[2024-01-24 13:45:46,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,621] [INFO] DQC Reference Directory: /var/lib/cwl/stg63f94c47-cfdc-41fd-858d-42081690e6ff/dqc_reference
[2024-01-24 13:45:48,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:48,109] [INFO] Task started: Prodigal
[2024-01-24 13:45:48,109] [INFO] Running command: gunzip -c /var/lib/cwl/stg26aafae2-54e3-4770-9f8a-189b37457324/GCF_009707995.1_ASM970799v1_genomic.fna.gz | prodigal -d GCF_009707995.1_ASM970799v1_genomic.fna/cds.fna -a GCF_009707995.1_ASM970799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:56,552] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:56,552] [INFO] Task started: HMMsearch
[2024-01-24 13:45:56,552] [INFO] Running command: hmmsearch --tblout GCF_009707995.1_ASM970799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63f94c47-cfdc-41fd-858d-42081690e6ff/dqc_reference/reference_markers.hmm GCF_009707995.1_ASM970799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:56,894] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:56,895] [INFO] Found 6/6 markers.
[2024-01-24 13:45:56,920] [INFO] Query marker FASTA was written to GCF_009707995.1_ASM970799v1_genomic.fna/markers.fasta
[2024-01-24 13:45:56,921] [INFO] Task started: Blastn
[2024-01-24 13:45:56,921] [INFO] Running command: blastn -query GCF_009707995.1_ASM970799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63f94c47-cfdc-41fd-858d-42081690e6ff/dqc_reference/reference_markers.fasta -out GCF_009707995.1_ASM970799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:57,924] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:57,927] [INFO] Selected 9 target genomes.
[2024-01-24 13:45:57,928] [INFO] Target genome list was writen to GCF_009707995.1_ASM970799v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:57,941] [INFO] Task started: fastANI
[2024-01-24 13:45:57,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg26aafae2-54e3-4770-9f8a-189b37457324/GCF_009707995.1_ASM970799v1_genomic.fna.gz --refList GCF_009707995.1_ASM970799v1_genomic.fna/target_genomes.txt --output GCF_009707995.1_ASM970799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:04,086] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:04,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63f94c47-cfdc-41fd-858d-42081690e6ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:04,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63f94c47-cfdc-41fd-858d-42081690e6ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:04,096] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:04,096] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:04,097] [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	88.7531	741	856	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	88.7487	748	856	95	below_threshold
Corynebacterium minutissimum	strain=NBRC 15361	GCA_001552395.1	38301	38301	type	True	84.3531	654	856	95	below_threshold
Corynebacterium minutissimum	strain=ATCC 23348	GCA_000805675.1	38301	38301	type	True	84.2535	652	856	95	below_threshold
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	84.2204	669	856	95	below_threshold
Corynebacterium singulare	strain=IBS B52218	GCA_000833575.1	161899	161899	type	True	83.7466	640	856	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.6516	254	856	95	below_threshold
Corynebacterium maris	strain=DSM 45190	GCA_000442645.1	575200	575200	type	True	78.0635	207	856	95	below_threshold
Nonomuraea glycinis	strain=NEAU-BB2C19	GCA_020215885.1	2047744	2047744	type	True	75.6943	58	856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:04,099] [INFO] DFAST Taxonomy check result was written to GCF_009707995.1_ASM970799v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:04,099] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:04,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:04,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63f94c47-cfdc-41fd-858d-42081690e6ff/dqc_reference/checkm_data
[2024-01-24 13:46:04,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:04,129] [INFO] Task started: CheckM
[2024-01-24 13:46:04,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009707995.1_ASM970799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009707995.1_ASM970799v1_genomic.fna/checkm_input GCF_009707995.1_ASM970799v1_genomic.fna/checkm_result
[2024-01-24 13:46:34,213] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:34,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:34,232] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:34,232] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:34,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009707995.1_ASM970799v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:34,233] [INFO] Task started: Blastn
[2024-01-24 13:46:34,233] [INFO] Running command: blastn -query GCF_009707995.1_ASM970799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63f94c47-cfdc-41fd-858d-42081690e6ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_009707995.1_ASM970799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:35,562] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:35,566] [INFO] Selected 6 target genomes.
[2024-01-24 13:46:35,566] [INFO] Target genome list was writen to GCF_009707995.1_ASM970799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:35,577] [INFO] Task started: fastANI
[2024-01-24 13:46:35,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg26aafae2-54e3-4770-9f8a-189b37457324/GCF_009707995.1_ASM970799v1_genomic.fna.gz --refList GCF_009707995.1_ASM970799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009707995.1_ASM970799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:39,799] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:39,806] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:39,806] [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_002861385.1	s__Corynebacterium aurimucosum_C	96.4493	793	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	conclusive
GCF_001836165.1	s__Corynebacterium sp001836165	90.4698	753	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCF_000022905.1	s__Corynebacterium aurimucosum	89.602	754	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000988205.1	s__Corynebacterium minutissimum_A	89.0781	763	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.53	96.09	0.91	0.89	16	-
GCF_016728705.1	s__Corynebacterium sp001807205	88.7634	747	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCA_019114925.1	s__Corynebacterium faecipullorum	87.9411	529	856	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 13:46:39,809] [INFO] GTDB search result was written to GCF_009707995.1_ASM970799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:39,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:39,813] [INFO] DFAST_QC result json was written to GCF_009707995.1_ASM970799v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:39,813] [INFO] DFAST_QC completed!
[2024-01-24 13:46:39,813] [INFO] Total running time: 0h0m53s