[2024-01-24 12:47:22,203] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,204] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fd2c2cb-153d-4ef4-a7b0-62786499abef/dqc_reference
[2024-01-24 12:47:23,515] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,515] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,516] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe7001c3-ad4c-4e38-a485-d60e959ae5aa/GCF_024102595.1_ASM2410259v1_genomic.fna.gz | prodigal -d GCF_024102595.1_ASM2410259v1_genomic.fna/cds.fna -a GCF_024102595.1_ASM2410259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:30,846] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:30,846] [INFO] Task started: HMMsearch
[2024-01-24 12:47:30,846] [INFO] Running command: hmmsearch --tblout GCF_024102595.1_ASM2410259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fd2c2cb-153d-4ef4-a7b0-62786499abef/dqc_reference/reference_markers.hmm GCF_024102595.1_ASM2410259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:31,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:31,093] [INFO] Found 6/6 markers.
[2024-01-24 12:47:31,121] [INFO] Query marker FASTA was written to GCF_024102595.1_ASM2410259v1_genomic.fna/markers.fasta
[2024-01-24 12:47:31,122] [INFO] Task started: Blastn
[2024-01-24 12:47:31,122] [INFO] Running command: blastn -query GCF_024102595.1_ASM2410259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fd2c2cb-153d-4ef4-a7b0-62786499abef/dqc_reference/reference_markers.fasta -out GCF_024102595.1_ASM2410259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:32,022] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:32,027] [INFO] Selected 24 target genomes.
[2024-01-24 12:47:32,027] [INFO] Target genome list was writen to GCF_024102595.1_ASM2410259v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:32,078] [INFO] Task started: fastANI
[2024-01-24 12:47:32,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe7001c3-ad4c-4e38-a485-d60e959ae5aa/GCF_024102595.1_ASM2410259v1_genomic.fna.gz --refList GCF_024102595.1_ASM2410259v1_genomic.fna/target_genomes.txt --output GCF_024102595.1_ASM2410259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:43,031] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:43,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fd2c2cb-153d-4ef4-a7b0-62786499abef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:43,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fd2c2cb-153d-4ef4-a7b0-62786499abef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:43,050] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:43,050] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:43,050] [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
Corynebacterium coyleae	strain=DSM 44184	GCA_900105505.1	53374	53374	type	True	79.8048	285	771	95	below_threshold
Corynebacterium coyleae	strain=FDAARGOS 1425	GCA_019048165.1	53374	53374	type	True	79.6969	292	771	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	79.5772	305	771	95	below_threshold
Corynebacterium riegelii	strain=FDAARGOS_1114	GCA_016728505.1	156976	156976	type	True	79.5586	256	771	95	below_threshold
Corynebacterium imitans	strain=DSM 44264	GCA_000739455.1	156978	156978	type	True	79.4969	331	771	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	79.463	336	771	95	below_threshold
Corynebacterium gottingense	strain=DSM 103494	GCA_003693265.1	2041036	2041036	type	True	79.4302	302	771	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.3641	290	771	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	79.3233	323	771	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	79.2344	276	771	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	79.1916	272	771	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	78.9965	277	771	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	78.9901	279	771	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	78.5506	252	771	95	below_threshold
Corynebacterium aquatimens	strain=DSM 45632	GCA_015752125.1	1190508	1190508	type	True	78.5182	145	771	95	below_threshold
Corynebacterium tuscaniense	strain=CCUG 51321T	GCA_008693065.1	302449	302449	type	True	78.4921	155	771	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	78.2039	153	771	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	78.0933	169	771	95	below_threshold
Corynebacterium suranareeae	strain=N24	GCA_002355155.1	2506452	2506452	type	True	77.6974	78	771	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	77.4588	76	771	95	below_threshold
Corynebacterium diphtheriae		GCA_902809765.1	1717	1717	type	True	77.4093	79	771	95	below_threshold
Corynebacterium diphtheriae	strain=NCTC11397	GCA_001457455.1	1717	1717	type	True	77.4093	79	771	95	below_threshold
Corynebacterium renale	strain=NCTC7448	GCA_900478035.1	1724	1724	type	True	77.264	131	771	95	below_threshold
Corynebacterium renale	strain=DSM 20688	GCA_002563965.1	1724	1724	type	True	77.2608	132	771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:43,052] [INFO] DFAST Taxonomy check result was written to GCF_024102595.1_ASM2410259v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:43,053] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:43,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:43,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fd2c2cb-153d-4ef4-a7b0-62786499abef/dqc_reference/checkm_data
[2024-01-24 12:47:43,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:43,087] [INFO] Task started: CheckM
[2024-01-24 12:47:43,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024102595.1_ASM2410259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024102595.1_ASM2410259v1_genomic.fna/checkm_input GCF_024102595.1_ASM2410259v1_genomic.fna/checkm_result
[2024-01-24 12:48:10,186] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:10,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:10,208] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:10,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:10,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024102595.1_ASM2410259v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:10,209] [INFO] Task started: Blastn
[2024-01-24 12:48:10,209] [INFO] Running command: blastn -query GCF_024102595.1_ASM2410259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fd2c2cb-153d-4ef4-a7b0-62786499abef/dqc_reference/reference_markers_gtdb.fasta -out GCF_024102595.1_ASM2410259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:11,407] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:11,411] [INFO] Selected 15 target genomes.
[2024-01-24 12:48:11,411] [INFO] Target genome list was writen to GCF_024102595.1_ASM2410259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:11,422] [INFO] Task started: fastANI
[2024-01-24 12:48:11,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe7001c3-ad4c-4e38-a485-d60e959ae5aa/GCF_024102595.1_ASM2410259v1_genomic.fna.gz --refList GCF_024102595.1_ASM2410259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024102595.1_ASM2410259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:19,122] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:19,136] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:19,136] [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_001767255.1	s__Corynebacterium sp001767255	97.2705	716	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.41	96.75	0.92	0.92	4	conclusive
GCF_001875725.1	s__Corynebacterium sp001875725	89.8534	654	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001875665.1	s__Corynebacterium sp001875665	88.821	643	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105505.1	s__Corynebacterium coyleae	79.8048	285	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.88	97.68	0.93	0.91	16	-
GCF_001831515.1	s__Corynebacterium sp001831515	79.6701	342	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.57	96.57	0.93	0.93	2	-
GCF_016728505.1	s__Corynebacterium riegelii	79.5588	257	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.34	97.30	0.92	0.92	4	-
GCF_000739455.1	s__Corynebacterium imitans	79.5005	328	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003693265.1	s__Corynebacterium gottingense	79.4472	301	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	-
GCA_900156035.1	s__Corynebacterium afermentans	79.2199	278	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_900176865.1	s__Corynebacterium fournieri	79.1752	273	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490555.1	s__Corynebacterium sp014490555	78.9965	277	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_903645305.1	s__Corynebacterium sp001764565	78.8962	269	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
GCF_900103625.1	s__Corynebacterium mycetoides	78.5506	252	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008693065.1	s__Corynebacterium tuscaniense	78.4921	155	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.42	98.40	0.94	0.94	3	-
GCF_002563965.1	s__Corynebacterium renale	77.2608	132	771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.02	98.07	0.97	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:19,138] [INFO] GTDB search result was written to GCF_024102595.1_ASM2410259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:19,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:19,143] [INFO] DFAST_QC result json was written to GCF_024102595.1_ASM2410259v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:19,143] [INFO] DFAST_QC completed!
[2024-01-24 12:48:19,143] [INFO] Total running time: 0h0m57s