[2024-01-25 17:35:50,650] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:50,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:50,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d646815-b0f2-4bf9-b6ff-7571db72a3b8/dqc_reference
[2024-01-25 17:35:51,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:51,761] [INFO] Task started: Prodigal
[2024-01-25 17:35:51,761] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ae4108c-51e1-4970-a684-69ff09041a77/GCF_000177535.2_ASM17753v2_genomic.fna.gz | prodigal -d GCF_000177535.2_ASM17753v2_genomic.fna/cds.fna -a GCF_000177535.2_ASM17753v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:59,088] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:59,088] [INFO] Task started: HMMsearch
[2024-01-25 17:35:59,088] [INFO] Running command: hmmsearch --tblout GCF_000177535.2_ASM17753v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d646815-b0f2-4bf9-b6ff-7571db72a3b8/dqc_reference/reference_markers.hmm GCF_000177535.2_ASM17753v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:59,273] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:59,274] [INFO] Found 6/6 markers.
[2024-01-25 17:35:59,294] [INFO] Query marker FASTA was written to GCF_000177535.2_ASM17753v2_genomic.fna/markers.fasta
[2024-01-25 17:35:59,294] [INFO] Task started: Blastn
[2024-01-25 17:35:59,294] [INFO] Running command: blastn -query GCF_000177535.2_ASM17753v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d646815-b0f2-4bf9-b6ff-7571db72a3b8/dqc_reference/reference_markers.fasta -out GCF_000177535.2_ASM17753v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:59,989] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:59,991] [INFO] Selected 21 target genomes.
[2024-01-25 17:35:59,992] [INFO] Target genome list was writen to GCF_000177535.2_ASM17753v2_genomic.fna/target_genomes.txt
[2024-01-25 17:36:00,077] [INFO] Task started: fastANI
[2024-01-25 17:36:00,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ae4108c-51e1-4970-a684-69ff09041a77/GCF_000177535.2_ASM17753v2_genomic.fna.gz --refList GCF_000177535.2_ASM17753v2_genomic.fna/target_genomes.txt --output GCF_000177535.2_ASM17753v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:10,471] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:10,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d646815-b0f2-4bf9-b6ff-7571db72a3b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:10,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d646815-b0f2-4bf9-b6ff-7571db72a3b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:10,483] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:36:10,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:10,483] [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 resistens	strain=DSM 45100	GCA_000177535.2	258224	258224	type	True	100.0	865	867	95	conclusive
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	80.9498	220	867	95	below_threshold
Corynebacterium auriscanis	strain=CIP 106629	GCA_000767255.1	99807	99807	type	True	80.3091	447	867	95	below_threshold
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	79.7704	154	867	95	below_threshold
Corynebacterium urealyticum	strain=DSM 7109	GCA_000069945.1	43771	43771	type	True	79.6023	153	867	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	79.6005	153	867	95	below_threshold
Corynebacterium urogenitale	strain=LMM-1652	GCA_009026825.1	2487892	2487892	type	True	79.0864	172	867	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.8601	107	867	95	below_threshold
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	78.7267	191	867	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	78.6172	75	867	95	below_threshold
Corynebacterium dentalis	strain=Marseille-P4122	GCA_900232865.1	2014528	2014528	type	True	78.5912	152	867	95	below_threshold
Corynebacterium casei	strain=LMG S-19264	GCA_000550785.1	160386	160386	type	True	78.533	71	867	95	below_threshold
Corynebacterium terpenotabidum	strain=Y-11	GCA_000418365.1	89154	89154	type	True	78.0543	84	867	95	below_threshold
Corynebacterium nuruki	strain=S6-4	GCA_007970465.1	1032851	1032851	type	True	77.7858	104	867	95	below_threshold
Corynebacterium pelargi	strain=136/3	GCA_004114895.1	1471400	1471400	type	True	77.6456	89	867	95	below_threshold
Corynebacterium doosanense	strain=CAU 212	GCA_000767055.1	1121358	1121358	type	True	77.2822	86	867	95	below_threshold
Corynebacterium nuruki	strain=S6-4	GCA_000213935.2	1032851	1032851	type	True	76.946	102	867	95	below_threshold
Corynebacterium pelargi	strain=CCM 8517	GCA_014635485.1	1471400	1471400	type	True	76.7582	81	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:10,484] [INFO] DFAST Taxonomy check result was written to GCF_000177535.2_ASM17753v2_genomic.fna/tc_result.tsv
