[2024-01-24 11:51:23,821] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,823] [INFO] DQC Reference Directory: /var/lib/cwl/stgf645136c-30a2-4990-ba20-cd1abb08a1e8/dqc_reference
[2024-01-24 11:51:25,190] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,196] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,196] [INFO] Running command: gunzip -c /var/lib/cwl/stgde7beea8-4e61-4064-baea-ec9bc4ed9ac9/GCF_021083255.1_ASM2108325v1_genomic.fna.gz | prodigal -d GCF_021083255.1_ASM2108325v1_genomic.fna/cds.fna -a GCF_021083255.1_ASM2108325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:38,448] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:38,449] [INFO] Task started: HMMsearch
[2024-01-24 11:51:38,449] [INFO] Running command: hmmsearch --tblout GCF_021083255.1_ASM2108325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf645136c-30a2-4990-ba20-cd1abb08a1e8/dqc_reference/reference_markers.hmm GCF_021083255.1_ASM2108325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:38,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:38,758] [INFO] Found 6/6 markers.
[2024-01-24 11:51:38,800] [INFO] Query marker FASTA was written to GCF_021083255.1_ASM2108325v1_genomic.fna/markers.fasta
[2024-01-24 11:51:38,800] [INFO] Task started: Blastn
[2024-01-24 11:51:38,801] [INFO] Running command: blastn -query GCF_021083255.1_ASM2108325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf645136c-30a2-4990-ba20-cd1abb08a1e8/dqc_reference/reference_markers.fasta -out GCF_021083255.1_ASM2108325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:40,072] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:40,078] [INFO] Selected 13 target genomes.
[2024-01-24 11:51:40,079] [INFO] Target genome list was writen to GCF_021083255.1_ASM2108325v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:40,082] [INFO] Task started: fastANI
[2024-01-24 11:51:40,083] [INFO] Running command: fastANI --query /var/lib/cwl/stgde7beea8-4e61-4064-baea-ec9bc4ed9ac9/GCF_021083255.1_ASM2108325v1_genomic.fna.gz --refList GCF_021083255.1_ASM2108325v1_genomic.fna/target_genomes.txt --output GCF_021083255.1_ASM2108325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:55,132] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:55,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf645136c-30a2-4990-ba20-cd1abb08a1e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:55,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf645136c-30a2-4990-ba20-cd1abb08a1e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:55,149] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:55,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:55,150] [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 alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	99.9903	1514	1528	95	conclusive
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	99.9892	1521	1528	95	conclusive
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	86.9427	1096	1528	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	86.3756	1036	1528	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	86.2767	1041	1528	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	86.1601	1093	1528	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.9939	1077	1528	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	85.8638	1041	1528	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	85.758	1058	1528	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	85.6494	1064	1528	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	85.6028	1065	1528	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	85.2276	1016	1528	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.1673	1048	1528	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:55,153] [INFO] DFAST Taxonomy check result was written to GCF_021083255.1_ASM2108325v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:55,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:55,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:55,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf645136c-30a2-4990-ba20-cd1abb08a1e8/dqc_reference/checkm_data
[2024-01-24 11:51:55,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:55,209] [INFO] Task started: CheckM
[2024-01-24 11:51:55,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021083255.1_ASM2108325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021083255.1_ASM2108325v1_genomic.fna/checkm_input GCF_021083255.1_ASM2108325v1_genomic.fna/checkm_result
[2024-01-24 11:53:06,995] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:06,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:07,019] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:07,019] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:07,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021083255.1_ASM2108325v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:07,020] [INFO] Task started: Blastn
[2024-01-24 11:53:07,020] [INFO] Running command: blastn -query GCF_021083255.1_ASM2108325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf645136c-30a2-4990-ba20-cd1abb08a1e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_021083255.1_ASM2108325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:09,022] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:09,026] [INFO] Selected 14 target genomes.
[2024-01-24 11:53:09,026] [INFO] Target genome list was writen to GCF_021083255.1_ASM2108325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:09,033] [INFO] Task started: fastANI
[2024-01-24 11:53:09,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgde7beea8-4e61-4064-baea-ec9bc4ed9ac9/GCF_021083255.1_ASM2108325v1_genomic.fna.gz --refList GCF_021083255.1_ASM2108325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021083255.1_ASM2108325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:24,829] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:24,848] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:24,848] [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_900112035.1	s__Nocardioides alpinus	99.9892	1521	1528	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_017872795.1	s__Nocardioides sp017872795	87.1164	1065	1528	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	86.9372	1097	1528	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	86.2112	1042	1528	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137245.1	s__Nocardioides glacieisoli	86.1698	1092	1528	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735675.1	s__Nocardioides sp016735675	85.994	1077	1528	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	85.9882	992	1528	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779655.1	s__Nocardioides ganghwensis	85.758	1058	1528	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907475.1	s__Nocardioides cavernae	85.6151	1064	1528	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105585.1	s__Nocardioides exalbidus	85.4585	1055	1528	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	85.3362	1054	1528	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	85.2149	1018	1528	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	85.0778	968	1528	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017916455.1	s__Nocardioides sp017916455	84.7751	935	1528	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:24,850] [INFO] GTDB search result was written to GCF_021083255.1_ASM2108325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:24,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:24,854] [INFO] DFAST_QC result json was written to GCF_021083255.1_ASM2108325v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:24,854] [INFO] DFAST_QC completed!
[2024-01-24 11:53:24,855] [INFO] Total running time: 0h2m1s