[2024-01-24 15:27:12,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e11a334-06a2-44bc-907f-394e315771c4/dqc_reference
[2024-01-24 15:27:13,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:13,943] [INFO] Task started: Prodigal
[2024-01-24 15:27:13,943] [INFO] Running command: gunzip -c /var/lib/cwl/stga4d1720f-9309-4248-8962-22c5e5ca2117/GCF_003955685.1_ASM395568v1_genomic.fna.gz | prodigal -d GCF_003955685.1_ASM395568v1_genomic.fna/cds.fna -a GCF_003955685.1_ASM395568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:23,821] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:23,821] [INFO] Task started: HMMsearch
[2024-01-24 15:27:23,821] [INFO] Running command: hmmsearch --tblout GCF_003955685.1_ASM395568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e11a334-06a2-44bc-907f-394e315771c4/dqc_reference/reference_markers.hmm GCF_003955685.1_ASM395568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:24,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:24,114] [INFO] Found 6/6 markers.
[2024-01-24 15:27:24,162] [INFO] Query marker FASTA was written to GCF_003955685.1_ASM395568v1_genomic.fna/markers.fasta
[2024-01-24 15:27:24,162] [INFO] Task started: Blastn
[2024-01-24 15:27:24,162] [INFO] Running command: blastn -query GCF_003955685.1_ASM395568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e11a334-06a2-44bc-907f-394e315771c4/dqc_reference/reference_markers.fasta -out GCF_003955685.1_ASM395568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:25,304] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:25,307] [INFO] Selected 6 target genomes.
[2024-01-24 15:27:25,308] [INFO] Target genome list was writen to GCF_003955685.1_ASM395568v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:25,311] [INFO] Task started: fastANI
[2024-01-24 15:27:25,311] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d1720f-9309-4248-8962-22c5e5ca2117/GCF_003955685.1_ASM395568v1_genomic.fna.gz --refList GCF_003955685.1_ASM395568v1_genomic.fna/target_genomes.txt --output GCF_003955685.1_ASM395568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:29,710] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:29,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e11a334-06a2-44bc-907f-394e315771c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:29,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e11a334-06a2-44bc-907f-394e315771c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:29,720] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:29,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:29,721] [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 marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	85.3499	700	1002	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	85.327	696	1002	95	below_threshold
Corynebacterium comes	strain=2019	GCA_009734405.1	2675218	2675218	type	True	85.0447	744	1002	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	84.1808	615	1002	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	84.1269	628	1002	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	83.9531	641	1002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:29,723] [INFO] DFAST Taxonomy check result was written to GCF_003955685.1_ASM395568v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:29,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:29,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:29,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e11a334-06a2-44bc-907f-394e315771c4/dqc_reference/checkm_data
[2024-01-24 15:27:29,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:29,766] [INFO] Task started: CheckM
[2024-01-24 15:27:29,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003955685.1_ASM395568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003955685.1_ASM395568v1_genomic.fna/checkm_input GCF_003955685.1_ASM395568v1_genomic.fna/checkm_result
[2024-01-24 15:28:03,211] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:03,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:03,231] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:03,232] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:03,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003955685.1_ASM395568v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:03,233] [INFO] Task started: Blastn
[2024-01-24 15:28:03,233] [INFO] Running command: blastn -query GCF_003955685.1_ASM395568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e11a334-06a2-44bc-907f-394e315771c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003955685.1_ASM395568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:04,911] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:04,914] [INFO] Selected 6 target genomes.
[2024-01-24 15:28:04,915] [INFO] Target genome list was writen to GCF_003955685.1_ASM395568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:04,921] [INFO] Task started: fastANI
[2024-01-24 15:28:04,921] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d1720f-9309-4248-8962-22c5e5ca2117/GCF_003955685.1_ASM395568v1_genomic.fna.gz --refList GCF_003955685.1_ASM395568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003955685.1_ASM395568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:09,046] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:09,055] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:09,055] [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_003955685.1	s__Corynebacterium sp003955685	100.0	1001	1002	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_000835165.1	s__Corynebacterium marinum	85.3499	700	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_009734405.1	s__Corynebacterium sp009734405	85.0447	744	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819445.1	s__Corynebacterium humireducens	84.1115	629	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_900177745.1	s__Corynebacterium pollutisoli	83.9384	642	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCA_012838985.1	s__Corynebacterium sp012838985	83.9195	537	1002	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 15:28:09,057] [INFO] GTDB search result was written to GCF_003955685.1_ASM395568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:09,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:09,060] [INFO] DFAST_QC result json was written to GCF_003955685.1_ASM395568v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:09,061] [INFO] DFAST_QC completed!
[2024-01-24 15:28:09,061] [INFO] Total running time: 0h0m56s