[2024-01-24 15:26:39,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg402cc13f-c149-41e5-8c78-8d0c5d0ec3b5/dqc_reference
[2024-01-24 15:26:41,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,030] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f51e1bd-d19f-4c21-a395-56bea8a05d86/GCF_003813985.1_ASM381398v1_genomic.fna.gz | prodigal -d GCF_003813985.1_ASM381398v1_genomic.fna/cds.fna -a GCF_003813985.1_ASM381398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:49,231] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:49,231] [INFO] Task started: HMMsearch
[2024-01-24 15:26:49,231] [INFO] Running command: hmmsearch --tblout GCF_003813985.1_ASM381398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg402cc13f-c149-41e5-8c78-8d0c5d0ec3b5/dqc_reference/reference_markers.hmm GCF_003813985.1_ASM381398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:49,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:49,460] [INFO] Found 6/6 markers.
[2024-01-24 15:26:49,488] [INFO] Query marker FASTA was written to GCF_003813985.1_ASM381398v1_genomic.fna/markers.fasta
[2024-01-24 15:26:49,488] [INFO] Task started: Blastn
[2024-01-24 15:26:49,488] [INFO] Running command: blastn -query GCF_003813985.1_ASM381398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg402cc13f-c149-41e5-8c78-8d0c5d0ec3b5/dqc_reference/reference_markers.fasta -out GCF_003813985.1_ASM381398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:50,300] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:50,303] [INFO] Selected 12 target genomes.
[2024-01-24 15:26:50,304] [INFO] Target genome list was writen to GCF_003813985.1_ASM381398v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:50,308] [INFO] Task started: fastANI
[2024-01-24 15:26:50,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f51e1bd-d19f-4c21-a395-56bea8a05d86/GCF_003813985.1_ASM381398v1_genomic.fna.gz --refList GCF_003813985.1_ASM381398v1_genomic.fna/target_genomes.txt --output GCF_003813985.1_ASM381398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:55,835] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:55,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg402cc13f-c149-41e5-8c78-8d0c5d0ec3b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:55,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg402cc13f-c149-41e5-8c78-8d0c5d0ec3b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:55,848] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:55,848] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:55,848] [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 gerontici	strain=W8	GCA_003813985.1	2079234	2079234	type	True	100.0	754	754	95	conclusive
Corynebacterium pseudopelargi	strain=812CH	GCA_003814005.1	2080757	2080757	type	True	82.2923	434	754	95	below_threshold
Corynebacterium pelargi	strain=136/3	GCA_004114895.1	1471400	1471400	type	True	82.2355	427	754	95	below_threshold
Corynebacterium pelargi	strain=CCM 8517	GCA_014635485.1	1471400	1471400	type	True	82.1016	409	754	95	below_threshold
Corynebacterium ulcerans	strain=NCTC7910	GCA_900187135.1	65058	65058	type	True	79.0509	107	754	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.9575	196	754	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.3864	169	754	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.2757	138	754	95	below_threshold
Corynebacterium liangguodongii	strain=2184	GCA_003070865.1	2079535	2079535	type	True	78.1897	112	754	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	78.0365	132	754	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	77.9346	134	754	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	77.8638	163	754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:55,850] [INFO] DFAST Taxonomy check result was written to GCF_003813985.1_ASM381398v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:55,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:55,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:55,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg402cc13f-c149-41e5-8c78-8d0c5d0ec3b5/dqc_reference/checkm_data
[2024-01-24 15:26:55,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:55,880] [INFO] Task started: CheckM
[2024-01-24 15:26:55,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003813985.1_ASM381398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003813985.1_ASM381398v1_genomic.fna/checkm_input GCF_003813985.1_ASM381398v1_genomic.fna/checkm_result
[2024-01-24 15:27:25,433] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:25,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:25,452] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:25,453] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:25,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003813985.1_ASM381398v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:25,454] [INFO] Task started: Blastn
[2024-01-24 15:27:25,454] [INFO] Running command: blastn -query GCF_003813985.1_ASM381398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg402cc13f-c149-41e5-8c78-8d0c5d0ec3b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003813985.1_ASM381398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:26,631] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:26,635] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:26,636] [INFO] Target genome list was writen to GCF_003813985.1_ASM381398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:26,673] [INFO] Task started: fastANI
[2024-01-24 15:27:26,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f51e1bd-d19f-4c21-a395-56bea8a05d86/GCF_003813985.1_ASM381398v1_genomic.fna.gz --refList GCF_003813985.1_ASM381398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003813985.1_ASM381398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:33,653] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:33,666] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:33,666] [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_003813985.1	s__Corynebacterium geronticis	100.0	754	754	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_004114895.1	s__Corynebacterium pelargi	82.2472	426	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003814005.1	s__Corynebacterium pseudopelargi	82.243	431	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	79.0035	196	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_900187135.1	s__Corynebacterium ulcerans	78.9473	105	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.3367	170	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.2726	139	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994655.1	s__Corynebacterium sp002994655	78.0389	141	754	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	77.9159	134	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	77.7757	131	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_012838985.1	s__Corynebacterium sp012838985	76.944	119	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:33,668] [INFO] GTDB search result was written to GCF_003813985.1_ASM381398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:33,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:33,672] [INFO] DFAST_QC result json was written to GCF_003813985.1_ASM381398v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:33,672] [INFO] DFAST_QC completed!
[2024-01-24 15:27:33,672] [INFO] Total running time: 0h0m54s