[2024-01-24 14:38:49,871] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:49,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:49,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bbc8032-c764-4e18-b234-c581a45c5131/dqc_reference
[2024-01-24 14:38:52,371] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:52,373] [INFO] Task started: Prodigal
[2024-01-24 14:38:52,373] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb5d7292-d19f-4c0e-a7c7-8d4ef9ec7a64/GCF_004331375.1_ASM433137v1_genomic.fna.gz | prodigal -d GCF_004331375.1_ASM433137v1_genomic.fna/cds.fna -a GCF_004331375.1_ASM433137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:21,042] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:21,042] [INFO] Task started: HMMsearch
[2024-01-24 14:39:21,042] [INFO] Running command: hmmsearch --tblout GCF_004331375.1_ASM433137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bbc8032-c764-4e18-b234-c581a45c5131/dqc_reference/reference_markers.hmm GCF_004331375.1_ASM433137v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:21,485] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:21,486] [INFO] Found 6/6 markers.
[2024-01-24 14:39:21,563] [INFO] Query marker FASTA was written to GCF_004331375.1_ASM433137v1_genomic.fna/markers.fasta
[2024-01-24 14:39:21,563] [INFO] Task started: Blastn
[2024-01-24 14:39:21,563] [INFO] Running command: blastn -query GCF_004331375.1_ASM433137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bbc8032-c764-4e18-b234-c581a45c5131/dqc_reference/reference_markers.fasta -out GCF_004331375.1_ASM433137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:22,850] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:22,854] [INFO] Selected 11 target genomes.
[2024-01-24 14:39:22,855] [INFO] Target genome list was writen to GCF_004331375.1_ASM433137v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:22,860] [INFO] Task started: fastANI
[2024-01-24 14:39:22,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb5d7292-d19f-4c0e-a7c7-8d4ef9ec7a64/GCF_004331375.1_ASM433137v1_genomic.fna.gz --refList GCF_004331375.1_ASM433137v1_genomic.fna/target_genomes.txt --output GCF_004331375.1_ASM433137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:49,599] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:49,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bbc8032-c764-4e18-b234-c581a45c5131/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:49,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bbc8032-c764-4e18-b234-c581a45c5131/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:49,610] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:49,611] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:39:49,611] [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
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	100.0	3087	3087	95	inconclusive
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	95.5274	2614	3087	95	inconclusive
Kribbella soli	strain=KCTC 29219	GCA_004331345.1	1124743	1124743	type	True	91.9954	2491	3087	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	87.9436	2249	3087	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	87.1541	2096	3087	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	87.0194	2146	3087	95	below_threshold
Kribbella jejuensis	strain=DSM 17305	GCA_006715085.1	236068	236068	type	True	86.7619	2004	3087	95	below_threshold
Kribbella solani	strain=DSM 17294	GCA_014205295.1	236067	236067	type	True	85.2732	1912	3087	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	84.5658	1974	3087	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	84.4496	1676	3087	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.6819	581	3087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:49,612] [INFO] DFAST Taxonomy check result was written to GCF_004331375.1_ASM433137v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:49,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:49,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:49,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bbc8032-c764-4e18-b234-c581a45c5131/dqc_reference/checkm_data
[2024-01-24 14:39:49,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:49,716] [INFO] Task started: CheckM
[2024-01-24 14:39:49,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331375.1_ASM433137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331375.1_ASM433137v1_genomic.fna/checkm_input GCF_004331375.1_ASM433137v1_genomic.fna/checkm_result
[2024-01-24 14:41:14,292] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:14,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:14,317] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:14,317] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:14,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331375.1_ASM433137v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:14,318] [INFO] Task started: Blastn
[2024-01-24 14:41:14,319] [INFO] Running command: blastn -query GCF_004331375.1_ASM433137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bbc8032-c764-4e18-b234-c581a45c5131/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331375.1_ASM433137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:16,408] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:16,426] [INFO] Selected 10 target genomes.
[2024-01-24 14:41:16,426] [INFO] Target genome list was writen to GCF_004331375.1_ASM433137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:16,435] [INFO] Task started: fastANI
[2024-01-24 14:41:16,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb5d7292-d19f-4c0e-a7c7-8d4ef9ec7a64/GCF_004331375.1_ASM433137v1_genomic.fna.gz --refList GCF_004331375.1_ASM433137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331375.1_ASM433137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:39,534] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:39,545] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:39,545] [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_004331435.1	s__Kribbella sindirgiensis	95.5274	2614	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.59	95.53	0.88	0.88	3	conclusive
GCF_004331345.1	s__Kribbella soli	91.9954	2491	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216905.1	s__Kribbella sp004216905	91.9907	2456	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366075.1	s__Kribbella sp004366075	91.5175	2351	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	97.22	95.50	0.92	0.87	3	-
GCF_011761605.1	s__Kribbella shirazensis	87.9701	2244	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876295.1	s__Kribbella aluminosa	87.1712	2093	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233875.1	s__Kribbella sp005233875	87.0189	2143	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365875.1	s__Kribbella sp004365875	86.8905	2137	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715085.1	s__Kribbella jejuensis	86.7558	2005	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365355.1	s__Kribbella sp004365355	86.6494	2124	3087	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:39,547] [INFO] GTDB search result was written to GCF_004331375.1_ASM433137v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:39,548] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:39,551] [INFO] DFAST_QC result json was written to GCF_004331375.1_ASM433137v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:39,551] [INFO] DFAST_QC completed!
[2024-01-24 14:41:39,552] [INFO] Total running time: 0h2m50s