[2024-01-24 13:37:05,129] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,131] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,131] [INFO] DQC Reference Directory: /var/lib/cwl/stge9ae85eb-60bb-4c1e-ae1d-30698266aae1/dqc_reference
[2024-01-24 13:37:06,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,563] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,564] [INFO] Running command: gunzip -c /var/lib/cwl/stgd784ade3-f58a-46ed-a57c-edc8d33a6019/GCF_014266025.1_ASM1426602v1_genomic.fna.gz | prodigal -d GCF_014266025.1_ASM1426602v1_genomic.fna/cds.fna -a GCF_014266025.1_ASM1426602v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:18,259] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:18,260] [INFO] Task started: HMMsearch
[2024-01-24 13:37:18,260] [INFO] Running command: hmmsearch --tblout GCF_014266025.1_ASM1426602v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9ae85eb-60bb-4c1e-ae1d-30698266aae1/dqc_reference/reference_markers.hmm GCF_014266025.1_ASM1426602v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:18,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:18,581] [INFO] Found 6/6 markers.
[2024-01-24 13:37:18,628] [INFO] Query marker FASTA was written to GCF_014266025.1_ASM1426602v1_genomic.fna/markers.fasta
[2024-01-24 13:37:18,629] [INFO] Task started: Blastn
[2024-01-24 13:37:18,629] [INFO] Running command: blastn -query GCF_014266025.1_ASM1426602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9ae85eb-60bb-4c1e-ae1d-30698266aae1/dqc_reference/reference_markers.fasta -out GCF_014266025.1_ASM1426602v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:20,047] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:20,050] [INFO] Selected 19 target genomes.
[2024-01-24 13:37:20,050] [INFO] Target genome list was writen to GCF_014266025.1_ASM1426602v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:20,058] [INFO] Task started: fastANI
[2024-01-24 13:37:20,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgd784ade3-f58a-46ed-a57c-edc8d33a6019/GCF_014266025.1_ASM1426602v1_genomic.fna.gz --refList GCF_014266025.1_ASM1426602v1_genomic.fna/target_genomes.txt --output GCF_014266025.1_ASM1426602v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:41,058] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:41,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9ae85eb-60bb-4c1e-ae1d-30698266aae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:41,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9ae85eb-60bb-4c1e-ae1d-30698266aae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:41,075] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:41,075] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:41,075] [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 deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	100.0	1380	1384	95	conclusive
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	99.9958	1377	1384	95	conclusive
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	83.4407	874	1384	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.4719	845	1384	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	82.4488	930	1384	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	82.4264	856	1384	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	82.4244	926	1384	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	82.2451	833	1384	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	82.2093	839	1384	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	82.0881	829	1384	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	82.0537	771	1384	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	82.0182	774	1384	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	81.9817	841	1384	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	81.9035	815	1384	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	81.2123	751	1384	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.8776	653	1384	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.5815	647	1384	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.4451	668	1384	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.0417	697	1384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:41,077] [INFO] DFAST Taxonomy check result was written to GCF_014266025.1_ASM1426602v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:41,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:41,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:41,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9ae85eb-60bb-4c1e-ae1d-30698266aae1/dqc_reference/checkm_data
[2024-01-24 13:37:41,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:41,120] [INFO] Task started: CheckM
[2024-01-24 13:37:41,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014266025.1_ASM1426602v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014266025.1_ASM1426602v1_genomic.fna/checkm_input GCF_014266025.1_ASM1426602v1_genomic.fna/checkm_result
[2024-01-24 13:38:38,852] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:38,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:38,872] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:38,872] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:38,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014266025.1_ASM1426602v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:38,873] [INFO] Task started: Blastn
[2024-01-24 13:38:38,873] [INFO] Running command: blastn -query GCF_014266025.1_ASM1426602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9ae85eb-60bb-4c1e-ae1d-30698266aae1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014266025.1_ASM1426602v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:41,202] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:41,206] [INFO] Selected 15 target genomes.
[2024-01-24 13:38:41,206] [INFO] Target genome list was writen to GCF_014266025.1_ASM1426602v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:41,241] [INFO] Task started: fastANI
[2024-01-24 13:38:41,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgd784ade3-f58a-46ed-a57c-edc8d33a6019/GCF_014266025.1_ASM1426602v1_genomic.fna.gz --refList GCF_014266025.1_ASM1426602v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014266025.1_ASM1426602v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:58,715] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:58,731] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:58,731] [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_014266025.1	s__Nocardioides deserti	100.0	1380	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_011250565.1	s__Nocardioides sp011250565	94.8147	1165	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	88.4125	1076	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_014127485.1	s__Nocardioides sp014127485	83.4017	877	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_013155365.1	s__Nocardioides sp013155365	82.5146	843	1384	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	82.5092	840	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_014212315.1	s__Nocardioides luti	82.425	856	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	82.2482	846	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002117935.1	s__Nocardioides sp002117935	82.2263	818	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013466985.1	s__Nocardioides ungokensis	82.0443	772	1384	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	82.0309	835	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_014191495.1	s__Nocardioides soli	82.0246	837	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	82.0081	775	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	81.1108	760	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916455.1	s__Nocardioides sp017916455	80.949	694	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:58,733] [INFO] GTDB search result was written to GCF_014266025.1_ASM1426602v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:58,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:58,738] [INFO] DFAST_QC result json was written to GCF_014266025.1_ASM1426602v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:58,738] [INFO] DFAST_QC completed!
[2024-01-24 13:38:58,738] [INFO] Total running time: 0h1m54s