[2024-01-24 14:30:46,706] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:46,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:46,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c435c39-019d-4831-a531-07bf0f3a98a3/dqc_reference
[2024-01-24 14:30:47,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:47,977] [INFO] Task started: Prodigal
[2024-01-24 14:30:47,977] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf6130ab-6662-4cb1-95b6-920566f04fb0/GCF_016889465.1_ASM1688946v1_genomic.fna.gz | prodigal -d GCF_016889465.1_ASM1688946v1_genomic.fna/cds.fna -a GCF_016889465.1_ASM1688946v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:55,589] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:55,589] [INFO] Task started: HMMsearch
[2024-01-24 14:30:55,589] [INFO] Running command: hmmsearch --tblout GCF_016889465.1_ASM1688946v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c435c39-019d-4831-a531-07bf0f3a98a3/dqc_reference/reference_markers.hmm GCF_016889465.1_ASM1688946v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:55,834] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:55,836] [INFO] Found 6/6 markers.
[2024-01-24 14:30:55,862] [INFO] Query marker FASTA was written to GCF_016889465.1_ASM1688946v1_genomic.fna/markers.fasta
[2024-01-24 14:30:55,862] [INFO] Task started: Blastn
[2024-01-24 14:30:55,862] [INFO] Running command: blastn -query GCF_016889465.1_ASM1688946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c435c39-019d-4831-a531-07bf0f3a98a3/dqc_reference/reference_markers.fasta -out GCF_016889465.1_ASM1688946v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:56,666] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:56,669] [INFO] Selected 8 target genomes.
[2024-01-24 14:30:56,670] [INFO] Target genome list was writen to GCF_016889465.1_ASM1688946v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:56,678] [INFO] Task started: fastANI
[2024-01-24 14:30:56,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf6130ab-6662-4cb1-95b6-920566f04fb0/GCF_016889465.1_ASM1688946v1_genomic.fna.gz --refList GCF_016889465.1_ASM1688946v1_genomic.fna/target_genomes.txt --output GCF_016889465.1_ASM1688946v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:03,022] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:03,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c435c39-019d-4831-a531-07bf0f3a98a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:03,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c435c39-019d-4831-a531-07bf0f3a98a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:03,032] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:03,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:03,032] [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 macginleyi	strain=FDAARGOS_1195	GCA_016889465.1	38290	38290	type	True	100.0	827	831	95	conclusive
Corynebacterium macginleyi	strain=CCUG 32361	GCA_003688935.1	38290	38290	type	True	99.955	772	831	95	conclusive
Corynebacterium accolens	strain=DSM 44278	GCA_023520795.1	38284	38284	type	True	88.1964	684	831	95	below_threshold
Corynebacterium accolens	strain=ATCC 49725	GCA_000159115.1	38284	38284	type	True	88.0772	684	831	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	80.3599	449	831	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	79.3977	248	831	95	below_threshold
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	77.9875	113	831	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	77.8073	119	831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:03,034] [INFO] DFAST Taxonomy check result was written to GCF_016889465.1_ASM1688946v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:03,034] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:03,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:03,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c435c39-019d-4831-a531-07bf0f3a98a3/dqc_reference/checkm_data
[2024-01-24 14:31:03,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:03,066] [INFO] Task started: CheckM
[2024-01-24 14:31:03,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016889465.1_ASM1688946v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016889465.1_ASM1688946v1_genomic.fna/checkm_input GCF_016889465.1_ASM1688946v1_genomic.fna/checkm_result
[2024-01-24 14:31:32,432] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:32,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:32,450] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:32,450] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:32,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016889465.1_ASM1688946v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:32,451] [INFO] Task started: Blastn
[2024-01-24 14:31:32,451] [INFO] Running command: blastn -query GCF_016889465.1_ASM1688946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c435c39-019d-4831-a531-07bf0f3a98a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016889465.1_ASM1688946v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:33,639] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:33,643] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:33,643] [INFO] Target genome list was writen to GCF_016889465.1_ASM1688946v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:33,653] [INFO] Task started: fastANI
[2024-01-24 14:31:33,653] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf6130ab-6662-4cb1-95b6-920566f04fb0/GCF_016889465.1_ASM1688946v1_genomic.fna.gz --refList GCF_016889465.1_ASM1688946v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016889465.1_ASM1688946v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:40,924] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:40,934] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:40,934] [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_003688935.1	s__Corynebacterium macginleyi	99.9628	771	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.68	97.89	0.95	0.93	26	conclusive
GCF_000159115.1	s__Corynebacterium accolens	88.0636	685	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.20	96.99	0.95	0.94	10	-
GCF_000478175.1	s__Corynebacterium sp000478175	87.9969	697	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.95	99.95	0.99	0.98	3	-
GCF_016127015.1	s__Corynebacterium aurimucosum_E	80.2473	434	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.91	96.45	0.92	0.89	6	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	80.1953	444	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	79.8758	420	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCA_900539985.1	s__Corynebacterium sp900539985	79.8029	393	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_000022905.1	s__Corynebacterium aurimucosum	79.1602	262	831	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	78.6728	224	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCF_000159135.1	s__Corynebacterium striatum	78.6052	228	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_001941425.1	s__Corynebacterium ammoniagenes	78.0011	134	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.70	98.81	0.99	0.95	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:40,935] [INFO] GTDB search result was written to GCF_016889465.1_ASM1688946v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:40,936] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:40,940] [INFO] DFAST_QC result json was written to GCF_016889465.1_ASM1688946v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:40,940] [INFO] DFAST_QC completed!
[2024-01-24 14:31:40,940] [INFO] Total running time: 0h0m54s