] Query marker FASTA was written to GCF_016735675.1_ASM1673567v1_genomic.fna/markers.fasta
[2024-01-25 20:15:47,789] [INFO] Task started: Blastn
[2024-01-25 20:15:47,789] [INFO] Running command: blastn -query GCF_016735675.1_ASM1673567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d7574fd-da6d-46d5-af11-f74dbe4a6f04/dqc_reference/reference_markers.fasta -out GCF_016735675.1_ASM1673567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:48,969] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:48,971] [INFO] Selected 14 target genomes.
[2024-01-25 20:15:48,971] [INFO] Target genome list was writen to GCF_016735675.1_ASM1673567v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:48,976] [INFO] Task started: fastANI
[2024-01-25 20:15:48,976] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf6ab96c-8b64-4868-a8b0-54f983053af6/GCF_016735675.1_ASM1673567v1_genomic.fna.gz --refList GCF_016735675.1_ASM1673567v1_genomic.fna/target_genomes.txt --output GCF_016735675.1_ASM1673567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:05,194] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:05,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d7574fd-da6d-46d5-af11-f74dbe4a6f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:05,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d7574fd-da6d-46d5-af11-f74dbe4a6f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:05,205] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:16:05,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:05,205] [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
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	100.0	1405	1406	95	conclusive
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	90.0994	1170	1406	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	87.4618	1116	1406	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	86.0252	1065	1406	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	86.0107	1080	1406	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	85.9435	1087	1406	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	85.9355	1009	1406	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	85.7657	1065	1406	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	85.7214	1061	1406	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	85.7058	979	1406	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.6312	1051	1406	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	85.6149	1041	1406	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	85.555	1027	1406	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	85.4876	1041	1406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:05,214] [INFO] DFAST Taxonomy check result was written to GCF_016735675.1_ASM1673567v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:05,214] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:05,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:05,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d7574fd-da6d-46d5-af11-f74dbe4a6f04/dqc_reference/checkm_data
[2024-01-25 20:16:05,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:05,257] [INFO] Task started: CheckM
[2024-01-25 20:16:05,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016735675.1_ASM1673567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016735675.1_ASM1673567v1_genomic.fna/checkm_input GCF_016735675.1_ASM1673567v1_genomic.fna/checkm_result
[2024-01-25 20:17:05,253] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:05,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:05,295] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:05,295] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:05,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016735675.1_ASM1673567v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:05,297] [INFO] Task started: Blastn
[2024-01-25 20:17:05,297] [INFO] Running command: blastn -query GCF_016735675.1_ASM1673567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d7574fd-da6d-46d5-af11-f74dbe4a6f04/dqc_reference/reference_markers_gtdb.fasta -out GCF_016735675.1_ASM1673567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:07,465] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:07,469] [INFO] Selected 16 target genomes.
[2024-01-25 20:17:07,469] [INFO] Target genome list was writen to GCF_016735675.1_ASM1673567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:07,512] [INFO] Task started: fastANI
[2024-01-25 20:17:07,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf6ab96c-8b64-4868-a8b0-54f983053af6/GCF_016735675.1_ASM1673567v1_genomic.fna.gz --refList GCF_016735675.1_ASM1673567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016735675.1_ASM1673567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:25,758] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:25,768] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:25,768] [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_016735675.1	s__Nocardioides sp016735675	100.0	1405	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004137245.1	s__Nocardioides glacieisoli	90.0728	1172	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137345.1	s__Nocardioides sp004137345	87.462	1116	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428125.1	s__Nocardioides sp001428125	86.1265	1003	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699265.1	s__Nocardioides sp009699265	86.0973	991	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112035.1	s__Nocardioides alpinus	86.0041	1081	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900105585.1	s__Nocardioides exalbidus	85.9542	1086	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137255.1	s__Nocardioides oleivorans	85.9198	1055	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017310035.1	s__Nocardioides sp017310035	85.8168	1026	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907475.1	s__Nocardioides cavernae	85.7236	1061	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003633575.1	s__Nocardioides sp003633575	85.7214	1069	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425025.1	s__Nocardioides sp001425025	85.6084	1046	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410035.1	s__Nocardioides cavernae_A	85.5885	1056	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785795.1	s__Nocardioides eburneiflavus	85.5359	1028	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779665.1	s__Nocardioides hwasunensis	85.4984	1040	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086465.1	s__Nocardioides sp014265965	85.1407	976	1406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:25,770] [INFO] GTDB search result was written to GCF_016735675.1_ASM1673567v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:25,772] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:25,778] [INFO] DFAST_QC result json was written to GCF_016735675.1_ASM1673567v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:25,778] [INFO] DFAST_QC completed!
[2024-01-25 20:17:25,778] [INFO] Total running time: 0h1m50s