[2024-01-24 11:13:04,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgce7b20f4-d022-43d9-bf78-2a7053c74603/dqc_reference
[2024-01-24 11:13:05,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,615] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,615] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a81e1ff-311b-45cd-8968-8797ee362de9/GCF_015352445.1_ASM1535244v1_genomic.fna.gz | prodigal -d GCF_015352445.1_ASM1535244v1_genomic.fna/cds.fna -a GCF_015352445.1_ASM1535244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:19,266] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:19,266] [INFO] Task started: HMMsearch
[2024-01-24 11:13:19,267] [INFO] Running command: hmmsearch --tblout GCF_015352445.1_ASM1535244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce7b20f4-d022-43d9-bf78-2a7053c74603/dqc_reference/reference_markers.hmm GCF_015352445.1_ASM1535244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:19,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:19,623] [INFO] Found 6/6 markers.
[2024-01-24 11:13:19,673] [INFO] Query marker FASTA was written to GCF_015352445.1_ASM1535244v1_genomic.fna/markers.fasta
[2024-01-24 11:13:19,674] [INFO] Task started: Blastn
[2024-01-24 11:13:19,674] [INFO] Running command: blastn -query GCF_015352445.1_ASM1535244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce7b20f4-d022-43d9-bf78-2a7053c74603/dqc_reference/reference_markers.fasta -out GCF_015352445.1_ASM1535244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:20,837] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:20,841] [INFO] Selected 21 target genomes.
[2024-01-24 11:13:20,842] [INFO] Target genome list was writen to GCF_015352445.1_ASM1535244v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:20,853] [INFO] Task started: fastANI
[2024-01-24 11:13:20,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a81e1ff-311b-45cd-8968-8797ee362de9/GCF_015352445.1_ASM1535244v1_genomic.fna.gz --refList GCF_015352445.1_ASM1535244v1_genomic.fna/target_genomes.txt --output GCF_015352445.1_ASM1535244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:40,942] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:40,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce7b20f4-d022-43d9-bf78-2a7053c74603/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:40,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce7b20f4-d022-43d9-bf78-2a7053c74603/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:40,962] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:40,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:40,963] [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 agariphilus	strain=KCTC 19276	GCA_015352445.1	433664	433664	type	True	100.0	1535	1539	95	conclusive
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	83.7928	1039	1539	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.5481	716	1539	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	80.4928	705	1539	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.3596	712	1539	95	below_threshold
Nocardioides cynanchi	strain=SB3-45	GCA_008761635.1	2558918	2558918	type	True	80.3397	672	1539	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	80.2573	658	1539	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	80.1609	662	1539	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	80.0349	642	1539	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.9867	672	1539	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.9707	658	1539	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	79.9376	728	1539	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	79.7791	647	1539	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	79.7791	613	1539	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.7518	649	1539	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	79.7482	636	1539	95	below_threshold
Nocardioides rotundus	strain=MCCC 1A10561	GCA_019931675.1	1774216	1774216	type	True	79.6237	558	1539	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.521	563	1539	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	79.4913	558	1539	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	79.4713	538	1539	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.2657	550	1539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:40,964] [INFO] DFAST Taxonomy check result was written to GCF_015352445.1_ASM1535244v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:40,965] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:40,965] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:40,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce7b20f4-d022-43d9-bf78-2a7053c74603/dqc_reference/checkm_data
[2024-01-24 11:13:40,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:41,014] [INFO] Task started: CheckM
[2024-01-24 11:13:41,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015352445.1_ASM1535244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015352445.1_ASM1535244v1_genomic.fna/checkm_input GCF_015352445.1_ASM1535244v1_genomic.fna/checkm_result
[2024-01-24 11:14:27,213] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:27,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:27,236] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:27,237] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:27,237] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015352445.1_ASM1535244v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:27,238] [INFO] Task started: Blastn
[2024-01-24 11:14:27,238] [INFO] Running command: blastn -query GCF_015352445.1_ASM1535244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce7b20f4-d022-43d9-bf78-2a7053c74603/dqc_reference/reference_markers_gtdb.fasta -out GCF_015352445.1_ASM1535244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:29,072] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:29,077] [INFO] Selected 22 target genomes.
[2024-01-24 11:14:29,077] [INFO] Target genome list was writen to GCF_015352445.1_ASM1535244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:29,106] [INFO] Task started: fastANI
[2024-01-24 11:14:29,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a81e1ff-311b-45cd-8968-8797ee362de9/GCF_015352445.1_ASM1535244v1_genomic.fna.gz --refList GCF_015352445.1_ASM1535244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015352445.1_ASM1535244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:49,064] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:49,084] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:49,084] [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_015352445.1	s__Nocardioides agariphilus	100.0	1535	1539	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_015352455.1	s__Nocardioides islandensis	83.7995	1038	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	80.523	719	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	80.4795	674	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422805.1	s__Nocardioides halotolerans	80.4711	708	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466985.1	s__Nocardioides ungokensis	80.3866	708	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212315.1	s__Nocardioides luti	80.3708	694	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008761635.1	s__Nocardioides cynanchi	80.3393	672	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924665.1	s__Nocardioides sp016924665	80.3311	652	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805925.1	s__Nocardioides sp902805925	80.3289	540	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564375.1	s__Nocardioides euryhalodurans	80.2915	654	1539	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	80.0897	671	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070375.1	s__Nocardioides kribbensis	79.9944	646	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_001425175.1	s__Nocardioides sp001425175	79.9478	701	1539	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	79.8606	593	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_003633575.1	s__Nocardioides sp003633575	79.8259	666	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047285.1	s__Nocardioides allogilvus	79.804	580	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.72	98.72	0.92	0.92	2	-
GCF_013410035.1	s__Nocardioides cavernae_A	79.7243	644	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752505.1	s__Marmoricola aurantiacus	79.5376	553	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194625.1	s__Nocardioides solisilvae	79.4297	542	1539	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	79.4244	578	1539	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	79.1783	549	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:49,086] [INFO] GTDB search result was written to GCF_015352445.1_ASM1535244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:49,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:49,091] [INFO] DFAST_QC result json was written to GCF_015352445.1_ASM1535244v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:49,091] [INFO] DFAST_QC completed!
[2024-01-24 11:14:49,091] [INFO] Total running time: 0h1m45s