[2024-01-25 17:36:10,485] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:10,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:10,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d646815-b0f2-4bf9-b6ff-7571db72a3b8/dqc_reference/checkm_data
[2024-01-25 17:36:10,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:10,513] [INFO] Task started: CheckM
[2024-01-25 17:36:10,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000177535.2_ASM17753v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000177535.2_ASM17753v2_genomic.fna/checkm_input GCF_000177535.2_ASM17753v2_genomic.fna/checkm_result
[2024-01-25 17:36:35,977] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:35,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:35,994] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:35,994] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:35,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000177535.2_ASM17753v2_genomic.fna/markers.fasta)
[2024-01-25 17:36:35,995] [INFO] Task started: Blastn
[2024-01-25 17:36:35,995] [INFO] Running command: blastn -query GCF_000177535.2_ASM17753v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d646815-b0f2-4bf9-b6ff-7571db72a3b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000177535.2_ASM17753v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:37,100] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:37,107] [INFO] Selected 21 target genomes.
[2024-01-25 17:36:37,107] [INFO] Target genome list was writen to GCF_000177535.2_ASM17753v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:37,117] [INFO] Task started: fastANI
[2024-01-25 17:36:37,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ae4108c-51e1-4970-a684-69ff09041a77/GCF_000177535.2_ASM17753v2_genomic.fna.gz --refList GCF_000177535.2_ASM17753v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000177535.2_ASM17753v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:47,234] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:47,245] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:47,245] [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_000177535.2	s__Corynebacterium resistens	100.0	865	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000767255.1	s__Corynebacterium auriscanis	80.3051	447	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.87	97.87	0.94	0.94	2	-
GCF_000738265.1	s__Corynebacterium jeikeium_A	79.6743	191	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCF_000069945.1	s__Corynebacterium urealyticum	79.5457	155	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	-
GCF_000738175.1	s__Corynebacterium jeikeium_C	79.347	203	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009026825.1	s__Corynebacterium sp009026825	79.1239	172	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000525655.1	s__Corynebacterium falsenii	78.8859	194	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.72	98.72	0.95	0.95	2	-
GCF_900232865.1	s__Corynebacterium dentalis	78.5912	152	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.56	98.56	0.96	0.96	2	-
GCF_000550785.1	s__Corynebacterium casei	78.4714	71	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.58	0.94	0.92	5	-
GCF_014490555.1	s__Corynebacterium sp014490555	78.3581	71	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_001815985.1	s__Corynebacterium sp001815985	78.3496	142	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.95	96.87	0.95	0.94	3	-
GCF_000418365.1	s__Corynebacterium terpenotabidum	78.2043	85	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001812805.1	s__Corynebacterium sp001812805	77.9967	75	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970465.1	s__Corynebacterium nuruki	77.9853	105	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.35	98.70	0.99	0.98	3	-
GCF_000159135.1	s__Corynebacterium striatum	77.8817	94	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCA_019120635.1	s__Corynebacterium intestinavium	77.8402	135	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114895.1	s__Corynebacterium pelargi	77.7163	87	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012837295.1	s__Corynebacterium sp012837295	76.4166	62	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:47,246] [INFO] GTDB search result was written to GCF_000177535.2_ASM17753v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:47,247] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:47,250] [INFO] DFAST_QC result json was written to GCF_000177535.2_ASM17753v2_genomic.fna/dqc_result.json
[2024-01-25 17:36:47,250] [INFO] DFAST_QC completed!
[2024-01-25 17:36:47,251] [INFO] Total running time: 0h0m57s