[2024-01-24 13:49:28,664] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:28,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:28,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg2eaa49ba-ea25-4e9d-8ec7-b52ad7db6bf1/dqc_reference
[2024-01-24 13:49:29,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:29,930] [INFO] Task started: Prodigal
[2024-01-24 13:49:29,930] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe8ea9cd-898a-42b3-bc90-156e0bf45f58/GCF_004785795.1_ASM478579v1_genomic.fna.gz | prodigal -d GCF_004785795.1_ASM478579v1_genomic.fna/cds.fna -a GCF_004785795.1_ASM478579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:44,427] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:44,427] [INFO] Task started: HMMsearch
[2024-01-24 13:49:44,427] [INFO] Running command: hmmsearch --tblout GCF_004785795.1_ASM478579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2eaa49ba-ea25-4e9d-8ec7-b52ad7db6bf1/dqc_reference/reference_markers.hmm GCF_004785795.1_ASM478579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:44,740] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:44,741] [INFO] Found 6/6 markers.
[2024-01-24 13:49:44,792] [INFO] Query marker FASTA was written to GCF_004785795.1_ASM478579v1_genomic.fna/markers.fasta
[2024-01-24 13:49:44,793] [INFO] Task started: Blastn
[2024-01-24 13:49:44,793] [INFO] Running command: blastn -query GCF_004785795.1_ASM478579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2eaa49ba-ea25-4e9d-8ec7-b52ad7db6bf1/dqc_reference/reference_markers.fasta -out GCF_004785795.1_ASM478579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:46,107] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:46,110] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:46,111] [INFO] Target genome list was writen to GCF_004785795.1_ASM478579v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:46,116] [INFO] Task started: fastANI
[2024-01-24 13:49:46,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe8ea9cd-898a-42b3-bc90-156e0bf45f58/GCF_004785795.1_ASM478579v1_genomic.fna.gz --refList GCF_004785795.1_ASM478579v1_genomic.fna/target_genomes.txt --output GCF_004785795.1_ASM478579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:01,089] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:01,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2eaa49ba-ea25-4e9d-8ec7-b52ad7db6bf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:01,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2eaa49ba-ea25-4e9d-8ec7-b52ad7db6bf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:01,100] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:01,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:01,101] [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 eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	100.0	1661	1665	95	conclusive
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	91.3584	1212	1665	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	88.6294	1063	1665	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	86.5275	1084	1665	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	86.4177	1089	1665	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	86.2853	1057	1665	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	86.2135	1011	1665	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	85.6168	1023	1665	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.5416	1060	1665	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	85.4775	1057	1665	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.4444	1041	1665	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	85.1783	1014	1665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:01,103] [INFO] DFAST Taxonomy check result was written to GCF_004785795.1_ASM478579v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:01,104] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:01,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:01,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2eaa49ba-ea25-4e9d-8ec7-b52ad7db6bf1/dqc_reference/checkm_data
[2024-01-24 13:50:01,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:01,158] [INFO] Task started: CheckM
[2024-01-24 13:50:01,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004785795.1_ASM478579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004785795.1_ASM478579v1_genomic.fna/checkm_input GCF_004785795.1_ASM478579v1_genomic.fna/checkm_result
[2024-01-24 13:51:38,081] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:38,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:38,109] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:38,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:38,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004785795.1_ASM478579v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:38,111] [INFO] Task started: Blastn
[2024-01-24 13:51:38,111] [INFO] Running command: blastn -query GCF_004785795.1_ASM478579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2eaa49ba-ea25-4e9d-8ec7-b52ad7db6bf1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004785795.1_ASM478579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:40,220] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:40,224] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:40,224] [INFO] Target genome list was writen to GCF_004785795.1_ASM478579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:40,246] [INFO] Task started: fastANI
[2024-01-24 13:51:40,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe8ea9cd-898a-42b3-bc90-156e0bf45f58/GCF_004785795.1_ASM478579v1_genomic.fna.gz --refList GCF_004785795.1_ASM478579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004785795.1_ASM478579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:57,667] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:57,682] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:57,682] [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_004785795.1	s__Nocardioides eburneiflavus	100.0	1661	1665	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_014779655.1	s__Nocardioides ganghwensis	91.3584	1212	1665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014653115.1	s__Nocardioides flavus	88.656	1061	1665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155335.1	s__Nocardioides sp013155335	86.6322	1088	1665	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	86.5133	1086	1665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017310035.1	s__Nocardioides sp017310035	86.4491	1058	1665	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	86.4199	1032	1665	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	86.129	988	1665	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	86.0743	987	1665	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	85.8349	943	1665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_900105585.1	s__Nocardioides exalbidus	85.582	1026	1665	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	85.5086	1017	1665	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	85.4776	1057	1665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016735675.1	s__Nocardioides sp016735675	85.4347	1041	1665	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	85.1664	1015	1665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:57,684] [INFO] GTDB search result was written to GCF_004785795.1_ASM478579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:57,684] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:57,688] [INFO] DFAST_QC result json was written to GCF_004785795.1_ASM478579v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:57,688] [INFO] DFAST_QC completed!
[2024-01-24 13:51:57,688] [INFO] Total running time: 0h2m29s