[2024-01-24 12:45:18,939] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:18,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:18,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cb54aca-102c-4414-ab52-ebf65e761536/dqc_reference
[2024-01-24 12:45:20,147] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:20,148] [INFO] Task started: Prodigal
[2024-01-24 12:45:20,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg76e2ddb3-9bb4-4281-b2c3-b939a7997bb7/GCF_024160105.1_ASM2416010v1_genomic.fna.gz | prodigal -d GCF_024160105.1_ASM2416010v1_genomic.fna/cds.fna -a GCF_024160105.1_ASM2416010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:27,427] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:27,427] [INFO] Task started: HMMsearch
[2024-01-24 12:45:27,428] [INFO] Running command: hmmsearch --tblout GCF_024160105.1_ASM2416010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cb54aca-102c-4414-ab52-ebf65e761536/dqc_reference/reference_markers.hmm GCF_024160105.1_ASM2416010v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:27,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:27,669] [INFO] Found 6/6 markers.
[2024-01-24 12:45:27,691] [INFO] Query marker FASTA was written to GCF_024160105.1_ASM2416010v1_genomic.fna/markers.fasta
[2024-01-24 12:45:27,691] [INFO] Task started: Blastn
[2024-01-24 12:45:27,691] [INFO] Running command: blastn -query GCF_024160105.1_ASM2416010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb54aca-102c-4414-ab52-ebf65e761536/dqc_reference/reference_markers.fasta -out GCF_024160105.1_ASM2416010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:28,793] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:28,797] [INFO] Selected 12 target genomes.
[2024-01-24 12:45:28,798] [INFO] Target genome list was writen to GCF_024160105.1_ASM2416010v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:28,816] [INFO] Task started: fastANI
[2024-01-24 12:45:28,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e2ddb3-9bb4-4281-b2c3-b939a7997bb7/GCF_024160105.1_ASM2416010v1_genomic.fna.gz --refList GCF_024160105.1_ASM2416010v1_genomic.fna/target_genomes.txt --output GCF_024160105.1_ASM2416010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:34,802] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:34,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cb54aca-102c-4414-ab52-ebf65e761536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:34,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cb54aca-102c-4414-ab52-ebf65e761536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:34,816] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:34,816] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:34,816] [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 bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	82.8335	535	768	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	81.9196	516	768	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	81.6332	466	768	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	81.6217	480	768	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	81.3872	473	768	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	81.31	488	768	95	below_threshold
Corynebacterium hadale	strain=NBT06-6	GCA_002273005.1	2026255	2026255	type	True	81.3062	454	768	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	81.2168	468	768	95	below_threshold
Corynebacterium imitans	strain=DSM 44264	GCA_000739455.1	156978	156978	type	True	80.9557	465	768	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	80.9479	473	768	95	below_threshold
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	80.9413	433	768	95	below_threshold
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	79.9081	386	768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:34,818] [INFO] DFAST Taxonomy check result was written to GCF_024160105.1_ASM2416010v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:34,818] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:34,818] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:34,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cb54aca-102c-4414-ab52-ebf65e761536/dqc_reference/checkm_data
[2024-01-24 12:45:34,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:34,844] [INFO] Task started: CheckM
[2024-01-24 12:45:34,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024160105.1_ASM2416010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024160105.1_ASM2416010v1_genomic.fna/checkm_input GCF_024160105.1_ASM2416010v1_genomic.fna/checkm_result
[2024-01-24 12:46:01,100] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:01,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:01,122] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:01,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:01,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024160105.1_ASM2416010v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:01,124] [INFO] Task started: Blastn
[2024-01-24 12:46:01,124] [INFO] Running command: blastn -query GCF_024160105.1_ASM2416010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb54aca-102c-4414-ab52-ebf65e761536/dqc_reference/reference_markers_gtdb.fasta -out GCF_024160105.1_ASM2416010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:02,701] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:02,706] [INFO] Selected 11 target genomes.
[2024-01-24 12:46:02,706] [INFO] Target genome list was writen to GCF_024160105.1_ASM2416010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:02,724] [INFO] Task started: fastANI
[2024-01-24 12:46:02,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e2ddb3-9bb4-4281-b2c3-b939a7997bb7/GCF_024160105.1_ASM2416010v1_genomic.fna.gz --refList GCF_024160105.1_ASM2416010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024160105.1_ASM2416010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:08,306] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:08,323] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:08,323] [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_900078305.2	s__Corynebacterium bouchesdurhonense	82.8178	536	768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	81.9484	514	768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287505.1	s__Corynebacterium glaucum_A	81.6431	510	768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351335.1	s__Corynebacterium lipophilum	81.6364	479	768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900411315.1	s__Corynebacterium senegalense	81.6181	467	768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807265.1	s__Corynebacterium sp001807265	81.6131	492	768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCA_900156035.1	s__Corynebacterium afermentans	81.4277	472	768	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	81.3101	488	768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003693265.1	s__Corynebacterium gottingense	81.2856	423	768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	-
GCF_001831515.1	s__Corynebacterium sp001831515	81.0769	477	768	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	80.9557	465	768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:08,338] [INFO] GTDB search result was written to GCF_024160105.1_ASM2416010v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:08,338] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:08,343] [INFO] DFAST_QC result json was written to GCF_024160105.1_ASM2416010v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:08,344] [INFO] DFAST_QC completed!
[2024-01-24 12:46:08,344] [INFO] Total running time: 0h0m49s