[2024-01-25 17:49:35,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:35,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:35,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg7767a0dc-9644-4433-b2ce-a39079fa1a5e/dqc_reference
[2024-01-25 17:49:36,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:36,782] [INFO] Task started: Prodigal
[2024-01-25 17:49:36,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg187e7559-4702-465d-8bb7-e361568e8e9b/GCF_024453815.1_ASM2445381v1_genomic.fna.gz | prodigal -d GCF_024453815.1_ASM2445381v1_genomic.fna/cds.fna -a GCF_024453815.1_ASM2445381v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:43,544] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:43,544] [INFO] Task started: HMMsearch
[2024-01-25 17:49:43,544] [INFO] Running command: hmmsearch --tblout GCF_024453815.1_ASM2445381v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7767a0dc-9644-4433-b2ce-a39079fa1a5e/dqc_reference/reference_markers.hmm GCF_024453815.1_ASM2445381v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:43,733] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:43,734] [INFO] Found 6/6 markers.
[2024-01-25 17:49:43,755] [INFO] Query marker FASTA was written to GCF_024453815.1_ASM2445381v1_genomic.fna/markers.fasta
[2024-01-25 17:49:43,755] [INFO] Task started: Blastn
[2024-01-25 17:49:43,756] [INFO] Running command: blastn -query GCF_024453815.1_ASM2445381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7767a0dc-9644-4433-b2ce-a39079fa1a5e/dqc_reference/reference_markers.fasta -out GCF_024453815.1_ASM2445381v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:44,556] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:44,558] [INFO] Selected 25 target genomes.
[2024-01-25 17:49:44,558] [INFO] Target genome list was writen to GCF_024453815.1_ASM2445381v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:44,600] [INFO] Task started: fastANI
[2024-01-25 17:49:44,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg187e7559-4702-465d-8bb7-e361568e8e9b/GCF_024453815.1_ASM2445381v1_genomic.fna.gz --refList GCF_024453815.1_ASM2445381v1_genomic.fna/target_genomes.txt --output GCF_024453815.1_ASM2445381v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:56,060] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:56,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7767a0dc-9644-4433-b2ce-a39079fa1a5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:56,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7767a0dc-9644-4433-b2ce-a39079fa1a5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:56,074] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:49:56,074] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:49:56,075] [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
Corynebacterium riegelii	strain=FDAARGOS_1114	GCA_016728505.1	156976	156976	type	True	80.3704	259	796	95	below_threshold
Corynebacterium coyleae	strain=DSM 44184	GCA_900105505.1	53374	53374	type	True	80.0976	299	796	95	below_threshold
Corynebacterium coyleae	strain=FDAARGOS 1425	GCA_019048165.1	53374	53374	type	True	80.0742	300	796	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	79.8664	352	796	95	below_threshold
Corynebacterium imitans	strain=DSM 44264	GCA_000739455.1	156978	156978	type	True	79.8046	349	796	95	below_threshold
Corynebacterium godavarianum	strain=PRD07	GCA_016785885.1	2054421	2054421	type	True	79.729	330	796	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	79.5695	332	796	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	79.4891	330	796	95	below_threshold
Corynebacterium gottingense	strain=DSM 103494	GCA_003693265.1	2041036	2041036	type	True	79.3424	312	796	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	79.3041	295	796	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	79.2814	286	796	95	below_threshold
Corynebacterium aquatimens	strain=DSM 45632	GCA_015752125.1	1190508	1190508	type	True	79.2099	162	796	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	79.1921	289	796	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	79.1101	294	796	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	79.0967	282	796	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	78.9888	254	796	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	78.9475	288	796	95	below_threshold
Corynebacterium tuscaniense	strain=CCUG 51321T	GCA_008693065.1	302449	302449	type	True	78.8883	159	796	95	below_threshold
Corynebacterium liangguodongii	strain=2184	GCA_003070865.1	2079535	2079535	type	True	78.7583	215	796	95	below_threshold
Corynebacterium diphtheriae	strain=NCTC11397	GCA_001457455.1	1717	1717	type	True	78.5189	84	796	95	below_threshold
Corynebacterium diphtheriae		GCA_902809765.1	1717	1717	type	True	78.4885	84	796	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	78.4113	144	796	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	78.2302	158	796	95	below_threshold
Corynebacterium suranareeae	strain=N24	GCA_002355155.1	2506452	2506452	type	True	78.0769	80	796	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	77.573	77	796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:56,076] [INFO] DFAST Taxonomy check result was written to GCF_024453815.1_ASM2445381v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:56,077] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:56,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:56,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7767a0dc-9644-4433-b2ce-a39079fa1a5e/dqc_reference/checkm_data
[2024-01-25 17:49:56,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:56,108] [INFO] Task started: CheckM
[2024-01-25 17:49:56,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024453815.1_ASM2445381v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024453815.1_ASM2445381v1_genomic.fna/checkm_input GCF_024453815.1_ASM2445381v1_genomic.fna/checkm_result
[2024-01-25 17:50:19,659] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:19,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:19,689] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:19,690] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:19,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024453815.1_ASM2445381v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:19,691] [INFO] Task started: Blastn
[2024-01-25 17:50:19,691] [INFO] Running command: blastn -query GCF_024453815.1_ASM2445381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7767a0dc-9644-4433-b2ce-a39079fa1a5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_024453815.1_ASM2445381v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:20,900] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:20,903] [INFO] Selected 15 target genomes.
[2024-01-25 17:50:20,903] [INFO] Target genome list was writen to GCF_024453815.1_ASM2445381v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:20,942] [INFO] Task started: fastANI
[2024-01-25 17:50:20,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg187e7559-4702-465d-8bb7-e361568e8e9b/GCF_024453815.1_ASM2445381v1_genomic.fna.gz --refList GCF_024453815.1_ASM2445381v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024453815.1_ASM2445381v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:28,529] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:28,538] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:28,539] [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	97.9488	757	796	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	89.7194	665	796	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	88.5716	648	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016728505.1	s__Corynebacterium riegelii	80.3723	258	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.34	97.30	0.92	0.92	4	-
GCF_001831515.1	s__Corynebacterium sp001831515	79.9599	346	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.57	96.57	0.93	0.93	2	-
GCF_000739455.1	s__Corynebacterium imitans	79.8713	348	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015351335.1	s__Corynebacterium lipophilum	79.2961	296	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577555.1	s__Corynebacterium jeddahense	79.2647	287	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645305.1	s__Corynebacterium sp001764565	79.2584	275	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
GCA_900156035.1	s__Corynebacterium afermentans	79.1931	292	796	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	79.1046	282	796	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	79.0947	295	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_900103625.1	s__Corynebacterium mycetoides	78.9799	255	796	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	78.9155	158	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.42	98.40	0.94	0.94	3	-
GCF_003070865.1	s__Corynebacterium liangguodongii	78.7591	215	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:28,541] [INFO] GTDB search result was written to GCF_024453815.1_ASM2445381v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:28,542] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:28,545] [INFO] DFAST_QC result json was written to GCF_024453815.1_ASM2445381v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:28,546] [INFO] DFAST_QC completed!
[2024-01-25 17:50:28,546] [INFO] Total running time: 0h0m53s