[2024-01-24 14:46:49,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:49,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:49,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a035dc7-9f1b-4dac-b635-15ac4a8c158e/dqc_reference
[2024-01-24 14:46:53,979] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:53,980] [INFO] Task started: Prodigal
[2024-01-24 14:46:53,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b3c51b6-8776-46da-aaf9-0154a1faa4fd/GCF_014644415.1_ASM1464441v1_genomic.fna.gz | prodigal -d GCF_014644415.1_ASM1464441v1_genomic.fna/cds.fna -a GCF_014644415.1_ASM1464441v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:03,899] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:03,899] [INFO] Task started: HMMsearch
[2024-01-24 14:47:03,899] [INFO] Running command: hmmsearch --tblout GCF_014644415.1_ASM1464441v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a035dc7-9f1b-4dac-b635-15ac4a8c158e/dqc_reference/reference_markers.hmm GCF_014644415.1_ASM1464441v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:04,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:04,283] [INFO] Found 6/6 markers.
[2024-01-24 14:47:04,320] [INFO] Query marker FASTA was written to GCF_014644415.1_ASM1464441v1_genomic.fna/markers.fasta
[2024-01-24 14:47:04,321] [INFO] Task started: Blastn
[2024-01-24 14:47:04,321] [INFO] Running command: blastn -query GCF_014644415.1_ASM1464441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a035dc7-9f1b-4dac-b635-15ac4a8c158e/dqc_reference/reference_markers.fasta -out GCF_014644415.1_ASM1464441v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:10,734] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:10,737] [INFO] Selected 26 target genomes.
[2024-01-24 14:47:10,738] [INFO] Target genome list was writen to GCF_014644415.1_ASM1464441v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:10,789] [INFO] Task started: fastANI
[2024-01-24 14:47:10,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b3c51b6-8776-46da-aaf9-0154a1faa4fd/GCF_014644415.1_ASM1464441v1_genomic.fna.gz --refList GCF_014644415.1_ASM1464441v1_genomic.fna/target_genomes.txt --output GCF_014644415.1_ASM1464441v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:34,701] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:34,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a035dc7-9f1b-4dac-b635-15ac4a8c158e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:34,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a035dc7-9f1b-4dac-b635-15ac4a8c158e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:34,724] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:34,724] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:34,724] [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	80.2166	594	1214	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	80.1738	635	1214	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	80.1267	644	1214	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	79.8946	571	1214	95	below_threshold
Marmoricola solisilvae	strain=KIS18-7	GCA_003725775.1	1542737	1542737	type	True	79.8596	515	1214	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.8018	523	1214	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	79.7847	599	1214	95	below_threshold
Nocardioides massiliensis	strain=GD13	GCA_900067705.2	1325935	1325935	type	True	79.782	380	1214	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	79.774	604	1214	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	79.6529	566	1214	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	79.6303	641	1214	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.601	638	1214	95	below_threshold
Nocardioides rotundus	strain=MCCC 1A10561	GCA_019931675.1	1774216	1774216	type	True	79.5605	533	1214	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	79.5252	645	1214	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	79.5075	549	1214	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	79.5007	644	1214	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.4647	549	1214	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.4544	629	1214	95	below_threshold
Nocardioides cynanchi	strain=SB3-45	GCA_008761635.1	2558918	2558918	type	True	79.4042	521	1214	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	79.398	616	1214	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.3303	620	1214	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.2815	554	1214	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	79.235	522	1214	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	79.2095	571	1214	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.206	522	1214	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.1739	498	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:34,748] [INFO] DFAST Taxonomy check result was written to GCF_014644415.1_ASM1464441v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:34,748] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:34,749] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:34,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a035dc7-9f1b-4dac-b635-15ac4a8c158e/dqc_reference/checkm_data
[2024-01-24 14:47:34,750] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:34,789] [INFO] Task started: CheckM
[2024-01-24 14:47:34,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644415.1_ASM1464441v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644415.1_ASM1464441v1_genomic.fna/checkm_input GCF_014644415.1_ASM1464441v1_genomic.fna/checkm_result
[2024-01-24 14:48:32,809] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:32,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:32,833] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:32,833] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:32,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644415.1_ASM1464441v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:32,834] [INFO] Task started: Blastn
[2024-01-24 14:48:32,834] [INFO] Running command: blastn -query GCF_014644415.1_ASM1464441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a035dc7-9f1b-4dac-b635-15ac4a8c158e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644415.1_ASM1464441v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:34,780] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:34,786] [INFO] Selected 22 target genomes.
[2024-01-24 14:48:34,786] [INFO] Target genome list was writen to GCF_014644415.1_ASM1464441v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:34,803] [INFO] Task started: fastANI
[2024-01-24 14:48:34,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b3c51b6-8776-46da-aaf9-0154a1faa4fd/GCF_014644415.1_ASM1464441v1_genomic.fna.gz --refList GCF_014644415.1_ASM1464441v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644415.1_ASM1464441v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:55,661] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:55,679] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:55,679] [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_014644415.1	s__Marmoricola endophyticus	100.0	1214	1214	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_003674065.1	s__Marmoricola mangrovicus	80.8898	681	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720335.1	s__Marmoricola aequoreus	80.2391	592	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466785.1	s__Nocardioides marinisabuli	80.1546	605	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001424755.1	s__Marmoricola sp001424755	80.1473	647	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104965.1	s__Marmoricola scoriae	80.1292	644	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744365.1	s__Marmoricola sp017744365	79.8734	605	1214	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	79.8443	516	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842875.1	s__Nocardioides sp014842875	79.8297	520	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900067705.2	s__Nocardioides_A massiliensis	79.7661	381	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212315.1	s__Nocardioides luti	79.7178	609	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557055.1	s__Nocardioides sp009557055	79.7011	554	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011420305.2	s__Nocardioides sp011420305	79.6436	557	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_013409425.1	s__Nocardioides perillae	79.5816	574	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046535.1	s__Nocardioides anomalus	79.5289	644	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009823805.1	s__Nocardioides sp009823805	79.5152	642	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729525.1	s__Nocardioides sp002729525	79.4432	581	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395785.1	s__Nocardioides_B mesophilus	79.4329	554	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191495.1	s__Nocardioides soli	79.3203	622	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_015352455.1	s__Nocardioides islandensis	79.2266	569	1214	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	79.2085	525	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805865.1	s__Marmoricola_A sp902805865	78.6308	365	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:55,681] [INFO] GTDB search result was written to GCF_014644415.1_ASM1464441v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:55,682] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:55,687] [INFO] DFAST_QC result json was written to GCF_014644415.1_ASM1464441v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:55,687] [INFO] DFAST_QC completed!
[2024-01-24 14:48:55,687] [INFO] Total running time: 0h2m6s