[2024-01-24 12:29:52,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:52,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:52,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bd24957-9ad6-4ba8-a27c-c275c7ecf93c/dqc_reference
[2024-01-24 12:29:53,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:53,861] [INFO] Task started: Prodigal
[2024-01-24 12:29:53,861] [INFO] Running command: gunzip -c /var/lib/cwl/stg74a3a4d8-e36b-42cd-a35a-312f71cc7bac/GCF_013466985.1_ASM1346698v1_genomic.fna.gz | prodigal -d GCF_013466985.1_ASM1346698v1_genomic.fna/cds.fna -a GCF_013466985.1_ASM1346698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:06,995] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:06,996] [INFO] Task started: HMMsearch
[2024-01-24 12:30:06,996] [INFO] Running command: hmmsearch --tblout GCF_013466985.1_ASM1346698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bd24957-9ad6-4ba8-a27c-c275c7ecf93c/dqc_reference/reference_markers.hmm GCF_013466985.1_ASM1346698v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:07,260] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:07,262] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg74a3a4d8-e36b-42cd-a35a-312f71cc7bac/GCF_013466985.1_ASM1346698v1_genomic.fna.gz]
[2024-01-24 12:30:07,304] [INFO] Query marker FASTA was written to GCF_013466985.1_ASM1346698v1_genomic.fna/markers.fasta
[2024-01-24 12:30:07,304] [INFO] Task started: Blastn
[2024-01-24 12:30:07,304] [INFO] Running command: blastn -query GCF_013466985.1_ASM1346698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bd24957-9ad6-4ba8-a27c-c275c7ecf93c/dqc_reference/reference_markers.fasta -out GCF_013466985.1_ASM1346698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:08,438] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:08,443] [INFO] Selected 22 target genomes.
[2024-01-24 12:30:08,444] [INFO] Target genome list was writen to GCF_013466985.1_ASM1346698v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:08,453] [INFO] Task started: fastANI
[2024-01-24 12:30:08,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a3a4d8-e36b-42cd-a35a-312f71cc7bac/GCF_013466985.1_ASM1346698v1_genomic.fna.gz --refList GCF_013466985.1_ASM1346698v1_genomic.fna/target_genomes.txt --output GCF_013466985.1_ASM1346698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:29,524] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:29,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bd24957-9ad6-4ba8-a27c-c275c7ecf93c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:29,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bd24957-9ad6-4ba8-a27c-c275c7ecf93c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:29,553] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:29,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:29,554] [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 ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	100.0	1541	1541	95	conclusive
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	83.9446	978	1541	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	83.826	938	1541	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	83.2711	933	1541	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	81.9165	852	1541	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	81.8642	788	1541	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	81.8614	812	1541	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.8589	797	1541	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	81.8477	783	1541	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	81.8314	803	1541	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	81.7846	848	1541	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	81.1407	690	1541	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	81.1029	799	1541	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	81.0107	709	1541	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.976	690	1541	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.9371	740	1541	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	80.9167	728	1541	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	80.8221	743	1541	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.6133	694	1541	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.5816	732	1541	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.0369	645	1541	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.8749	720	1541	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:29,556] [INFO] DFAST Taxonomy check result was written to GCF_013466985.1_ASM1346698v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:29,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:29,557] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:29,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bd24957-9ad6-4ba8-a27c-c275c7ecf93c/dqc_reference/checkm_data
[2024-01-24 12:30:29,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:29,600] [INFO] Task started: CheckM
[2024-01-24 12:30:29,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013466985.1_ASM1346698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013466985.1_ASM1346698v1_genomic.fna/checkm_input GCF_013466985.1_ASM1346698v1_genomic.fna/checkm_result
[2024-01-24 12:31:46,460] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:46,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:46,481] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:46,482] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:46,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013466985.1_ASM1346698v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:46,483] [INFO] Task started: Blastn
[2024-01-24 12:31:46,483] [INFO] Running command: blastn -query GCF_013466985.1_ASM1346698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bd24957-9ad6-4ba8-a27c-c275c7ecf93c/dqc_reference/reference_markers_gtdb.fasta -out GCF_013466985.1_ASM1346698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:48,311] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:48,314] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:48,314] [INFO] Target genome list was writen to GCF_013466985.1_ASM1346698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:48,325] [INFO] Task started: fastANI
[2024-01-24 12:31:48,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a3a4d8-e36b-42cd-a35a-312f71cc7bac/GCF_013466985.1_ASM1346698v1_genomic.fna.gz --refList GCF_013466985.1_ASM1346698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013466985.1_ASM1346698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:04,954] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:04,967] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:04,967] [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_013466985.1	s__Nocardioides ungokensis	100.0	1541	1541	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_013409645.1	s__Nocardioides panaciterrulae	83.9166	979	1541	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	83.8275	938	1541	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	83.295	931	1541	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	82.5552	871	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014127485.1	s__Nocardioides sp014127485	82.2816	800	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_001425175.1	s__Nocardioides sp001425175	82.1763	897	1541	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	82.0398	764	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620705.1	s__Nocardioides sp000620705	81.9454	839	1541	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	81.87	781	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013466785.1	s__Nocardioides marinisabuli	81.8499	798	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	81.7853	848	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907435.1	s__Nocardioides salarius	81.6891	817	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_011420305.2	s__Nocardioides sp011420305	81.6339	747	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_016907475.1	s__Nocardioides cavernae	80.9172	727	1541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004919105.1	s__Nocardioides sp004919105	80.2927	689	1541	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 12:32:04,969] [INFO] GTDB search result was written to GCF_013466985.1_ASM1346698v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:04,970] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:04,977] [INFO] DFAST_QC result json was written to GCF_013466985.1_ASM1346698v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:04,977] [INFO] DFAST_QC completed!
[2024-01-24 12:32:04,977] [INFO] Total running time: 0h2m12s