[2024-01-25 19:41:50,803] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:50,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:50,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg27fd88f6-bb33-442b-ba42-b0db65e36d1d/dqc_reference
[2024-01-25 19:41:51,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:51,982] [INFO] Task started: Prodigal
[2024-01-25 19:41:51,983] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c236d3b-240e-48f8-a373-9ee9cca6a93f/GCF_001941345.1_ASM194134v1_genomic.fna.gz | prodigal -d GCF_001941345.1_ASM194134v1_genomic.fna/cds.fna -a GCF_001941345.1_ASM194134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:00,082] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:00,083] [INFO] Task started: HMMsearch
[2024-01-25 19:42:00,083] [INFO] Running command: hmmsearch --tblout GCF_001941345.1_ASM194134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27fd88f6-bb33-442b-ba42-b0db65e36d1d/dqc_reference/reference_markers.hmm GCF_001941345.1_ASM194134v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:00,292] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:00,293] [INFO] Found 6/6 markers.
[2024-01-25 19:42:00,318] [INFO] Query marker FASTA was written to GCF_001941345.1_ASM194134v1_genomic.fna/markers.fasta
[2024-01-25 19:42:00,319] [INFO] Task started: Blastn
[2024-01-25 19:42:00,319] [INFO] Running command: blastn -query GCF_001941345.1_ASM194134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27fd88f6-bb33-442b-ba42-b0db65e36d1d/dqc_reference/reference_markers.fasta -out GCF_001941345.1_ASM194134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:00,991] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:00,994] [INFO] Selected 9 target genomes.
[2024-01-25 19:42:00,995] [INFO] Target genome list was writen to GCF_001941345.1_ASM194134v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:01,001] [INFO] Task started: fastANI
[2024-01-25 19:42:01,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c236d3b-240e-48f8-a373-9ee9cca6a93f/GCF_001941345.1_ASM194134v1_genomic.fna.gz --refList GCF_001941345.1_ASM194134v1_genomic.fna/target_genomes.txt --output GCF_001941345.1_ASM194134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:06,006] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:06,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27fd88f6-bb33-442b-ba42-b0db65e36d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:06,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27fd88f6-bb33-442b-ba42-b0db65e36d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:06,014] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:06,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:06,014] [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 stationis	strain=622=DSM 20302	GCA_001941345.1	1705	1705	type	True	100.0	953	953	95	conclusive
Corynebacterium casei	strain=LMG S-19264	GCA_000550785.1	160386	160386	type	True	82.983	661	953	95	below_threshold
Corynebacterium ammoniagenes	strain=DSM 20306 = 9.6	GCA_001941425.1	1697	1697	type	True	82.8622	654	953	95	below_threshold
Corynebacterium ammoniagenes	strain=DSM 20306	GCA_000164115.1	1697	1697	type	True	82.7331	648	953	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.8193	193	953	95	below_threshold
Corynebacterium accolens	strain=DSM 44278	GCA_023520795.1	38284	38284	type	True	78.7304	176	953	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	78.6939	234	953	95	below_threshold
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	78.5446	244	953	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	78.5044	165	953	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:06,015] [INFO] DFAST Taxonomy check result was written to GCF_001941345.1_ASM194134v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:06,016] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:06,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:06,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27fd88f6-bb33-442b-ba42-b0db65e36d1d/dqc_reference/checkm_data
[2024-01-25 19:42:06,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:06,046] [INFO] Task started: CheckM
[2024-01-25 19:42:06,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001941345.1_ASM194134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001941345.1_ASM194134v1_genomic.fna/checkm_input GCF_001941345.1_ASM194134v1_genomic.fna/checkm_result
[2024-01-25 19:42:32,814] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:32,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:32,829] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:32,829] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:32,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001941345.1_ASM194134v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:32,830] [INFO] Task started: Blastn
[2024-01-25 19:42:32,830] [INFO] Running command: blastn -query GCF_001941345.1_ASM194134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27fd88f6-bb33-442b-ba42-b0db65e36d1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001941345.1_ASM194134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:33,789] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:33,791] [INFO] Selected 8 target genomes.
[2024-01-25 19:42:33,791] [INFO] Target genome list was writen to GCF_001941345.1_ASM194134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:33,802] [INFO] Task started: fastANI
[2024-01-25 19:42:33,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c236d3b-240e-48f8-a373-9ee9cca6a93f/GCF_001941345.1_ASM194134v1_genomic.fna.gz --refList GCF_001941345.1_ASM194134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001941345.1_ASM194134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:38,853] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:38,859] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:38,859] [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_001941345.1	s__Corynebacterium stationis	100.0	953	953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.14	0.93	0.87	11	conclusive
GCF_002967075.1	s__Corynebacterium sp002967075	94.3785	812	953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550785.1	s__Corynebacterium casei	82.9485	661	953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.58	0.94	0.92	5	-
GCF_001941425.1	s__Corynebacterium ammoniagenes	82.8855	653	953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.70	98.81	0.99	0.95	5	-
GCF_000980815.1	s__Corynebacterium camporealensis	78.7498	237	953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000159135.1	s__Corynebacterium striatum	78.489	188	953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_000159115.1	s__Corynebacterium accolens	78.24	176	953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.20	96.99	0.95	0.94	10	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	77.9581	188	953	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:38,861] [INFO] GTDB search result was written to GCF_001941345.1_ASM194134v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:38,861] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:38,863] [INFO] DFAST_QC result json was written to GCF_001941345.1_ASM194134v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:38,864] [INFO] DFAST_QC completed!
[2024-01-25 19:42:38,864] [INFO] Total running time: 0h0m48s