[2024-01-25 18:16:05,903] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:05,904] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:05,905] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcf92ec6-8a34-4d0d-abc4-728b91d6083a/dqc_reference
[2024-01-25 18:16:07,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:07,064] [INFO] Task started: Prodigal
[2024-01-25 18:16:07,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg79bc8b81-8ba0-46de-9d7a-c3526d5f6d08/GCF_014779665.1_ASM1477966v1_genomic.fna.gz | prodigal -d GCF_014779665.1_ASM1477966v1_genomic.fna/cds.fna -a GCF_014779665.1_ASM1477966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:18,163] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:18,164] [INFO] Task started: HMMsearch
[2024-01-25 18:16:18,164] [INFO] Running command: hmmsearch --tblout GCF_014779665.1_ASM1477966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcf92ec6-8a34-4d0d-abc4-728b91d6083a/dqc_reference/reference_markers.hmm GCF_014779665.1_ASM1477966v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:18,516] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:18,517] [INFO] Found 6/6 markers.
[2024-01-25 18:16:18,562] [INFO] Query marker FASTA was written to GCF_014779665.1_ASM1477966v1_genomic.fna/markers.fasta
[2024-01-25 18:16:18,562] [INFO] Task started: Blastn
[2024-01-25 18:16:18,562] [INFO] Running command: blastn -query GCF_014779665.1_ASM1477966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcf92ec6-8a34-4d0d-abc4-728b91d6083a/dqc_reference/reference_markers.fasta -out GCF_014779665.1_ASM1477966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:19,788] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:19,791] [INFO] Selected 16 target genomes.
[2024-01-25 18:16:19,791] [INFO] Target genome list was writen to GCF_014779665.1_ASM1477966v1_genomic.fna/target_genomes.txt
[2024-01-25 18:16:19,804] [INFO] Task started: fastANI
[2024-01-25 18:16:19,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg79bc8b81-8ba0-46de-9d7a-c3526d5f6d08/GCF_014779665.1_ASM1477966v1_genomic.fna.gz --refList GCF_014779665.1_ASM1477966v1_genomic.fna/target_genomes.txt --output GCF_014779665.1_ASM1477966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:37,415] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:37,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcf92ec6-8a34-4d0d-abc4-728b91d6083a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:37,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcf92ec6-8a34-4d0d-abc4-728b91d6083a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:37,428] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:37,428] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:37,428] [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 hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	100.0	1464	1466	95	conclusive
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	87.2874	1146	1466	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	85.592	1022	1466	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	85.5281	1029	1466	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.5233	1041	1466	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	85.5178	968	1466	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	85.5147	999	1466	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	85.4387	995	1466	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	85.405	988	1466	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	85.3417	992	1466	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.334	1025	1466	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	85.2841	1019	1466	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	85.274	1024	1466	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	85.2208	935	1466	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	85.1973	949	1466	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	84.6091	960	1466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:37,429] [INFO] DFAST Taxonomy check result was written to GCF_014779665.1_ASM1477966v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:37,430] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:37,430] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:37,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcf92ec6-8a34-4d0d-abc4-728b91d6083a/dqc_reference/checkm_data
[2024-01-25 18:16:37,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:37,473] [INFO] Task started: CheckM
[2024-01-25 18:16:37,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014779665.1_ASM1477966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014779665.1_ASM1477966v1_genomic.fna/checkm_input GCF_014779665.1_ASM1477966v1_genomic.fna/checkm_result
[2024-01-25 18:17:41,304] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:41,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:41,345] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:41,345] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:41,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014779665.1_ASM1477966v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:41,347] [INFO] Task started: Blastn
[2024-01-25 18:17:41,347] [INFO] Running command: blastn -query GCF_014779665.1_ASM1477966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcf92ec6-8a34-4d0d-abc4-728b91d6083a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014779665.1_ASM1477966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:43,379] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:43,382] [INFO] Selected 18 target genomes.
[2024-01-25 18:17:43,382] [INFO] Target genome list was writen to GCF_014779665.1_ASM1477966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:43,396] [INFO] Task started: fastANI
[2024-01-25 18:17:43,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg79bc8b81-8ba0-46de-9d7a-c3526d5f6d08/GCF_014779665.1_ASM1477966v1_genomic.fna.gz --refList GCF_014779665.1_ASM1477966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014779665.1_ASM1477966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:18:03,262] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:03,274] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:18:03,274] [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_014779665.1	s__Nocardioides hwasunensis	100.0	1464	1466	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_900105585.1	s__Nocardioides exalbidus	87.2763	1147	1466	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	85.6016	943	1466	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	85.6011	953	1466	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	85.5374	1086	1466	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	85.5277	1041	1466	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	85.5208	997	1466	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	85.5044	1031	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014779655.1	s__Nocardioides ganghwensis	85.4642	993	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013155375.1	s__Nocardioides sp013155375	85.4431	1048	1466	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	85.407	989	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	85.3536	1030	1466	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	85.3376	992	1466	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	85.3142	1017	1466	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	85.2735	1020	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014653115.1	s__Nocardioides flavus	85.2537	932	1466	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	85.2409	966	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017872795.1	s__Nocardioides sp017872795	85.063	984	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:18:03,277] [INFO] GTDB search result was written to GCF_014779665.1_ASM1477966v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:18:03,277] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:18:03,289] [INFO] DFAST_QC result json was written to GCF_014779665.1_ASM1477966v1_genomic.fna/dqc_result.json
[2024-01-25 18:18:03,290] [INFO] DFAST_QC completed!
[2024-01-25 18:18:03,290] [INFO] Total running time: 0h1m57s