[2024-01-25 20:02:05,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:05,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:05,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg81221458-5de2-40fe-8951-4872ec2a0280/dqc_reference
[2024-01-25 20:02:06,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:06,879] [INFO] Task started: Prodigal
[2024-01-25 20:02:06,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg168318f7-6fb0-4241-b7f4-5ca8113edd50/GCF_902702935.1_FRC0190_genomic.fna.gz | prodigal -d GCF_902702935.1_FRC0190_genomic.fna/cds.fna -a GCF_902702935.1_FRC0190_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:14,061] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:14,061] [INFO] Task started: HMMsearch
[2024-01-25 20:02:14,061] [INFO] Running command: hmmsearch --tblout GCF_902702935.1_FRC0190_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81221458-5de2-40fe-8951-4872ec2a0280/dqc_reference/reference_markers.hmm GCF_902702935.1_FRC0190_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:14,242] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:14,243] [INFO] Found 6/6 markers.
[2024-01-25 20:02:14,262] [INFO] Query marker FASTA was written to GCF_902702935.1_FRC0190_genomic.fna/markers.fasta
[2024-01-25 20:02:14,263] [INFO] Task started: Blastn
[2024-01-25 20:02:14,263] [INFO] Running command: blastn -query GCF_902702935.1_FRC0190_genomic.fna/markers.fasta -db /var/lib/cwl/stg81221458-5de2-40fe-8951-4872ec2a0280/dqc_reference/reference_markers.fasta -out GCF_902702935.1_FRC0190_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:14,909] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:14,911] [INFO] Selected 6 target genomes.
[2024-01-25 20:02:14,912] [INFO] Target genome list was writen to GCF_902702935.1_FRC0190_genomic.fna/target_genomes.txt
[2024-01-25 20:02:14,916] [INFO] Task started: fastANI
[2024-01-25 20:02:14,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg168318f7-6fb0-4241-b7f4-5ca8113edd50/GCF_902702935.1_FRC0190_genomic.fna.gz --refList GCF_902702935.1_FRC0190_genomic.fna/target_genomes.txt --output GCF_902702935.1_FRC0190_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:18,396] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:18,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81221458-5de2-40fe-8951-4872ec2a0280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:18,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81221458-5de2-40fe-8951-4872ec2a0280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:18,401] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:18,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:18,402] [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 rouxii	strain=FRC0190	GCA_902702935.1	2719119	2719119	type	True	100.0	816	817	95	conclusive
Corynebacterium diphtheriae		GCA_902809765.1	1717	1717	type	True	92.8993	700	817	95	below_threshold
Corynebacterium diphtheriae	strain=NCTC11397	GCA_001457455.1	1717	1717	type	True	92.8897	699	817	95	below_threshold
Corynebacterium diphtheriae subsp. diphtheriae	strain=FDAARGOS_1554	GCA_020736085.1	2315257	1717	type	True	92.8845	701	817	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	92.8566	694	817	95	below_threshold
Corynebacterium belfantii		GCA_900205605.1	2014537	2014537	type	True	91.9503	671	817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:18,403] [INFO] DFAST Taxonomy check result was written to GCF_902702935.1_FRC0190_genomic.fna/tc_result.tsv
[2024-01-25 20:02:18,403] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:18,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:18,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81221458-5de2-40fe-8951-4872ec2a0280/dqc_reference/checkm_data
[2024-01-25 20:02:18,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:18,428] [INFO] Task started: CheckM
[2024-01-25 20:02:18,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902702935.1_FRC0190_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902702935.1_FRC0190_genomic.fna/checkm_input GCF_902702935.1_FRC0190_genomic.fna/checkm_result
[2024-01-25 20:02:43,682] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:43,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:43,702] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:43,702] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:43,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902702935.1_FRC0190_genomic.fna/markers.fasta)
[2024-01-25 20:02:43,703] [INFO] Task started: Blastn
[2024-01-25 20:02:43,703] [INFO] Running command: blastn -query GCF_902702935.1_FRC0190_genomic.fna/markers.fasta -db /var/lib/cwl/stg81221458-5de2-40fe-8951-4872ec2a0280/dqc_reference/reference_markers_gtdb.fasta -out GCF_902702935.1_FRC0190_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:44,613] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:44,616] [INFO] Selected 19 target genomes.
[2024-01-25 20:02:44,616] [INFO] Target genome list was writen to GCF_902702935.1_FRC0190_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:44,634] [INFO] Task started: fastANI
[2024-01-25 20:02:44,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg168318f7-6fb0-4241-b7f4-5ca8113edd50/GCF_902702935.1_FRC0190_genomic.fna.gz --refList GCF_902702935.1_FRC0190_genomic.fna/target_genomes_gtdb.txt --output GCF_902702935.1_FRC0190_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:55,559] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:55,568] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:55,568] [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_902702935.1	s__Corynebacterium rouxii	100.0	816	817	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_001457455.1	s__Corynebacterium diphtheriae	92.8896	699	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_900187135.1	s__Corynebacterium ulcerans	80.1279	172	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	-
GCF_011612265.2	s__Corynebacterium matruchotii	79.5361	73	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.18	0.97	0.91	9	-
GCF_004382825.2	s__Corynebacterium silvaticum	79.4944	184	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	79.4232	143	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_002155265.1	s__Corynebacterium pseudotuberculosis	79.3954	155	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.58	98.61	0.99	0.97	131	-
GCF_003814005.1	s__Corynebacterium pseudopelargi	78.8877	131	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177535.2	s__Corynebacterium resistens	78.805	72	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590555.1	s__Corynebacterium argentoratense	78.6809	92	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.97	98.97	0.98	0.98	3	-
GCF_001643015.1	s__Corynebacterium crudilactis	78.4628	101	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177745.1	s__Corynebacterium pollutisoli	78.0941	85	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_003716585.1	s__Corynebacterium alimapuense	77.806	64	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014267345.1	s__Corynebacterium sp014267345	77.5422	76	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:55,570] [INFO] GTDB search result was written to GCF_902702935.1_FRC0190_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:55,570] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:55,573] [INFO] DFAST_QC result json was written to GCF_902702935.1_FRC0190_genomic.fna/dqc_result.json
[2024-01-25 20:02:55,573] [INFO] DFAST_QC completed!
[2024-01-25 20:02:55,573] [INFO] Total running time: 0h0m50s