[2024-01-24 13:22:16,741] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:16,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:16,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ebecc83-0933-449b-b500-0140db72d0e1/dqc_reference
[2024-01-24 13:22:18,112] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:18,113] [INFO] Task started: Prodigal
[2024-01-24 13:22:18,113] [INFO] Running command: gunzip -c /var/lib/cwl/stg16a95624-fc6a-4961-a3d4-805ebb3993db/GCF_006007965.1_ASM600796v1_genomic.fna.gz | prodigal -d GCF_006007965.1_ASM600796v1_genomic.fna/cds.fna -a GCF_006007965.1_ASM600796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:28,889] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:28,890] [INFO] Task started: HMMsearch
[2024-01-24 13:22:28,890] [INFO] Running command: hmmsearch --tblout GCF_006007965.1_ASM600796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ebecc83-0933-449b-b500-0140db72d0e1/dqc_reference/reference_markers.hmm GCF_006007965.1_ASM600796v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:29,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:29,214] [INFO] Found 6/6 markers.
[2024-01-24 13:22:29,244] [INFO] Query marker FASTA was written to GCF_006007965.1_ASM600796v1_genomic.fna/markers.fasta
[2024-01-24 13:22:29,245] [INFO] Task started: Blastn
[2024-01-24 13:22:29,245] [INFO] Running command: blastn -query GCF_006007965.1_ASM600796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ebecc83-0933-449b-b500-0140db72d0e1/dqc_reference/reference_markers.fasta -out GCF_006007965.1_ASM600796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:30,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:30,573] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:30,573] [INFO] Target genome list was writen to GCF_006007965.1_ASM600796v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:30,584] [INFO] Task started: fastANI
[2024-01-24 13:22:30,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg16a95624-fc6a-4961-a3d4-805ebb3993db/GCF_006007965.1_ASM600796v1_genomic.fna.gz --refList GCF_006007965.1_ASM600796v1_genomic.fna/target_genomes.txt --output GCF_006007965.1_ASM600796v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:43,572] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:43,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ebecc83-0933-449b-b500-0140db72d0e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:43,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ebecc83-0933-449b-b500-0140db72d0e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:43,586] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:43,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:43,586] [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 jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	100.0	1178	1178	95	conclusive
Nocardioides daphniae	strain=CCM 7403	GCA_014635145.1	402297	402297	type	True	87.251	925	1178	95	below_threshold
Nocardioides daphniae	strain=JCM 16608	GCA_004777465.1	402297	402297	type	True	87.2126	919	1178	95	below_threshold
Nocardioides malaquae	strain=Y6	GCA_015070385.1	2773426	2773426	type	True	83.6588	752	1178	95	below_threshold
Nocardioides gilvus	strain=XZ17	GCA_003194605.1	1735589	1735589	type	True	81.9922	735	1178	95	below_threshold
Nocardioides yefusunii	strain=HY056	GCA_004014875.1	2500546	2500546	type	True	81.3604	629	1178	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	81.2813	641	1178	95	below_threshold
Nocardioides houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	80.9017	640	1178	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.4737	586	1178	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.4278	577	1178	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	80.3785	541	1178	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	80.3618	581	1178	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.1439	565	1178	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.1429	579	1178	95	below_threshold
Nocardioides daejeonensis	strain=MJ31	GCA_003194585.1	1046556	1046556	type	True	79.6059	469	1178	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:43,594] [INFO] DFAST Taxonomy check result was written to GCF_006007965.1_ASM600796v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:43,595] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:43,595] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:43,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ebecc83-0933-449b-b500-0140db72d0e1/dqc_reference/checkm_data
[2024-01-24 13:22:43,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:43,638] [INFO] Task started: CheckM
[2024-01-24 13:22:43,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006007965.1_ASM600796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006007965.1_ASM600796v1_genomic.fna/checkm_input GCF_006007965.1_ASM600796v1_genomic.fna/checkm_result
[2024-01-24 13:24:00,943] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:00,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:00,968] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:00,968] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:00,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006007965.1_ASM600796v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:00,969] [INFO] Task started: Blastn
[2024-01-24 13:24:00,969] [INFO] Running command: blastn -query GCF_006007965.1_ASM600796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ebecc83-0933-449b-b500-0140db72d0e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_006007965.1_ASM600796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:03,192] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:03,196] [INFO] Selected 18 target genomes.
[2024-01-24 13:24:03,196] [INFO] Target genome list was writen to GCF_006007965.1_ASM600796v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:03,241] [INFO] Task started: fastANI
[2024-01-24 13:24:03,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg16a95624-fc6a-4961-a3d4-805ebb3993db/GCF_006007965.1_ASM600796v1_genomic.fna.gz --refList GCF_006007965.1_ASM600796v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006007965.1_ASM600796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:19,327] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:19,347] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:19,347] [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_006007965.1	s__Nocardioides sp006007965	100.0	1178	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004777465.1	s__Nocardioides daphniae	87.2264	918	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.94	99.94	1.00	1.00	2	-
GCF_003194605.1	s__Nocardioides gilvus	81.9724	737	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004014875.1	s__Nocardioides sp004014875	81.3497	630	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003194625.1	s__Nocardioides solisilvae	81.2605	643	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013624435.2	s__Nocardioides sp013624415	81.1512	687	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.04	99.04	0.95	0.95	2	-
GCF_002865585.1	s__Nocardioides houyundeii	80.8697	640	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	96.00	0.92	0.88	3	-
GCF_011420305.2	s__Nocardioides sp011420305	80.6406	607	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_001429625.1	s__Nocardioides sp001429625	80.5772	603	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155365.1	s__Nocardioides sp013155365	80.5731	612	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047295.1	s__Nocardioides sediminis	80.4997	574	1178	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	80.4195	578	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	80.3582	543	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155375.1	s__Nocardioides sp013155375	80.2562	568	1178	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	80.133	580	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620705.1	s__Nocardioides sp000620705	79.9611	560	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919105.1	s__Nocardioides sp004919105	79.8022	523	1178	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194585.1	s__Nocardioides daejeonensis	79.6046	470	1178	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 13:24:19,349] [INFO] GTDB search result was written to GCF_006007965.1_ASM600796v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:19,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:19,353] [INFO] DFAST_QC result json was written to GCF_006007965.1_ASM600796v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:19,353] [INFO] DFAST_QC completed!
[2024-01-24 13:24:19,353] [INFO] Total running time: 0h2m3s