[2024-01-25 18:39:50,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:50,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:50,558] [INFO] DQC Reference Directory: /var/lib/cwl/stgeffc4643-cf2f-475e-a4c4-4f01bd423262/dqc_reference
[2024-01-25 18:39:51,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:51,681] [INFO] Task started: Prodigal
[2024-01-25 18:39:51,681] [INFO] Running command: gunzip -c /var/lib/cwl/stgd98c7086-1921-4b75-adbe-b078889b0d91/GCF_014646375.1_ASM1464637v1_genomic.fna.gz | prodigal -d GCF_014646375.1_ASM1464637v1_genomic.fna/cds.fna -a GCF_014646375.1_ASM1464637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:00,349] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:00,349] [INFO] Task started: HMMsearch
[2024-01-25 18:40:00,349] [INFO] Running command: hmmsearch --tblout GCF_014646375.1_ASM1464637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeffc4643-cf2f-475e-a4c4-4f01bd423262/dqc_reference/reference_markers.hmm GCF_014646375.1_ASM1464637v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:00,558] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:00,560] [INFO] Found 6/6 markers.
[2024-01-25 18:40:00,589] [INFO] Query marker FASTA was written to GCF_014646375.1_ASM1464637v1_genomic.fna/markers.fasta
[2024-01-25 18:40:00,589] [INFO] Task started: Blastn
[2024-01-25 18:40:00,589] [INFO] Running command: blastn -query GCF_014646375.1_ASM1464637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeffc4643-cf2f-475e-a4c4-4f01bd423262/dqc_reference/reference_markers.fasta -out GCF_014646375.1_ASM1464637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:01,779] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:01,782] [INFO] Selected 19 target genomes.
[2024-01-25 18:40:01,783] [INFO] Target genome list was writen to GCF_014646375.1_ASM1464637v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:01,791] [INFO] Task started: fastANI
[2024-01-25 18:40:01,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgd98c7086-1921-4b75-adbe-b078889b0d91/GCF_014646375.1_ASM1464637v1_genomic.fna.gz --refList GCF_014646375.1_ASM1464637v1_genomic.fna/target_genomes.txt --output GCF_014646375.1_ASM1464637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:18,891] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:18,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeffc4643-cf2f-475e-a4c4-4f01bd423262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:18,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeffc4643-cf2f-475e-a4c4-4f01bd423262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:18,904] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:18,904] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:18,904] [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 phosphati	strain=CGMCC 4.7371	GCA_014646375.1	1867775	1867775	type	True	100.0	1165	1168	95	conclusive
Nocardioides jejuensis	strain=18JY15-6	GCA_004337475.1	2502782	2502782	type	True	86.2983	820	1168	95	below_threshold
Nocardioides cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	83.1013	731	1168	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.8665	624	1168	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.537	597	1168	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	80.4438	569	1168	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	80.4269	534	1168	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.3498	623	1168	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.2507	576	1168	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.146	568	1168	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.1341	570	1168	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	80.0995	552	1168	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.0847	595	1168	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	80.0678	541	1168	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	79.8177	587	1168	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	79.7927	588	1168	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.7693	518	1168	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.4612	488	1168	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.4423	573	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:18,908] [INFO] DFAST Taxonomy check result was written to GCF_014646375.1_ASM1464637v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:18,908] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:18,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:18,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeffc4643-cf2f-475e-a4c4-4f01bd423262/dqc_reference/checkm_data
[2024-01-25 18:40:18,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:18,947] [INFO] Task started: CheckM
[2024-01-25 18:40:18,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646375.1_ASM1464637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646375.1_ASM1464637v1_genomic.fna/checkm_input GCF_014646375.1_ASM1464637v1_genomic.fna/checkm_result
[2024-01-25 18:41:08,820] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:08,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:08,843] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:08,843] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:08,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646375.1_ASM1464637v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:08,844] [INFO] Task started: Blastn
[2024-01-25 18:41:08,845] [INFO] Running command: blastn -query GCF_014646375.1_ASM1464637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeffc4643-cf2f-475e-a4c4-4f01bd423262/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646375.1_ASM1464637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:10,819] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:10,822] [INFO] Selected 16 target genomes.
[2024-01-25 18:41:10,822] [INFO] Target genome list was writen to GCF_014646375.1_ASM1464637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:10,831] [INFO] Task started: fastANI
[2024-01-25 18:41:10,831] [INFO] Running command: fastANI --query /var/lib/cwl/stgd98c7086-1921-4b75-adbe-b078889b0d91/GCF_014646375.1_ASM1464637v1_genomic.fna.gz --refList GCF_014646375.1_ASM1464637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646375.1_ASM1464637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:25,483] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:25,492] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:25,493] [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_014646375.1	s__Nocardioides phosphati	100.0	1165	1168	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_003053885.1	s__Nocardioides sp003053885	88.7104	889	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337475.1	s__Nocardioides jejuensis	86.2699	822	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600895.1	s__Nocardioides sp003600895	83.1295	729	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426745.1	s__Nocardioides sp001426745	80.9294	614	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.99	98.75	0.96	0.95	3	-
GCF_011250565.1	s__Nocardioides sp011250565	80.5525	587	1168	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	80.5168	599	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_003057875.1	s__Nocardioides currus	80.4536	568	1168	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	80.432	595	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014180715.1	s__Nocardioides stalactiti	80.1498	531	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155365.1	s__Nocardioides sp013155365	80.1246	553	1168	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	80.1013	574	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_015070375.1	s__Nocardioides kribbensis	80.0951	553	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_013778305.1	s__Nocardioides sp013778305	80.0691	603	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016924665.1	s__Nocardioides sp016924665	79.8402	575	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466785.1	s__Nocardioides marinisabuli	79.823	586	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:25,494] [INFO] GTDB search result was written to GCF_014646375.1_ASM1464637v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:25,495] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:25,498] [INFO] DFAST_QC result json was written to GCF_014646375.1_ASM1464637v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:25,498] [INFO] DFAST_QC completed!
[2024-01-25 18:41:25,498] [INFO] Total running time: 0h1m35s