[2024-01-24 10:47:40,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,975] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dd43086-1227-4e99-8ff5-ad473cbf8c41/dqc_reference
[2024-01-24 10:47:44,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,787] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,788] [INFO] Running command: gunzip -c /var/lib/cwl/stgd068bff5-f17d-412f-bbdf-b1e5e5c30c78/GCF_015352455.1_ASM1535245v1_genomic.fna.gz | prodigal -d GCF_015352455.1_ASM1535245v1_genomic.fna/cds.fna -a GCF_015352455.1_ASM1535245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:01,614] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:01,615] [INFO] Task started: HMMsearch
[2024-01-24 10:48:01,615] [INFO] Running command: hmmsearch --tblout GCF_015352455.1_ASM1535245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dd43086-1227-4e99-8ff5-ad473cbf8c41/dqc_reference/reference_markers.hmm GCF_015352455.1_ASM1535245v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:01,956] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:01,958] [INFO] Found 6/6 markers.
[2024-01-24 10:48:02,006] [INFO] Query marker FASTA was written to GCF_015352455.1_ASM1535245v1_genomic.fna/markers.fasta
[2024-01-24 10:48:02,006] [INFO] Task started: Blastn
[2024-01-24 10:48:02,006] [INFO] Running command: blastn -query GCF_015352455.1_ASM1535245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dd43086-1227-4e99-8ff5-ad473cbf8c41/dqc_reference/reference_markers.fasta -out GCF_015352455.1_ASM1535245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:03,272] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:03,276] [INFO] Selected 22 target genomes.
[2024-01-24 10:48:03,276] [INFO] Target genome list was writen to GCF_015352455.1_ASM1535245v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:03,285] [INFO] Task started: fastANI
[2024-01-24 10:48:03,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgd068bff5-f17d-412f-bbdf-b1e5e5c30c78/GCF_015352455.1_ASM1535245v1_genomic.fna.gz --refList GCF_015352455.1_ASM1535245v1_genomic.fna/target_genomes.txt --output GCF_015352455.1_ASM1535245v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:25,837] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:25,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dd43086-1227-4e99-8ff5-ad473cbf8c41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:25,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dd43086-1227-4e99-8ff5-ad473cbf8c41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:25,859] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:25,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:25,860] [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 islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	100.0	1632	1636	95	conclusive
Nocardioides agariphilus	strain=KCTC 19276	GCA_015352445.1	433664	433664	type	True	83.7387	1057	1636	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.1477	776	1636	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	81.1018	771	1636	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.8902	792	1636	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	80.8699	707	1636	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	80.7002	798	1636	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	80.6856	770	1636	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	80.3543	721	1636	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	80.3298	668	1636	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	80.2924	715	1636	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.2278	741	1636	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.1454	732	1636	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.0836	698	1636	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.0424	703	1636	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.0228	658	1636	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.9519	646	1636	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	79.9487	731	1636	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.8906	734	1636	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	79.7242	640	1636	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	79.687	619	1636	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	79.4751	728	1636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:25,861] [INFO] DFAST Taxonomy check result was written to GCF_015352455.1_ASM1535245v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:25,862] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:25,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:25,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dd43086-1227-4e99-8ff5-ad473cbf8c41/dqc_reference/checkm_data
[2024-01-24 10:48:25,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:25,913] [INFO] Task started: CheckM
[2024-01-24 10:48:25,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015352455.1_ASM1535245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015352455.1_ASM1535245v1_genomic.fna/checkm_input GCF_015352455.1_ASM1535245v1_genomic.fna/checkm_result
[2024-01-24 10:49:36,855] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:36,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:36,876] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:36,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:36,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015352455.1_ASM1535245v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:36,877] [INFO] Task started: Blastn
[2024-01-24 10:49:36,878] [INFO] Running command: blastn -query GCF_015352455.1_ASM1535245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dd43086-1227-4e99-8ff5-ad473cbf8c41/dqc_reference/reference_markers_gtdb.fasta -out GCF_015352455.1_ASM1535245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:38,860] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:38,865] [INFO] Selected 21 target genomes.
[2024-01-24 10:49:38,865] [INFO] Target genome list was writen to GCF_015352455.1_ASM1535245v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:38,880] [INFO] Task started: fastANI
[2024-01-24 10:49:38,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgd068bff5-f17d-412f-bbdf-b1e5e5c30c78/GCF_015352455.1_ASM1535245v1_genomic.fna.gz --refList GCF_015352455.1_ASM1535245v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015352455.1_ASM1535245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:01,153] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:01,173] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:01,173] [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_015352455.1	s__Nocardioides islandensis	100.0	1632	1636	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_015352445.1	s__Nocardioides agariphilus	83.7443	1057	1636	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	81.1332	767	1636	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	80.8746	794	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620645.1	s__Nocardioides sp000620645	80.8597	737	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014127485.1	s__Nocardioides sp014127485	80.8324	712	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_000422805.1	s__Nocardioides halotolerans	80.6925	769	1636	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	80.6384	805	1636	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	80.6316	728	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250565.1	s__Nocardioides sp011250565	80.6256	695	1636	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	80.6225	725	1636	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	80.6125	753	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_014266025.1	s__Nocardioides deserti	80.51	705	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001425175.1	s__Nocardioides sp001425175	80.4967	814	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013177455.1	s__Nocardioides sp013177455	80.433	727	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_004564375.1	s__Nocardioides euryhalodurans	80.3576	721	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660455.1	s__Nocardioides ferulae	80.3492	708	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346315.1	s__Nocardioides litoris	79.9382	733	1636	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	79.7594	630	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725535.1	s__Marmoricola pocheonensis	79.6273	649	1636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803235.1	s__Nocardioides simplex_A	79.5946	703	1636	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 10:50:01,175] [INFO] GTDB search result was written to GCF_015352455.1_ASM1535245v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:01,175] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:01,180] [INFO] DFAST_QC result json was written to GCF_015352455.1_ASM1535245v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:01,180] [INFO] DFAST_QC completed!
[2024-01-24 10:50:01,180] [INFO] Total running time: 0h2m20s