[2024-01-24 11:18:04,903] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:04,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:04,906] [INFO] DQC Reference Directory: /var/lib/cwl/stge2b7b7e2-007e-4c68-942b-298e90991ad2/dqc_reference
[2024-01-24 11:18:06,094] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:06,095] [INFO] Task started: Prodigal
[2024-01-24 11:18:06,095] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e4d11be-a790-4851-9a9f-a4ac2212a882/GCF_013409645.1_ASM1340964v1_genomic.fna.gz | prodigal -d GCF_013409645.1_ASM1340964v1_genomic.fna/cds.fna -a GCF_013409645.1_ASM1340964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:18,029] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:18,030] [INFO] Task started: HMMsearch
[2024-01-24 11:18:18,030] [INFO] Running command: hmmsearch --tblout GCF_013409645.1_ASM1340964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2b7b7e2-007e-4c68-942b-298e90991ad2/dqc_reference/reference_markers.hmm GCF_013409645.1_ASM1340964v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:18,299] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:18,300] [INFO] Found 6/6 markers.
[2024-01-24 11:18:18,340] [INFO] Query marker FASTA was written to GCF_013409645.1_ASM1340964v1_genomic.fna/markers.fasta
[2024-01-24 11:18:18,340] [INFO] Task started: Blastn
[2024-01-24 11:18:18,340] [INFO] Running command: blastn -query GCF_013409645.1_ASM1340964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2b7b7e2-007e-4c68-942b-298e90991ad2/dqc_reference/reference_markers.fasta -out GCF_013409645.1_ASM1340964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:19,633] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:19,637] [INFO] Selected 20 target genomes.
[2024-01-24 11:18:19,638] [INFO] Target genome list was writen to GCF_013409645.1_ASM1340964v1_genomic.fna/target_genomes.txt
[2024-01-24 11:18:19,643] [INFO] Task started: fastANI
[2024-01-24 11:18:19,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4d11be-a790-4851-9a9f-a4ac2212a882/GCF_013409645.1_ASM1340964v1_genomic.fna.gz --refList GCF_013409645.1_ASM1340964v1_genomic.fna/target_genomes.txt --output GCF_013409645.1_ASM1340964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:39,282] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:39,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2b7b7e2-007e-4c68-942b-298e90991ad2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:39,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2b7b7e2-007e-4c68-942b-298e90991ad2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:39,300] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:18:39,300] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:18:39,300] [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 panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	100.0	1418	1423	95	conclusive
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	84.0651	966	1423	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.9351	876	1423	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	82.4193	787	1423	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	81.9991	777	1423	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	81.9341	768	1423	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	81.8987	816	1423	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.8571	802	1423	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	81.8486	835	1423	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	81.7707	770	1423	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	81.2592	699	1423	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	81.2243	697	1423	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	81.2103	747	1423	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	81.1821	748	1423	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.8344	687	1423	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.7022	677	1423	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	80.3734	705	1423	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.1529	660	1423	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.0968	618	1423	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.9546	684	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:39,302] [INFO] DFAST Taxonomy check result was written to GCF_013409645.1_ASM1340964v1_genomic.fna/tc_result.tsv
[2024-01-24 11:18:39,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:39,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:39,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2b7b7e2-007e-4c68-942b-298e90991ad2/dqc_reference/checkm_data
[2024-01-24 11:18:39,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:39,346] [INFO] Task started: CheckM
[2024-01-24 11:18:39,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409645.1_ASM1340964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409645.1_ASM1340964v1_genomic.fna/checkm_input GCF_013409645.1_ASM1340964v1_genomic.fna/checkm_result
[2024-01-24 11:19:51,335] [INFO] Task succeeded: CheckM
[2024-01-24 11:19:51,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:19:51,358] [INFO] ===== Completeness check finished =====
[2024-01-24 11:19:51,358] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:19:51,359] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409645.1_ASM1340964v1_genomic.fna/markers.fasta)
[2024-01-24 11:19:51,359] [INFO] Task started: Blastn
[2024-01-24 11:19:51,359] [INFO] Running command: blastn -query GCF_013409645.1_ASM1340964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2b7b7e2-007e-4c68-942b-298e90991ad2/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409645.1_ASM1340964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:19:53,444] [INFO] Task succeeded: Blastn
[2024-01-24 11:19:53,448] [INFO] Selected 20 target genomes.
[2024-01-24 11:19:53,448] [INFO] Target genome list was writen to GCF_013409645.1_ASM1340964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:19:53,458] [INFO] Task started: fastANI
[2024-01-24 11:19:53,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4d11be-a790-4851-9a9f-a4ac2212a882/GCF_013409645.1_ASM1340964v1_genomic.fna.gz --refList GCF_013409645.1_ASM1340964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409645.1_ASM1340964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:14,138] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:14,158] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:20:14,158] [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_013409645.1	s__Nocardioides panaciterrulae	100.0	1415	1423	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_013466985.1	s__Nocardioides ungokensis	84.0533	967	1423	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	82.4446	872	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117935.1	s__Nocardioides sp002117935	82.2209	817	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013177455.1	s__Nocardioides sp013177455	82.1943	782	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_000015265.1	s__Nocardioides sp000015265	82.1177	822	1423	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	82.0015	722	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_013778305.1	s__Nocardioides sp013778305	81.9602	803	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011250565.1	s__Nocardioides sp011250565	81.9515	763	1423	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	81.9497	827	1423	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	81.9377	767	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014191495.1	s__Nocardioides soli	81.912	815	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_003660455.1	s__Nocardioides ferulae	81.9005	828	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101465.1	s__Nocardioides lianchengensis	81.7747	797	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425175.1	s__Nocardioides sp001425175	81.7633	844	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009557055.1	s__Nocardioides sp009557055	81.7181	738	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013155365.1	s__Nocardioides sp013155365	81.7047	745	1423	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	81.187	749	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047295.1	s__Nocardioides sediminis	81.162	750	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017310035.1	s__Nocardioides sp017310035	80.7792	699	1423	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 11:20:14,160] [INFO] GTDB search result was written to GCF_013409645.1_ASM1340964v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:14,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:14,166] [INFO] DFAST_QC result json was written to GCF_013409645.1_ASM1340964v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:14,166] [INFO] DFAST_QC completed!
[2024-01-24 11:20:14,166] [INFO] Total running time: 0h2m9s