[2024-01-25 17:34:07,125] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ef785be-e41f-41b5-9028-c370a139a03c/dqc_reference
[2024-01-25 17:34:08,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,952] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a0a67d5-8f3c-4487-a5f2-78bd29eba5e7/GCF_026712185.1_ASM2671218v1_genomic.fna.gz | prodigal -d GCF_026712185.1_ASM2671218v1_genomic.fna/cds.fna -a GCF_026712185.1_ASM2671218v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:20,594] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:20,594] [INFO] Task started: HMMsearch
[2024-01-25 17:34:20,594] [INFO] Running command: hmmsearch --tblout GCF_026712185.1_ASM2671218v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ef785be-e41f-41b5-9028-c370a139a03c/dqc_reference/reference_markers.hmm GCF_026712185.1_ASM2671218v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:20,892] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:20,893] [INFO] Found 6/6 markers.
[2024-01-25 17:34:20,931] [INFO] Query marker FASTA was written to GCF_026712185.1_ASM2671218v1_genomic.fna/markers.fasta
[2024-01-25 17:34:20,932] [INFO] Task started: Blastn
[2024-01-25 17:34:20,932] [INFO] Running command: blastn -query GCF_026712185.1_ASM2671218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ef785be-e41f-41b5-9028-c370a139a03c/dqc_reference/reference_markers.fasta -out GCF_026712185.1_ASM2671218v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:22,220] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:22,230] [INFO] Selected 13 target genomes.
[2024-01-25 17:34:22,230] [INFO] Target genome list was writen to GCF_026712185.1_ASM2671218v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:22,326] [INFO] Task started: fastANI
[2024-01-25 17:34:22,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a0a67d5-8f3c-4487-a5f2-78bd29eba5e7/GCF_026712185.1_ASM2671218v1_genomic.fna.gz --refList GCF_026712185.1_ASM2671218v1_genomic.fna/target_genomes.txt --output GCF_026712185.1_ASM2671218v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:37,726] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:37,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ef785be-e41f-41b5-9028-c370a139a03c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:37,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ef785be-e41f-41b5-9028-c370a139a03c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:37,741] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:34:37,741] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:34:37,741] [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 cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	90.8039	1234	1501	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	90.7701	1242	1501	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	86.6279	1079	1501	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	86.3505	1085	1501	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	86.2586	1007	1501	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	85.763	1017	1501	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	85.6976	957	1501	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	85.6026	1043	1501	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.5915	1075	1501	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	85.5046	1004	1501	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.49	1040	1501	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	85.4727	1009	1501	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	85.2	1069	1501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:37,743] [INFO] DFAST Taxonomy check result was written to GCF_026712185.1_ASM2671218v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:37,745] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:37,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:37,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ef785be-e41f-41b5-9028-c370a139a03c/dqc_reference/checkm_data
[2024-01-25 17:34:37,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:37,801] [INFO] Task started: CheckM
[2024-01-25 17:34:37,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026712185.1_ASM2671218v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026712185.1_ASM2671218v1_genomic.fna/checkm_input GCF_026712185.1_ASM2671218v1_genomic.fna/checkm_result
[2024-01-25 17:35:43,907] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:43,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:43,932] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:43,932] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:43,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026712185.1_ASM2671218v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:43,934] [INFO] Task started: Blastn
[2024-01-25 17:35:43,934] [INFO] Running command: blastn -query GCF_026712185.1_ASM2671218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ef785be-e41f-41b5-9028-c370a139a03c/dqc_reference/reference_markers_gtdb.fasta -out GCF_026712185.1_ASM2671218v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:46,211] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:46,218] [INFO] Selected 14 target genomes.
[2024-01-25 17:35:46,218] [INFO] Target genome list was writen to GCF_026712185.1_ASM2671218v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:46,227] [INFO] Task started: fastANI
[2024-01-25 17:35:46,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a0a67d5-8f3c-4487-a5f2-78bd29eba5e7/GCF_026712185.1_ASM2671218v1_genomic.fna.gz --refList GCF_026712185.1_ASM2671218v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026712185.1_ASM2671218v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:02,235] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:02,245] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:36:02,245] [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_016907475.1	s__Nocardioides cavernae	90.804	1234	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013155335.1	s__Nocardioides sp013155335	88.7624	1204	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086465.1	s__Nocardioides sp014265965	86.9348	1041	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014779655.1	s__Nocardioides ganghwensis	86.6392	1078	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004785795.1	s__Nocardioides eburneiflavus	86.3396	1086	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653115.1	s__Nocardioides flavus	86.2672	1006	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410035.1	s__Nocardioides cavernae_A	85.8917	1059	1501	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	85.8286	968	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_001428125.1	s__Nocardioides sp001428125	85.736	1016	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425025.1	s__Nocardioides sp001425025	85.6974	1086	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105585.1	s__Nocardioides exalbidus	85.6161	1044	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137255.1	s__Nocardioides oleivorans	85.5364	1034	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633575.1	s__Nocardioides sp003633575	85.5201	1029	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916425.1	s__Nocardioides sp017916425	85.1406	957	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:02,246] [INFO] GTDB search result was written to GCF_026712185.1_ASM2671218v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:02,247] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:02,250] [INFO] DFAST_QC result json was written to GCF_026712185.1_ASM2671218v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:02,250] [INFO] DFAST_QC completed!
[2024-01-25 17:36:02,250] [INFO] Total running time: 0h1m55s