[2024-01-24 13:09:44,755] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:44,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:44,757] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb2f388c-805e-4401-86db-e4f4c7fbba11/dqc_reference
[2024-01-24 13:09:46,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:46,013] [INFO] Task started: Prodigal
[2024-01-24 13:09:46,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg731cd3ac-69e2-4606-b73b-1c7b52e33939/GCF_002273005.1_ASM227300v1_genomic.fna.gz | prodigal -d GCF_002273005.1_ASM227300v1_genomic.fna/cds.fna -a GCF_002273005.1_ASM227300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:54,270] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:54,271] [INFO] Task started: HMMsearch
[2024-01-24 13:09:54,271] [INFO] Running command: hmmsearch --tblout GCF_002273005.1_ASM227300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb2f388c-805e-4401-86db-e4f4c7fbba11/dqc_reference/reference_markers.hmm GCF_002273005.1_ASM227300v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:54,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:54,543] [INFO] Found 6/6 markers.
[2024-01-24 13:09:54,584] [INFO] Query marker FASTA was written to GCF_002273005.1_ASM227300v1_genomic.fna/markers.fasta
[2024-01-24 13:09:54,585] [INFO] Task started: Blastn
[2024-01-24 13:09:54,585] [INFO] Running command: blastn -query GCF_002273005.1_ASM227300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb2f388c-805e-4401-86db-e4f4c7fbba11/dqc_reference/reference_markers.fasta -out GCF_002273005.1_ASM227300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:55,564] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:55,567] [INFO] Selected 6 target genomes.
[2024-01-24 13:09:55,567] [INFO] Target genome list was writen to GCF_002273005.1_ASM227300v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:55,570] [INFO] Task started: fastANI
[2024-01-24 13:09:55,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg731cd3ac-69e2-4606-b73b-1c7b52e33939/GCF_002273005.1_ASM227300v1_genomic.fna.gz --refList GCF_002273005.1_ASM227300v1_genomic.fna/target_genomes.txt --output GCF_002273005.1_ASM227300v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:59,091] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:59,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb2f388c-805e-4401-86db-e4f4c7fbba11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:59,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb2f388c-805e-4401-86db-e4f4c7fbba11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:59,099] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:09:59,099] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:09:59,099] [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	100.0	863	865	95	inconclusive
Corynebacterium gottingense	strain=DSM 103494	GCA_003693265.1	2041036	2041036	type	True	97.3438	724	865	95	inconclusive
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	97.1168	775	865	95	inconclusive
Corynebacterium godavarianum	strain=PRD07	GCA_016785885.1	2054421	2054421	type	True	97.0395	787	865	95	inconclusive
Corynebacterium imitans	strain=DSM 44264	GCA_000739455.1	156978	156978	type	True	84.1636	648	865	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	84.0986	656	865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:59,100] [INFO] DFAST Taxonomy check result was written to GCF_002273005.1_ASM227300v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:59,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:59,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:59,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb2f388c-805e-4401-86db-e4f4c7fbba11/dqc_reference/checkm_data
[2024-01-24 13:09:59,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:59,129] [INFO] Task started: CheckM
[2024-01-24 13:09:59,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002273005.1_ASM227300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002273005.1_ASM227300v1_genomic.fna/checkm_input GCF_002273005.1_ASM227300v1_genomic.fna/checkm_result
[2024-01-24 13:10:28,053] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:28,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:28,075] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:28,075] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:28,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002273005.1_ASM227300v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:28,076] [INFO] Task started: Blastn
[2024-01-24 13:10:28,076] [INFO] Running command: blastn -query GCF_002273005.1_ASM227300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb2f388c-805e-4401-86db-e4f4c7fbba11/dqc_reference/reference_markers_gtdb.fasta -out GCF_002273005.1_ASM227300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:29,519] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:29,522] [INFO] Selected 9 target genomes.
[2024-01-24 13:10:29,523] [INFO] Target genome list was writen to GCF_002273005.1_ASM227300v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:29,529] [INFO] Task started: fastANI
[2024-01-24 13:10:29,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg731cd3ac-69e2-4606-b73b-1c7b52e33939/GCF_002273005.1_ASM227300v1_genomic.fna.gz --refList GCF_002273005.1_ASM227300v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002273005.1_ASM227300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:34,534] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:34,547] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:34,548] [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	97.3438	724	865	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	84.4728	656	865	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	84.1471	650	865	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	81.5035	440	865	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	81.4296	501	865	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	81.2474	487	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_015351335.1	s__Corynebacterium lipophilum	81.2311	478	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900156035.1	s__Corynebacterium afermentans	81.2233	463	865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	80.9151	459	865	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 13:10:34,549] [INFO] GTDB search result was written to GCF_002273005.1_ASM227300v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:34,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:34,555] [INFO] DFAST_QC result json was written to GCF_002273005.1_ASM227300v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:34,555] [INFO] DFAST_QC completed!
[2024-01-24 13:10:34,555] [INFO] Total running time: 0h0m50s