[2024-01-24 14:28:08,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,586] [INFO] DQC Reference Directory: /var/lib/cwl/stgfee77d43-5d4c-44b1-9455-cdbb957a787f/dqc_reference
[2024-01-24 14:28:10,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,416] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg96b5f95a-8054-40a5-aed5-b91b28db2b62/GCF_007992395.1_ASM799239v1_genomic.fna.gz | prodigal -d GCF_007992395.1_ASM799239v1_genomic.fna/cds.fna -a GCF_007992395.1_ASM799239v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:23,123] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:23,123] [INFO] Task started: HMMsearch
[2024-01-24 14:28:23,123] [INFO] Running command: hmmsearch --tblout GCF_007992395.1_ASM799239v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfee77d43-5d4c-44b1-9455-cdbb957a787f/dqc_reference/reference_markers.hmm GCF_007992395.1_ASM799239v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:23,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:23,428] [INFO] Found 6/6 markers.
[2024-01-24 14:28:23,509] [INFO] Query marker FASTA was written to GCF_007992395.1_ASM799239v1_genomic.fna/markers.fasta
[2024-01-24 14:28:23,509] [INFO] Task started: Blastn
[2024-01-24 14:28:23,509] [INFO] Running command: blastn -query GCF_007992395.1_ASM799239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee77d43-5d4c-44b1-9455-cdbb957a787f/dqc_reference/reference_markers.fasta -out GCF_007992395.1_ASM799239v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:24,916] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:24,919] [INFO] Selected 11 target genomes.
[2024-01-24 14:28:24,920] [INFO] Target genome list was writen to GCF_007992395.1_ASM799239v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:24,931] [INFO] Task started: fastANI
[2024-01-24 14:28:24,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b5f95a-8054-40a5-aed5-b91b28db2b62/GCF_007992395.1_ASM799239v1_genomic.fna.gz --refList GCF_007992395.1_ASM799239v1_genomic.fna/target_genomes.txt --output GCF_007992395.1_ASM799239v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:36,950] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:36,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfee77d43-5d4c-44b1-9455-cdbb957a787f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:36,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfee77d43-5d4c-44b1-9455-cdbb957a787f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:36,968] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:36,968] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:36,969] [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 szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	100.0	1383	1386	95	conclusive
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	99.9881	1386	1386	95	conclusive
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	85.2001	970	1386	95	below_threshold
Nocardioides psychrotolerans	strain=CGMCC 1.11156	GCA_900113685.1	1005945	1005945	type	True	84.1027	982	1386	95	below_threshold
Nocardioides psychrotolerans	strain=NBRC 108563	GCA_007992415.1	1005945	1005945	type	True	84.0993	975	1386	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	82.4943	850	1386	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	81.02	675	1386	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.7023	640	1386	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.4556	716	1386	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.4276	749	1386	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.0253	675	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:36,978] [INFO] DFAST Taxonomy check result was written to GCF_007992395.1_ASM799239v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:36,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:36,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:36,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfee77d43-5d4c-44b1-9455-cdbb957a787f/dqc_reference/checkm_data
[2024-01-24 14:28:36,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:37,044] [INFO] Task started: CheckM
[2024-01-24 14:28:37,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992395.1_ASM799239v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992395.1_ASM799239v1_genomic.fna/checkm_input GCF_007992395.1_ASM799239v1_genomic.fna/checkm_result
[2024-01-24 14:29:35,202] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:35,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:35,225] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:35,225] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:35,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992395.1_ASM799239v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:35,226] [INFO] Task started: Blastn
[2024-01-24 14:29:35,226] [INFO] Running command: blastn -query GCF_007992395.1_ASM799239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee77d43-5d4c-44b1-9455-cdbb957a787f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992395.1_ASM799239v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:37,229] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:37,233] [INFO] Selected 15 target genomes.
[2024-01-24 14:29:37,233] [INFO] Target genome list was writen to GCF_007992395.1_ASM799239v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:37,246] [INFO] Task started: fastANI
[2024-01-24 14:29:37,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b5f95a-8054-40a5-aed5-b91b28db2b62/GCF_007992395.1_ASM799239v1_genomic.fna.gz --refList GCF_007992395.1_ASM799239v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992395.1_ASM799239v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:53,125] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:53,138] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:53,138] [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_900103935.1	s__Nocardioides szechwanensis	99.9881	1386	1386	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_004522095.1	s__Nocardioides sp004522095	85.3	999	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015024225.1	s__Nocardioides sp015024225	85.1894	971	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_900113685.1	s__Nocardioides psychrotolerans	84.076	985	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	82.7871	843	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_014127485.1	s__Nocardioides sp014127485	82.5013	849	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_013177455.1	s__Nocardioides sp013177455	82.0829	834	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_011250565.1	s__Nocardioides sp011250565	82.0124	820	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346395.1	s__Nocardioides plantarum	81.9808	829	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087085.1	s__Nocardioides rubriscoriae	81.8579	873	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070375.1	s__Nocardioides kribbensis	81.8118	774	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_004522105.1	s__Nocardioides sp004522105	81.7807	824	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	81.7694	805	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001429625.1	s__Nocardioides sp001429625	81.3648	744	1386	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698575.1	s__Nocardioides sp002698575	80.9811	694	1386	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 14:29:53,140] [INFO] GTDB search result was written to GCF_007992395.1_ASM799239v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:53,141] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:53,146] [INFO] DFAST_QC result json was written to GCF_007992395.1_ASM799239v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:53,147] [INFO] DFAST_QC completed!
[2024-01-24 14:29:53,147] [INFO] Total running time: 0h1m45s