[2024-01-24 11:51:11,364] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg9574701d-c307-42ed-b801-d0a110245554/dqc_reference
[2024-01-24 11:51:12,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,909] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg23c1ff61-87d8-4073-a9ca-bc573faedf39/GCF_008087085.1_ASM808708v1_genomic.fna.gz | prodigal -d GCF_008087085.1_ASM808708v1_genomic.fna/cds.fna -a GCF_008087085.1_ASM808708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:26,435] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:26,435] [INFO] Task started: HMMsearch
[2024-01-24 11:51:26,435] [INFO] Running command: hmmsearch --tblout GCF_008087085.1_ASM808708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9574701d-c307-42ed-b801-d0a110245554/dqc_reference/reference_markers.hmm GCF_008087085.1_ASM808708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:26,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:26,716] [INFO] Found 6/6 markers.
[2024-01-24 11:51:26,758] [INFO] Query marker FASTA was written to GCF_008087085.1_ASM808708v1_genomic.fna/markers.fasta
[2024-01-24 11:51:26,758] [INFO] Task started: Blastn
[2024-01-24 11:51:26,758] [INFO] Running command: blastn -query GCF_008087085.1_ASM808708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9574701d-c307-42ed-b801-d0a110245554/dqc_reference/reference_markers.fasta -out GCF_008087085.1_ASM808708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:27,996] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:28,002] [INFO] Selected 20 target genomes.
[2024-01-24 11:51:28,002] [INFO] Target genome list was writen to GCF_008087085.1_ASM808708v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:28,010] [INFO] Task started: fastANI
[2024-01-24 11:51:28,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c1ff61-87d8-4073-a9ca-bc573faedf39/GCF_008087085.1_ASM808708v1_genomic.fna.gz --refList GCF_008087085.1_ASM808708v1_genomic.fna/target_genomes.txt --output GCF_008087085.1_ASM808708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:53,538] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:53,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9574701d-c307-42ed-b801-d0a110245554/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:53,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9574701d-c307-42ed-b801-d0a110245554/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:53,554] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:53,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:53,554] [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 rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	100.0	1589	1593	95	conclusive
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	86.2685	1069	1593	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	84.2015	1048	1593	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	82.0584	881	1593	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	81.9648	850	1593	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.8824	865	1593	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	81.8546	871	1593	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.7892	859	1593	95	below_threshold
Nocardioides psychrotolerans	strain=NBRC 108563	GCA_007992415.1	1005945	1005945	type	True	81.627	879	1593	95	below_threshold
Nocardioides psychrotolerans	strain=CGMCC 1.11156	GCA_900113685.1	1005945	1005945	type	True	81.6252	884	1593	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	81.395	807	1593	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	81.3553	916	1593	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	81.3535	911	1593	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	81.3185	833	1593	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.8567	742	1593	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	80.7556	741	1593	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.6678	774	1593	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.6344	785	1593	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.4502	741	1593	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.1042	651	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:53,563] [INFO] DFAST Taxonomy check result was written to GCF_008087085.1_ASM808708v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:53,563] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:53,564] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:53,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9574701d-c307-42ed-b801-d0a110245554/dqc_reference/checkm_data
[2024-01-24 11:51:53,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:53,610] [INFO] Task started: CheckM
[2024-01-24 11:51:53,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008087085.1_ASM808708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008087085.1_ASM808708v1_genomic.fna/checkm_input GCF_008087085.1_ASM808708v1_genomic.fna/checkm_result
[2024-01-24 11:52:56,512] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:56,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:56,530] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:56,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:56,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008087085.1_ASM808708v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:56,531] [INFO] Task started: Blastn
[2024-01-24 11:52:56,531] [INFO] Running command: blastn -query GCF_008087085.1_ASM808708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9574701d-c307-42ed-b801-d0a110245554/dqc_reference/reference_markers_gtdb.fasta -out GCF_008087085.1_ASM808708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:58,476] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:58,481] [INFO] Selected 13 target genomes.
[2024-01-24 11:52:58,481] [INFO] Target genome list was writen to GCF_008087085.1_ASM808708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:58,489] [INFO] Task started: fastANI
[2024-01-24 11:52:58,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c1ff61-87d8-4073-a9ca-bc573faedf39/GCF_008087085.1_ASM808708v1_genomic.fna.gz --refList GCF_008087085.1_ASM808708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008087085.1_ASM808708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:15,322] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:15,333] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:15,333] [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_008087085.1	s__Nocardioides rubriscoriae	100.0	1589	1593	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_006346395.1	s__Nocardioides plantarum	86.2384	1072	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346315.1	s__Nocardioides litoris	84.1645	1053	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005954645.2	s__Nocardioides dongxiaopingii	83.7402	980	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.98	98.98	0.96	0.96	2	-
GCF_004522105.1	s__Nocardioides sp004522105	83.5236	971	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522095.1	s__Nocardioides sp004522095	82.1325	895	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250565.1	s__Nocardioides sp011250565	81.948	827	1593	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	81.9288	854	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900113685.1	s__Nocardioides psychrotolerans	81.6068	887	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014266025.1	s__Nocardioides deserti	81.4703	798	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013177455.1	s__Nocardioides sp013177455	81.4424	834	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_900101465.1	s__Nocardioides lianchengensis	81.3249	921	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014191495.1	s__Nocardioides soli	80.9929	830	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:15,335] [INFO] GTDB search result was written to GCF_008087085.1_ASM808708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:15,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:15,339] [INFO] DFAST_QC result json was written to GCF_008087085.1_ASM808708v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:15,339] [INFO] DFAST_QC completed!
[2024-01-24 11:53:15,339] [INFO] Total running time: 0h2m4s