[2024-01-24 12:42:09,429] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,432] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg70f63172-4dfa-492c-b771-af338a0cfa56/dqc_reference
[2024-01-24 12:42:10,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,747] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg2aebbf16-1e19-48a8-a577-43baf2272a61/GCF_024138775.1_ASM2413877v1_genomic.fna.gz | prodigal -d GCF_024138775.1_ASM2413877v1_genomic.fna/cds.fna -a GCF_024138775.1_ASM2413877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:19,514] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:19,515] [INFO] Task started: HMMsearch
[2024-01-24 12:42:19,515] [INFO] Running command: hmmsearch --tblout GCF_024138775.1_ASM2413877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70f63172-4dfa-492c-b771-af338a0cfa56/dqc_reference/reference_markers.hmm GCF_024138775.1_ASM2413877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:19,741] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:19,742] [INFO] Found 6/6 markers.
[2024-01-24 12:42:19,767] [INFO] Query marker FASTA was written to GCF_024138775.1_ASM2413877v1_genomic.fna/markers.fasta
[2024-01-24 12:42:19,768] [INFO] Task started: Blastn
[2024-01-24 12:42:19,768] [INFO] Running command: blastn -query GCF_024138775.1_ASM2413877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70f63172-4dfa-492c-b771-af338a0cfa56/dqc_reference/reference_markers.fasta -out GCF_024138775.1_ASM2413877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:20,615] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:20,619] [INFO] Selected 8 target genomes.
[2024-01-24 12:42:20,619] [INFO] Target genome list was writen to GCF_024138775.1_ASM2413877v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:20,620] [INFO] Task started: fastANI
[2024-01-24 12:42:20,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aebbf16-1e19-48a8-a577-43baf2272a61/GCF_024138775.1_ASM2413877v1_genomic.fna.gz --refList GCF_024138775.1_ASM2413877v1_genomic.fna/target_genomes.txt --output GCF_024138775.1_ASM2413877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:25,551] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:25,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70f63172-4dfa-492c-b771-af338a0cfa56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:25,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70f63172-4dfa-492c-b771-af338a0cfa56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:25,563] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:42:25,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:25,563] [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 aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	100.0	893	894	95	conclusive
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	99.9128	884	894	95	conclusive
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	84.0573	671	894	95	below_threshold
Corynebacterium minutissimum	strain=NBRC 15361	GCA_001552395.1	38301	38301	type	True	84.051	649	894	95	below_threshold
Corynebacterium minutissimum	strain=ATCC 23348	GCA_000805675.1	38301	38301	type	True	83.9831	654	894	95	below_threshold
Corynebacterium singulare	strain=IBS B52218	GCA_000833575.1	161899	161899	type	True	83.5013	647	894	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	79.9506	362	894	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	79.9281	366	894	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:25,565] [INFO] DFAST Taxonomy check result was written to GCF_024138775.1_ASM2413877v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:25,565] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:25,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:25,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70f63172-4dfa-492c-b771-af338a0cfa56/dqc_reference/checkm_data
[2024-01-24 12:42:25,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:25,596] [INFO] Task started: CheckM
[2024-01-24 12:42:25,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024138775.1_ASM2413877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024138775.1_ASM2413877v1_genomic.fna/checkm_input GCF_024138775.1_ASM2413877v1_genomic.fna/checkm_result
[2024-01-24 12:42:55,671] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:55,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:55,693] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:55,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:55,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024138775.1_ASM2413877v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:55,694] [INFO] Task started: Blastn
[2024-01-24 12:42:55,694] [INFO] Running command: blastn -query GCF_024138775.1_ASM2413877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70f63172-4dfa-492c-b771-af338a0cfa56/dqc_reference/reference_markers_gtdb.fasta -out GCF_024138775.1_ASM2413877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:56,919] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:56,923] [INFO] Selected 6 target genomes.
[2024-01-24 12:42:56,923] [INFO] Target genome list was writen to GCF_024138775.1_ASM2413877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:56,925] [INFO] Task started: fastANI
[2024-01-24 12:42:56,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aebbf16-1e19-48a8-a577-43baf2272a61/GCF_024138775.1_ASM2413877v1_genomic.fna.gz --refList GCF_024138775.1_ASM2413877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024138775.1_ASM2413877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:01,133] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:01,140] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:01,140] [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_016728705.1	s__Corynebacterium sp001807205	99.917	883	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	conclusive
GCF_000022905.1	s__Corynebacterium aurimucosum	93.2986	811	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001836165.1	s__Corynebacterium sp001836165	92.4133	761	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCA_019114925.1	s__Corynebacterium faecipullorum	92.2091	550	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000988205.1	s__Corynebacterium minutissimum_A	89.6756	748	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.53	96.09	0.91	0.89	16	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	89.1423	739	894	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:01,142] [INFO] GTDB search result was written to GCF_024138775.1_ASM2413877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:01,143] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:01,145] [INFO] DFAST_QC result json was written to GCF_024138775.1_ASM2413877v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:01,145] [INFO] DFAST_QC completed!
[2024-01-24 12:43:01,145] [INFO] Total running time: 0h0m52s