[2024-01-24 15:11:03,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:11:03,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:11:03,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg97452638-82fa-4dd2-9b18-733ce96e7ef0/dqc_reference
[2024-01-24 15:11:04,371] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:11:04,371] [INFO] Task started: Prodigal
[2024-01-24 15:11:04,372] [INFO] Running command: gunzip -c /var/lib/cwl/stgacc17832-340b-4e0f-abe2-04d9fd682efe/GCF_003725535.1_ASM372553v1_genomic.fna.gz | prodigal -d GCF_003725535.1_ASM372553v1_genomic.fna/cds.fna -a GCF_003725535.1_ASM372553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:19,235] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:19,235] [INFO] Task started: HMMsearch
[2024-01-24 15:11:19,235] [INFO] Running command: hmmsearch --tblout GCF_003725535.1_ASM372553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97452638-82fa-4dd2-9b18-733ce96e7ef0/dqc_reference/reference_markers.hmm GCF_003725535.1_ASM372553v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:19,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:19,578] [INFO] Found 6/6 markers.
[2024-01-24 15:11:19,624] [INFO] Query marker FASTA was written to GCF_003725535.1_ASM372553v1_genomic.fna/markers.fasta
[2024-01-24 15:11:19,624] [INFO] Task started: Blastn
[2024-01-24 15:11:19,624] [INFO] Running command: blastn -query GCF_003725535.1_ASM372553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97452638-82fa-4dd2-9b18-733ce96e7ef0/dqc_reference/reference_markers.fasta -out GCF_003725535.1_ASM372553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:20,983] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:20,986] [INFO] Selected 23 target genomes.
[2024-01-24 15:11:20,987] [INFO] Target genome list was writen to GCF_003725535.1_ASM372553v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:21,040] [INFO] Task started: fastANI
[2024-01-24 15:11:21,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgacc17832-340b-4e0f-abe2-04d9fd682efe/GCF_003725535.1_ASM372553v1_genomic.fna.gz --refList GCF_003725535.1_ASM372553v1_genomic.fna/target_genomes.txt --output GCF_003725535.1_ASM372553v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:44,101] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:44,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97452638-82fa-4dd2-9b18-733ce96e7ef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:44,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97452638-82fa-4dd2-9b18-733ce96e7ef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:44,124] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:11:44,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:11:44,124] [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 solisilvae	strain=KIS18-7	GCA_003725775.1	1542737	1542737	type	True	81.895	787	1623	95	below_threshold
Marmoricola ginsengisoli	strain=Gsoil 097	GCA_003725695.1	661483	661483	type	True	81.6553	824	1623	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	80.4558	702	1623	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	80.4152	674	1623	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.2709	653	1623	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.1135	676	1623	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	80.0927	701	1623	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.0803	674	1623	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	80.0709	648	1623	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.0423	666	1623	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.039	576	1623	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	79.9763	673	1623	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.9169	712	1623	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	79.8167	617	1623	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	79.7918	673	1623	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	79.7496	652	1623	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.7467	652	1623	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	79.6452	716	1623	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.5928	609	1623	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.5437	734	1623	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	79.5181	703	1623	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.4846	630	1623	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.2755	615	1623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:44,126] [INFO] DFAST Taxonomy check result was written to GCF_003725535.1_ASM372553v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:44,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:44,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:44,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97452638-82fa-4dd2-9b18-733ce96e7ef0/dqc_reference/checkm_data
[2024-01-24 15:11:44,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:44,174] [INFO] Task started: CheckM
[2024-01-24 15:11:44,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003725535.1_ASM372553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003725535.1_ASM372553v1_genomic.fna/checkm_input GCF_003725535.1_ASM372553v1_genomic.fna/checkm_result
[2024-01-24 15:12:53,520] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:53,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:53,543] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:53,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:53,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003725535.1_ASM372553v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:53,545] [INFO] Task started: Blastn
[2024-01-24 15:12:53,545] [INFO] Running command: blastn -query GCF_003725535.1_ASM372553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97452638-82fa-4dd2-9b18-733ce96e7ef0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003725535.1_ASM372553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:55,740] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:55,744] [INFO] Selected 17 target genomes.
[2024-01-24 15:12:55,745] [INFO] Target genome list was writen to GCF_003725535.1_ASM372553v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:55,772] [INFO] Task started: fastANI
[2024-01-24 15:12:55,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgacc17832-340b-4e0f-abe2-04d9fd682efe/GCF_003725535.1_ASM372553v1_genomic.fna.gz --refList GCF_003725535.1_ASM372553v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003725535.1_ASM372553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:14,393] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:14,412] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:14,412] [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_003725535.1	s__Marmoricola pocheonensis	99.9983	1622	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017744365.1	s__Marmoricola sp017744365	82.3438	879	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725775.1	s__Marmoricola solisilvae	81.8961	787	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725695.1	s__Marmoricola ginsengisoli	81.6755	822	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872665.1	s__Marmoricola sp017872665	81.2517	767	1623	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	80.5187	755	1623	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	80.3684	680	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466985.1	s__Nocardioides ungokensis	80.2189	658	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191495.1	s__Nocardioides soli	80.1004	700	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_004519545.1	s__Nocardioides guangzhouensis	80.0969	678	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	80.0798	674	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720335.1	s__Marmoricola aequoreus	80.0236	654	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	79.9703	673	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_015024225.1	s__Nocardioides sp015024225	79.7809	673	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_900103935.1	s__Nocardioides szechwanensis	79.7506	652	1623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003674065.1	s__Marmoricola mangrovicus	79.7351	652	1623	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	79.5061	739	1623	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 15:13:14,414] [INFO] GTDB search result was written to GCF_003725535.1_ASM372553v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:14,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:14,420] [INFO] DFAST_QC result json was written to GCF_003725535.1_ASM372553v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:14,420] [INFO] DFAST_QC completed!
[2024-01-24 15:13:14,420] [INFO] Total running time: 0h2m11s