[2024-01-24 10:47:06,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,602] [INFO] DQC Reference Directory: /var/lib/cwl/stga865a59e-2510-446f-b6cc-2b3bb4a7d79c/dqc_reference
[2024-01-24 10:47:12,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,826] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d838ceb-0287-462a-9271-cdaa79958e2e/GCF_019754945.1_ASM1975494v1_genomic.fna.gz | prodigal -d GCF_019754945.1_ASM1975494v1_genomic.fna/cds.fna -a GCF_019754945.1_ASM1975494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:20,562] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:20,562] [INFO] Task started: HMMsearch
[2024-01-24 10:47:20,562] [INFO] Running command: hmmsearch --tblout GCF_019754945.1_ASM1975494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga865a59e-2510-446f-b6cc-2b3bb4a7d79c/dqc_reference/reference_markers.hmm GCF_019754945.1_ASM1975494v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:20,818] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:20,820] [INFO] Found 6/6 markers.
[2024-01-24 10:47:20,852] [INFO] Query marker FASTA was written to GCF_019754945.1_ASM1975494v1_genomic.fna/markers.fasta
[2024-01-24 10:47:20,852] [INFO] Task started: Blastn
[2024-01-24 10:47:20,852] [INFO] Running command: blastn -query GCF_019754945.1_ASM1975494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga865a59e-2510-446f-b6cc-2b3bb4a7d79c/dqc_reference/reference_markers.fasta -out GCF_019754945.1_ASM1975494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:21,689] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:21,694] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:21,695] [INFO] Target genome list was writen to GCF_019754945.1_ASM1975494v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:21,756] [INFO] Task started: fastANI
[2024-01-24 10:47:21,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d838ceb-0287-462a-9271-cdaa79958e2e/GCF_019754945.1_ASM1975494v1_genomic.fna.gz --refList GCF_019754945.1_ASM1975494v1_genomic.fna/target_genomes.txt --output GCF_019754945.1_ASM1975494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:27,625] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:27,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga865a59e-2510-446f-b6cc-2b3bb4a7d79c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:27,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga865a59e-2510-446f-b6cc-2b3bb4a7d79c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:27,638] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:27,638] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:27,638] [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 pseudokroppenstedtii	strain=MC-17X	GCA_019754945.1	2804917	2804917	type	True	100.0	819	819	95	conclusive
Corynebacterium kroppenstedtii	strain=FDAARGOS_1192	GCA_016889365.1	161879	161879	suspected-type	True	93.6492	780	819	95	below_threshold
Corynebacterium kroppenstedtii	strain=DSM 44385	GCA_000023145.1	161879	161879	suspected-type	True	93.6432	780	819	95	below_threshold
Corynebacterium parakroppenstedtii	strain=MC-26	GCA_019754935.1	2828363	2828363	type	True	92.7071	780	819	95	below_threshold
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	77.7939	80	819	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	77.6543	68	819	95	below_threshold
Corynebacterium gallinarum	strain=Sa1YVA5	GCA_014837045.1	2762214	2762214	type	True	77.2827	61	819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:27,646] [INFO] DFAST Taxonomy check result was written to GCF_019754945.1_ASM1975494v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:27,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:27,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:27,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga865a59e-2510-446f-b6cc-2b3bb4a7d79c/dqc_reference/checkm_data
[2024-01-24 10:47:27,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:27,679] [INFO] Task started: CheckM
[2024-01-24 10:47:27,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019754945.1_ASM1975494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019754945.1_ASM1975494v1_genomic.fna/checkm_input GCF_019754945.1_ASM1975494v1_genomic.fna/checkm_result
[2024-01-24 10:47:55,507] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:55,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:55,538] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:55,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:55,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019754945.1_ASM1975494v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:55,539] [INFO] Task started: Blastn
[2024-01-24 10:47:55,540] [INFO] Running command: blastn -query GCF_019754945.1_ASM1975494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga865a59e-2510-446f-b6cc-2b3bb4a7d79c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019754945.1_ASM1975494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:56,745] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:56,750] [INFO] Selected 5 target genomes.
[2024-01-24 10:47:56,750] [INFO] Target genome list was writen to GCF_019754945.1_ASM1975494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:56,766] [INFO] Task started: fastANI
[2024-01-24 10:47:56,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d838ceb-0287-462a-9271-cdaa79958e2e/GCF_019754945.1_ASM1975494v1_genomic.fna.gz --refList GCF_019754945.1_ASM1975494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019754945.1_ASM1975494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:00,156] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:00,163] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:00,163] [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_016889405.1	s__Corynebacterium kroppenstedtii_C	98.5843	791	819	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_000023145.1	s__Corynebacterium kroppenstedtii	93.6432	780	819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001552955.1	s__Corynebacterium kroppenstedtii_A	92.695	778	819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.92	99.91	0.99	0.98	4	-
GCA_003243515.1	s__Corynebacterium kroppenstedtii_B	92.1704	714	819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016894245.1	s__Corynebacterium sp902373425	90.1688	762	819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:00,165] [INFO] GTDB search result was written to GCF_019754945.1_ASM1975494v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:00,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:00,169] [INFO] DFAST_QC result json was written to GCF_019754945.1_ASM1975494v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:00,169] [INFO] DFAST_QC completed!
[2024-01-24 10:48:00,169] [INFO] Total running time: 0h0m54s