[2024-01-24 15:27:21,358] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:21,361] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:21,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg15b7f183-e0b5-45ee-b977-37738461acba/dqc_reference
[2024-01-24 15:27:22,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:22,714] [INFO] Task started: Prodigal
[2024-01-24 15:27:22,714] [INFO] Running command: gunzip -c /var/lib/cwl/stgfeb827aa-e746-40e5-a2e4-c5806dfbf2d2/GCF_030440305.1_ASM3044030v1_genomic.fna.gz | prodigal -d GCF_030440305.1_ASM3044030v1_genomic.fna/cds.fna -a GCF_030440305.1_ASM3044030v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:31,834] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:31,835] [INFO] Task started: HMMsearch
[2024-01-24 15:27:31,835] [INFO] Running command: hmmsearch --tblout GCF_030440305.1_ASM3044030v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15b7f183-e0b5-45ee-b977-37738461acba/dqc_reference/reference_markers.hmm GCF_030440305.1_ASM3044030v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:32,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:32,076] [INFO] Found 6/6 markers.
[2024-01-24 15:27:32,106] [INFO] Query marker FASTA was written to GCF_030440305.1_ASM3044030v1_genomic.fna/markers.fasta
[2024-01-24 15:27:32,106] [INFO] Task started: Blastn
[2024-01-24 15:27:32,106] [INFO] Running command: blastn -query GCF_030440305.1_ASM3044030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15b7f183-e0b5-45ee-b977-37738461acba/dqc_reference/reference_markers.fasta -out GCF_030440305.1_ASM3044030v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:33,106] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:33,110] [INFO] Selected 6 target genomes.
[2024-01-24 15:27:33,110] [INFO] Target genome list was writen to GCF_030440305.1_ASM3044030v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:33,113] [INFO] Task started: fastANI
[2024-01-24 15:27:33,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb827aa-e746-40e5-a2e4-c5806dfbf2d2/GCF_030440305.1_ASM3044030v1_genomic.fna.gz --refList GCF_030440305.1_ASM3044030v1_genomic.fna/target_genomes.txt --output GCF_030440305.1_ASM3044030v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:37,072] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:37,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15b7f183-e0b5-45ee-b977-37738461acba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:37,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15b7f183-e0b5-45ee-b977-37738461acba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:37,079] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:27:37,079] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:27:37,080] [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 hadale	strain=NBT06-6	GCA_002273005.1	2026255	2026255	type	True	99.95	863	912	95	inconclusive
Corynebacterium gottingense	strain=DSM 103494	GCA_003693265.1	2041036	2041036	type	True	97.3455	741	912	95	inconclusive
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	97.0884	785	912	95	inconclusive
Corynebacterium godavarianum	strain=PRD07	GCA_016785885.1	2054421	2054421	type	True	97.0729	798	912	95	inconclusive
Corynebacterium imitans	strain=DSM 44264	GCA_000739455.1	156978	156978	type	True	84.4081	659	912	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	84.3734	667	912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:37,081] [INFO] DFAST Taxonomy check result was written to GCF_030440305.1_ASM3044030v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:37,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:37,082] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:37,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15b7f183-e0b5-45ee-b977-37738461acba/dqc_reference/checkm_data
[2024-01-24 15:27:37,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:37,111] [INFO] Task started: CheckM
[2024-01-24 15:27:37,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030440305.1_ASM3044030v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030440305.1_ASM3044030v1_genomic.fna/checkm_input GCF_030440305.1_ASM3044030v1_genomic.fna/checkm_result
[2024-01-24 15:28:07,267] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:07,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:07,288] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:07,288] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:07,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030440305.1_ASM3044030v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:07,289] [INFO] Task started: Blastn
[2024-01-24 15:28:07,290] [INFO] Running command: blastn -query GCF_030440305.1_ASM3044030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15b7f183-e0b5-45ee-b977-37738461acba/dqc_reference/reference_markers_gtdb.fasta -out GCF_030440305.1_ASM3044030v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:08,701] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:08,704] [INFO] Selected 9 target genomes.
[2024-01-24 15:28:08,704] [INFO] Target genome list was writen to GCF_030440305.1_ASM3044030v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:08,714] [INFO] Task started: fastANI
[2024-01-24 15:28:08,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb827aa-e746-40e5-a2e4-c5806dfbf2d2/GCF_030440305.1_ASM3044030v1_genomic.fna.gz --refList GCF_030440305.1_ASM3044030v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030440305.1_ASM3044030v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:13,912] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:13,927] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:13,928] [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_003693265.1	s__Corynebacterium gottingense	97.3396	742	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	conclusive
GCF_001831515.1	s__Corynebacterium sp001831515	84.5625	652	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.57	96.57	0.93	0.93	2	-
GCF_000739455.1	s__Corynebacterium imitans	84.4081	659	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000577555.1	s__Corynebacterium jeddahense	81.7908	442	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	81.7586	513	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807265.1	s__Corynebacterium sp001807265	81.5009	483	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCA_900156035.1	s__Corynebacterium afermentans	81.4225	460	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_015351335.1	s__Corynebacterium lipophilum	81.3617	492	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	81.1632	449	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:13,929] [INFO] GTDB search result was written to GCF_030440305.1_ASM3044030v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:13,930] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:13,934] [INFO] DFAST_QC result json was written to GCF_030440305.1_ASM3044030v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:13,935] [INFO] DFAST_QC completed!
[2024-01-24 15:28:13,935] [INFO] Total running time: 0h0m53s