[2024-01-24 13:31:33,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bb3c1d9-7bbb-4419-92e0-77ad538ddaba/dqc_reference
[2024-01-24 13:31:34,821] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,822] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,822] [INFO] Running command: gunzip -c /var/lib/cwl/stgf163138b-0ae5-4d17-bb9f-23597c512119/GCF_015319165.1_ASM1531916v1_genomic.fna.gz | prodigal -d GCF_015319165.1_ASM1531916v1_genomic.fna/cds.fna -a GCF_015319165.1_ASM1531916v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:48,323] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:48,324] [INFO] Task started: HMMsearch
[2024-01-24 13:31:48,324] [INFO] Running command: hmmsearch --tblout GCF_015319165.1_ASM1531916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bb3c1d9-7bbb-4419-92e0-77ad538ddaba/dqc_reference/reference_markers.hmm GCF_015319165.1_ASM1531916v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:48,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:48,635] [INFO] Found 6/6 markers.
[2024-01-24 13:31:48,677] [INFO] Query marker FASTA was written to GCF_015319165.1_ASM1531916v1_genomic.fna/markers.fasta
[2024-01-24 13:31:48,678] [INFO] Task started: Blastn
[2024-01-24 13:31:48,678] [INFO] Running command: blastn -query GCF_015319165.1_ASM1531916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bb3c1d9-7bbb-4419-92e0-77ad538ddaba/dqc_reference/reference_markers.fasta -out GCF_015319165.1_ASM1531916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:49,921] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:49,925] [INFO] Selected 19 target genomes.
[2024-01-24 13:31:49,925] [INFO] Target genome list was writen to GCF_015319165.1_ASM1531916v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:49,933] [INFO] Task started: fastANI
[2024-01-24 13:31:49,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgf163138b-0ae5-4d17-bb9f-23597c512119/GCF_015319165.1_ASM1531916v1_genomic.fna.gz --refList GCF_015319165.1_ASM1531916v1_genomic.fna/target_genomes.txt --output GCF_015319165.1_ASM1531916v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:08,488] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:08,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bb3c1d9-7bbb-4419-92e0-77ad538ddaba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:08,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bb3c1d9-7bbb-4419-92e0-77ad538ddaba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:08,510] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:08,510] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:08,511] [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 acrostichi	strain=CBS4Y-1	GCA_015319165.1	2784339	2784339	type	True	100.0	1426	1427	95	conclusive
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	81.5365	790	1427	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.4706	789	1427	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	81.4562	789	1427	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.4515	781	1427	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	81.4447	804	1427	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.5764	702	1427	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.549	696	1427	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	80.3208	706	1427	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	80.1732	695	1427	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.0625	657	1427	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	80.0364	698	1427	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.0143	646	1427	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	79.9186	738	1427	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.816	601	1427	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.6295	634	1427	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.4794	608	1427	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.4132	558	1427	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.4072	642	1427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:08,512] [INFO] DFAST Taxonomy check result was written to GCF_015319165.1_ASM1531916v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:08,513] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:08,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:08,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bb3c1d9-7bbb-4419-92e0-77ad538ddaba/dqc_reference/checkm_data
[2024-01-24 13:32:08,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:08,556] [INFO] Task started: CheckM
[2024-01-24 13:32:08,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015319165.1_ASM1531916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015319165.1_ASM1531916v1_genomic.fna/checkm_input GCF_015319165.1_ASM1531916v1_genomic.fna/checkm_result
[2024-01-24 13:33:19,475] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:19,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:19,499] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:19,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:19,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015319165.1_ASM1531916v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:19,500] [INFO] Task started: Blastn
[2024-01-24 13:33:19,500] [INFO] Running command: blastn -query GCF_015319165.1_ASM1531916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bb3c1d9-7bbb-4419-92e0-77ad538ddaba/dqc_reference/reference_markers_gtdb.fasta -out GCF_015319165.1_ASM1531916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:21,793] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:21,796] [INFO] Selected 20 target genomes.
[2024-01-24 13:33:21,797] [INFO] Target genome list was writen to GCF_015319165.1_ASM1531916v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:21,845] [INFO] Task started: fastANI
[2024-01-24 13:33:21,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgf163138b-0ae5-4d17-bb9f-23597c512119/GCF_015319165.1_ASM1531916v1_genomic.fna.gz --refList GCF_015319165.1_ASM1531916v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015319165.1_ASM1531916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:41,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:41,726] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:41,727] [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_015319165.1	s__Nocardioides acrostichi	100.0	1426	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001627335.1	s__Nocardioides sp001627335	81.5107	711	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_013408145.1	s__Nocardioides marinus	81.4997	793	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_016907435.1	s__Nocardioides salarius	81.4792	800	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013466785.1	s__Nocardioides marinisabuli	81.4658	779	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCA_009701885.1	s__Nocardioides sp009701885	81.2387	773	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	80.5341	699	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003660455.1	s__Nocardioides ferulae	80.312	707	1427	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	80.1776	694	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409425.1	s__Nocardioides perillae	80.1718	645	1427	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	80.0993	722	1427	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	80.0926	715	1427	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	80.0319	659	1427	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	79.9289	737	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506435.1	s__Nocardioides sp902506435	79.8652	666	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018459925.1	s__Nocardioides aquaticus	79.7903	653	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429625.1	s__Nocardioides sp001429625	79.6296	644	1427	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	79.5466	584	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424755.1	s__Marmoricola sp001424755	79.3928	613	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014108865.1	s__Nocardioides sp014108865	78.7465	560	1427	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 13:33:41,742] [INFO] GTDB search result was written to GCF_015319165.1_ASM1531916v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:41,742] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:41,747] [INFO] DFAST_QC result json was written to GCF_015319165.1_ASM1531916v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:41,747] [INFO] DFAST_QC completed!
[2024-01-24 13:33:41,747] [INFO] Total running time: 0h2m8s