[2024-01-24 11:04:47,848] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:04:47,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:04:47,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg62482428-bb00-4ec5-81f0-89f038664c63/dqc_reference
[2024-01-24 11:04:49,045] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:04:49,046] [INFO] Task started: Prodigal
[2024-01-24 11:04:49,046] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e2b6f16-7cf3-49ab-9b82-38ef5853e841/GCF_016889365.1_ASM1688936v1_genomic.fna.gz | prodigal -d GCF_016889365.1_ASM1688936v1_genomic.fna/cds.fna -a GCF_016889365.1_ASM1688936v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:04:56,507] [INFO] Task succeeded: Prodigal
[2024-01-24 11:04:56,507] [INFO] Task started: HMMsearch
[2024-01-24 11:04:56,508] [INFO] Running command: hmmsearch --tblout GCF_016889365.1_ASM1688936v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62482428-bb00-4ec5-81f0-89f038664c63/dqc_reference/reference_markers.hmm GCF_016889365.1_ASM1688936v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:04:56,730] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:04:56,732] [INFO] Found 6/6 markers.
[2024-01-24 11:04:56,755] [INFO] Query marker FASTA was written to GCF_016889365.1_ASM1688936v1_genomic.fna/markers.fasta
[2024-01-24 11:04:56,756] [INFO] Task started: Blastn
[2024-01-24 11:04:56,756] [INFO] Running command: blastn -query GCF_016889365.1_ASM1688936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62482428-bb00-4ec5-81f0-89f038664c63/dqc_reference/reference_markers.fasta -out GCF_016889365.1_ASM1688936v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:04:57,547] [INFO] Task succeeded: Blastn
[2024-01-24 11:04:57,551] [INFO] Selected 10 target genomes.
[2024-01-24 11:04:57,552] [INFO] Target genome list was writen to GCF_016889365.1_ASM1688936v1_genomic.fna/target_genomes.txt
[2024-01-24 11:04:57,559] [INFO] Task started: fastANI
[2024-01-24 11:04:57,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e2b6f16-7cf3-49ab-9b82-38ef5853e841/GCF_016889365.1_ASM1688936v1_genomic.fna.gz --refList GCF_016889365.1_ASM1688936v1_genomic.fna/target_genomes.txt --output GCF_016889365.1_ASM1688936v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:02,960] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:02,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62482428-bb00-4ec5-81f0-89f038664c63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:02,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62482428-bb00-4ec5-81f0-89f038664c63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:02,972] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:02,972] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:02,972] [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 kroppenstedtii	strain=FDAARGOS_1192	GCA_016889365.1	161879	161879	suspected-type	True	100.0	814	815	95	conclusive
Corynebacterium kroppenstedtii	strain=DSM 44385	GCA_000023145.1	161879	161879	suspected-type	True	99.9999	812	815	95	conclusive
Corynebacterium pseudokroppenstedtii	strain=MC-17X	GCA_019754945.1	2804917	2804917	type	True	93.687	777	815	95	below_threshold
Corynebacterium parakroppenstedtii	strain=MC-26	GCA_019754935.1	2828363	2828363	type	True	93.1949	771	815	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.174	59	815	95	below_threshold
Corynebacterium kalinowskii	strain=1959	GCA_009734385.1	2675216	2675216	type	True	78.2502	55	815	95	below_threshold
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	78.2389	82	815	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	77.768	73	815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:02,974] [INFO] DFAST Taxonomy check result was written to GCF_016889365.1_ASM1688936v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:02,977] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:02,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:02,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62482428-bb00-4ec5-81f0-89f038664c63/dqc_reference/checkm_data
[2024-01-24 11:05:02,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:03,191] [INFO] Task started: CheckM
[2024-01-24 11:05:03,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016889365.1_ASM1688936v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016889365.1_ASM1688936v1_genomic.fna/checkm_input GCF_016889365.1_ASM1688936v1_genomic.fna/checkm_result
[2024-01-24 11:05:30,406] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:30,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:30,430] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:30,430] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:30,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016889365.1_ASM1688936v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:30,431] [INFO] Task started: Blastn
[2024-01-24 11:05:30,431] [INFO] Running command: blastn -query GCF_016889365.1_ASM1688936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62482428-bb00-4ec5-81f0-89f038664c63/dqc_reference/reference_markers_gtdb.fasta -out GCF_016889365.1_ASM1688936v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:31,532] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:31,536] [INFO] Selected 6 target genomes.
[2024-01-24 11:05:31,536] [INFO] Target genome list was writen to GCF_016889365.1_ASM1688936v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:31,542] [INFO] Task started: fastANI
[2024-01-24 11:05:31,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e2b6f16-7cf3-49ab-9b82-38ef5853e841/GCF_016889365.1_ASM1688936v1_genomic.fna.gz --refList GCF_016889365.1_ASM1688936v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016889365.1_ASM1688936v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:34,944] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:34,952] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:05:34,952] [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_000023145.1	s__Corynebacterium kroppenstedtii	99.9947	814	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_016889405.1	s__Corynebacterium kroppenstedtii_C	94.0613	789	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552955.1	s__Corynebacterium kroppenstedtii_A	93.2072	781	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.92	99.91	0.99	0.98	4	-
GCA_003243515.1	s__Corynebacterium kroppenstedtii_B	92.7207	724	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016894245.1	s__Corynebacterium sp902373425	90.202	772	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCA_019209935.1	s__Corynebacterium sp019209935	77.0738	65	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.84	95.84	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:05:34,954] [INFO] GTDB search result was written to GCF_016889365.1_ASM1688936v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:34,954] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:34,957] [INFO] DFAST_QC result json was written to GCF_016889365.1_ASM1688936v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:34,957] [INFO] DFAST_QC completed!
[2024-01-24 11:05:34,957] [INFO] Total running time: 0h0m47s