[2024-01-24 14:12:03,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:03,530] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:03,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg41f98f71-9b76-4b43-a35a-e5037de1821a/dqc_reference
[2024-01-24 14:12:04,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:04,894] [INFO] Task started: Prodigal
[2024-01-24 14:12:04,895] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0070602-7a78-4b6b-9924-08cbfff2a995/GCF_000720335.1_ASM72033v1_genomic.fna.gz | prodigal -d GCF_000720335.1_ASM72033v1_genomic.fna/cds.fna -a GCF_000720335.1_ASM72033v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:16,676] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:16,677] [INFO] Task started: HMMsearch
[2024-01-24 14:12:16,677] [INFO] Running command: hmmsearch --tblout GCF_000720335.1_ASM72033v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41f98f71-9b76-4b43-a35a-e5037de1821a/dqc_reference/reference_markers.hmm GCF_000720335.1_ASM72033v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:17,059] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:17,060] [INFO] Found 6/6 markers.
[2024-01-24 14:12:17,097] [INFO] Query marker FASTA was written to GCF_000720335.1_ASM72033v1_genomic.fna/markers.fasta
[2024-01-24 14:12:17,097] [INFO] Task started: Blastn
[2024-01-24 14:12:17,098] [INFO] Running command: blastn -query GCF_000720335.1_ASM72033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41f98f71-9b76-4b43-a35a-e5037de1821a/dqc_reference/reference_markers.fasta -out GCF_000720335.1_ASM72033v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:18,442] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:18,446] [INFO] Selected 21 target genomes.
[2024-01-24 14:12:18,446] [INFO] Target genome list was writen to GCF_000720335.1_ASM72033v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:18,458] [INFO] Task started: fastANI
[2024-01-24 14:12:18,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0070602-7a78-4b6b-9924-08cbfff2a995/GCF_000720335.1_ASM72033v1_genomic.fna.gz --refList GCF_000720335.1_ASM72033v1_genomic.fna/target_genomes.txt --output GCF_000720335.1_ASM72033v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:40,178] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:40,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41f98f71-9b76-4b43-a35a-e5037de1821a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:40,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41f98f71-9b76-4b43-a35a-e5037de1821a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:40,208] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:40,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:40,208] [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
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	100.0	1369	1372	95	conclusive
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	83.3279	876	1372	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	83.2718	856	1372	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	80.6943	721	1372	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.6041	663	1372	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	80.511	693	1372	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.1806	654	1372	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	80.1012	696	1372	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.0867	667	1372	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.0832	697	1372	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	80.0615	639	1372	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.9749	646	1372	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	79.9481	596	1372	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.9083	661	1372	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.8976	678	1372	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.892	715	1372	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	79.8889	694	1372	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	79.8193	725	1372	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	79.8068	699	1372	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.7969	734	1372	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	79.585	642	1372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:40,210] [INFO] DFAST Taxonomy check result was written to GCF_000720335.1_ASM72033v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:40,210] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:40,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:40,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41f98f71-9b76-4b43-a35a-e5037de1821a/dqc_reference/checkm_data
[2024-01-24 14:12:40,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:40,253] [INFO] Task started: CheckM
[2024-01-24 14:12:40,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000720335.1_ASM72033v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000720335.1_ASM72033v1_genomic.fna/checkm_input GCF_000720335.1_ASM72033v1_genomic.fna/checkm_result
[2024-01-24 14:13:37,532] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:37,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:37,555] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:37,556] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:37,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000720335.1_ASM72033v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:37,556] [INFO] Task started: Blastn
[2024-01-24 14:13:37,557] [INFO] Running command: blastn -query GCF_000720335.1_ASM72033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41f98f71-9b76-4b43-a35a-e5037de1821a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000720335.1_ASM72033v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:39,714] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:39,719] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:39,719] [INFO] Target genome list was writen to GCF_000720335.1_ASM72033v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:39,738] [INFO] Task started: fastANI
[2024-01-24 14:13:39,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0070602-7a78-4b6b-9924-08cbfff2a995/GCF_000720335.1_ASM72033v1_genomic.fna.gz --refList GCF_000720335.1_ASM72033v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000720335.1_ASM72033v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:52,558] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:52,576] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:52,577] [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_000720335.1	s__Marmoricola aequoreus	100.0	1369	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900104965.1	s__Marmoricola scoriae	83.3566	874	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752505.1	s__Marmoricola aurantiacus	83.3157	853	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424755.1	s__Marmoricola sp001424755	83.1851	876	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426045.1	s__Marmoricola sp000426045	81.1819	780	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409425.1	s__Nocardioides perillae	80.5735	685	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	80.0846	731	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_003194625.1	s__Nocardioides solisilvae	79.8815	604	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744365.1	s__Marmoricola sp017744365	79.8662	662	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660455.1	s__Nocardioides ferulae	79.8572	719	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725535.1	s__Marmoricola pocheonensis	79.8497	680	1372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101465.1	s__Nocardioides lianchengensis	79.751	740	1372	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 14:13:52,579] [INFO] GTDB search result was written to GCF_000720335.1_ASM72033v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:52,579] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:52,586] [INFO] DFAST_QC result json was written to GCF_000720335.1_ASM72033v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:52,586] [INFO] DFAST_QC completed!
[2024-01-24 14:13:52,586] [INFO] Total running time: 0h1m49s