[2024-01-24 14:54:55,229] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:55,231] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:55,231] [INFO] DQC Reference Directory: /var/lib/cwl/stgad32fa2a-edf6-46b2-a3df-47abb7d9470f/dqc_reference
[2024-01-24 14:54:56,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:56,563] [INFO] Task started: Prodigal
[2024-01-24 14:54:56,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg1da65850-0cc9-40bd-be44-cf4f4befd6bf/GCF_015024225.1_ASM1502422v1_genomic.fna.gz | prodigal -d GCF_015024225.1_ASM1502422v1_genomic.fna/cds.fna -a GCF_015024225.1_ASM1502422v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:09,087] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:09,087] [INFO] Task started: HMMsearch
[2024-01-24 14:55:09,088] [INFO] Running command: hmmsearch --tblout GCF_015024225.1_ASM1502422v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad32fa2a-edf6-46b2-a3df-47abb7d9470f/dqc_reference/reference_markers.hmm GCF_015024225.1_ASM1502422v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:09,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:09,405] [INFO] Found 6/6 markers.
[2024-01-24 14:55:09,448] [INFO] Query marker FASTA was written to GCF_015024225.1_ASM1502422v1_genomic.fna/markers.fasta
[2024-01-24 14:55:09,449] [INFO] Task started: Blastn
[2024-01-24 14:55:09,449] [INFO] Running command: blastn -query GCF_015024225.1_ASM1502422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad32fa2a-edf6-46b2-a3df-47abb7d9470f/dqc_reference/reference_markers.fasta -out GCF_015024225.1_ASM1502422v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:10,805] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:10,811] [INFO] Selected 14 target genomes.
[2024-01-24 14:55:10,812] [INFO] Target genome list was writen to GCF_015024225.1_ASM1502422v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:10,820] [INFO] Task started: fastANI
[2024-01-24 14:55:10,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg1da65850-0cc9-40bd-be44-cf4f4befd6bf/GCF_015024225.1_ASM1502422v1_genomic.fna.gz --refList GCF_015024225.1_ASM1502422v1_genomic.fna/target_genomes.txt --output GCF_015024225.1_ASM1502422v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:27,340] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:27,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad32fa2a-edf6-46b2-a3df-47abb7d9470f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:27,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad32fa2a-edf6-46b2-a3df-47abb7d9470f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:27,352] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:27,353] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:27,353] [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 lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	100.0	1545	1561	95	conclusive
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	85.0777	974	1561	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	85.0321	997	1561	95	below_threshold
Nocardioides psychrotolerans	strain=NBRC 108563	GCA_007992415.1	1005945	1005945	type	True	83.7694	919	1561	95	below_threshold
Nocardioides psychrotolerans	strain=CGMCC 1.11156	GCA_900113685.1	1005945	1005945	type	True	83.6723	937	1561	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	82.062	815	1561	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	81.9591	917	1561	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	81.9541	827	1561	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	81.6139	875	1561	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.8765	792	1561	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.5236	665	1561	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.3101	690	1561	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.1143	795	1561	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.9781	722	1561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:27,354] [INFO] DFAST Taxonomy check result was written to GCF_015024225.1_ASM1502422v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:27,355] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:27,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:27,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad32fa2a-edf6-46b2-a3df-47abb7d9470f/dqc_reference/checkm_data
[2024-01-24 14:55:27,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:27,412] [INFO] Task started: CheckM
[2024-01-24 14:55:27,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015024225.1_ASM1502422v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015024225.1_ASM1502422v1_genomic.fna/checkm_input GCF_015024225.1_ASM1502422v1_genomic.fna/checkm_result
[2024-01-24 14:56:28,024] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:28,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:28,043] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:28,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:28,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015024225.1_ASM1502422v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:28,044] [INFO] Task started: Blastn
[2024-01-24 14:56:28,044] [INFO] Running command: blastn -query GCF_015024225.1_ASM1502422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad32fa2a-edf6-46b2-a3df-47abb7d9470f/dqc_reference/reference_markers_gtdb.fasta -out GCF_015024225.1_ASM1502422v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:30,053] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:30,057] [INFO] Selected 14 target genomes.
[2024-01-24 14:56:30,058] [INFO] Target genome list was writen to GCF_015024225.1_ASM1502422v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:30,082] [INFO] Task started: fastANI
[2024-01-24 14:56:30,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg1da65850-0cc9-40bd-be44-cf4f4befd6bf/GCF_015024225.1_ASM1502422v1_genomic.fna.gz --refList GCF_015024225.1_ASM1502422v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015024225.1_ASM1502422v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:47,227] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:47,239] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:47,239] [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_015024225.1	s__Nocardioides sp015024225	100.0	1547	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	conclusive
GCF_004522095.1	s__Nocardioides sp004522095	90.9891	1320	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103935.1	s__Nocardioides szechwanensis	85.0281	997	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900113685.1	s__Nocardioides psychrotolerans	83.6594	940	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014127485.1	s__Nocardioides sp014127485	82.6879	874	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_014212315.1	s__Nocardioides luti	82.5209	851	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117935.1	s__Nocardioides sp002117935	82.2246	828	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014266025.1	s__Nocardioides deserti	82.13	860	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	82.0392	995	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006346395.1	s__Nocardioides plantarum	81.9294	921	1561	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	81.9227	827	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_011420305.2	s__Nocardioides sp011420305	81.523	790	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_006346315.1	s__Nocardioides litoris	81.5206	886	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	81.4899	935	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:47,241] [INFO] GTDB search result was written to GCF_015024225.1_ASM1502422v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:47,241] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:47,245] [INFO] DFAST_QC result json was written to GCF_015024225.1_ASM1502422v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:47,245] [INFO] DFAST_QC completed!
[2024-01-24 14:56:47,245] [INFO] Total running time: 0h1m52s