[2024-01-25 19:24:50,704] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:50,708] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:50,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg7854cab2-fe44-4f51-9c82-faf5f2eaf053/dqc_reference
[2024-01-25 19:24:51,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:51,818] [INFO] Task started: Prodigal
[2024-01-25 19:24:51,819] [INFO] Running command: gunzip -c /var/lib/cwl/stgf045c2fc-2757-473d-a729-1724bad1b5a8/GCF_016342265.1_ASM1634226v1_genomic.fna.gz | prodigal -d GCF_016342265.1_ASM1634226v1_genomic.fna/cds.fna -a GCF_016342265.1_ASM1634226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:24:59,045] [INFO] Task succeeded: Prodigal
[2024-01-25 19:24:59,045] [INFO] Task started: HMMsearch
[2024-01-25 19:24:59,045] [INFO] Running command: hmmsearch --tblout GCF_016342265.1_ASM1634226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7854cab2-fe44-4f51-9c82-faf5f2eaf053/dqc_reference/reference_markers.hmm GCF_016342265.1_ASM1634226v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:24:59,240] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:24:59,242] [INFO] Found 6/6 markers.
[2024-01-25 19:24:59,269] [INFO] Query marker FASTA was written to GCF_016342265.1_ASM1634226v1_genomic.fna/markers.fasta
[2024-01-25 19:24:59,269] [INFO] Task started: Blastn
[2024-01-25 19:24:59,269] [INFO] Running command: blastn -query GCF_016342265.1_ASM1634226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7854cab2-fe44-4f51-9c82-faf5f2eaf053/dqc_reference/reference_markers.fasta -out GCF_016342265.1_ASM1634226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:00,222] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:00,242] [INFO] Selected 17 target genomes.
[2024-01-25 19:25:00,243] [INFO] Target genome list was writen to GCF_016342265.1_ASM1634226v1_genomic.fna/target_genomes.txt
[2024-01-25 19:25:00,306] [INFO] Task started: fastANI
[2024-01-25 19:25:00,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgf045c2fc-2757-473d-a729-1724bad1b5a8/GCF_016342265.1_ASM1634226v1_genomic.fna.gz --refList GCF_016342265.1_ASM1634226v1_genomic.fna/target_genomes.txt --output GCF_016342265.1_ASM1634226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:08,870] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:08,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7854cab2-fe44-4f51-9c82-faf5f2eaf053/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:08,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7854cab2-fe44-4f51-9c82-faf5f2eaf053/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:08,881] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:25:08,881] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:25:08,881] [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 halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.9001	318	905	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.8883	315	905	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.849	312	905	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.8478	317	905	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.8413	286	905	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	78.8023	318	905	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	78.7977	298	905	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	78.7219	300	905	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.6793	210	905	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.5764	299	905	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_000183325.2	36808	36808	type	True	78.5508	207	905	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	78.3651	239	905	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	78.3	245	905	95	below_threshold
Corynebacterium gallinarum	strain=Sa1YVA5	GCA_014837045.1	2762214	2762214	type	True	77.8751	242	905	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	77.774	256	905	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	77.7641	256	905	95	below_threshold
Nocardia aurantia	strain=RB56	GCA_009604425.1	2585199	2585199	type	True	76.4857	165	905	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:08,883] [INFO] DFAST Taxonomy check result was written to GCF_016342265.1_ASM1634226v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:08,883] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:08,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:08,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7854cab2-fe44-4f51-9c82-faf5f2eaf053/dqc_reference/checkm_data
[2024-01-25 19:25:08,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:08,913] [INFO] Task started: CheckM
[2024-01-25 19:25:08,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016342265.1_ASM1634226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016342265.1_ASM1634226v1_genomic.fna/checkm_input GCF_016342265.1_ASM1634226v1_genomic.fna/checkm_result
[2024-01-25 19:25:34,351] [INFO] Task succeeded: CheckM
[2024-01-25 19:25:34,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:25:34,368] [INFO] ===== Completeness check finished =====
[2024-01-25 19:25:34,368] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:25:34,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016342265.1_ASM1634226v1_genomic.fna/markers.fasta)
[2024-01-25 19:25:34,369] [INFO] Task started: Blastn
[2024-01-25 19:25:34,369] [INFO] Running command: blastn -query GCF_016342265.1_ASM1634226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7854cab2-fe44-4f51-9c82-faf5f2eaf053/dqc_reference/reference_markers_gtdb.fasta -out GCF_016342265.1_ASM1634226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:35,789] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:35,792] [INFO] Selected 10 target genomes.
[2024-01-25 19:25:35,792] [INFO] Target genome list was writen to GCF_016342265.1_ASM1634226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:25:35,821] [INFO] Task started: fastANI
[2024-01-25 19:25:35,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgf045c2fc-2757-473d-a729-1724bad1b5a8/GCF_016342265.1_ASM1634226v1_genomic.fna.gz --refList GCF_016342265.1_ASM1634226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016342265.1_ASM1634226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:25:41,755] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:41,762] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:25:41,763] [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_016342265.1	s__Corynebacterium sp016342265	100.0	905	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019209935.1	s__Corynebacterium sp019209935	91.0287	770	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.84	95.84	0.96	0.96	2	-
GCF_016342275.1	s__Corynebacterium sp016342275	87.6725	782	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595275.1	s__Corynebacterium sp016595275	86.7855	745	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819445.1	s__Corynebacterium humireducens	78.9222	312	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.8861	319	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.8413	286	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_900177745.1	s__Corynebacterium pollutisoli	78.7892	319	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_002994655.1	s__Corynebacterium sp002994655	78.7554	277	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011305.1	s__Corynebacterium efficiens	77.7491	258	905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:25:41,764] [INFO] GTDB search result was written to GCF_016342265.1_ASM1634226v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:25:41,765] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:25:41,768] [INFO] DFAST_QC result json was written to GCF_016342265.1_ASM1634226v1_genomic.fna/dqc_result.json
[2024-01-25 19:25:41,768] [INFO] DFAST_QC completed!
[2024-01-25 19:25:41,768] [INFO] Total running time: 0h0m51s