[2024-01-25 18:46:50,767] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:50,769] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:50,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a821e28-b73e-4e85-a469-a8f04def4295/dqc_reference
[2024-01-25 18:46:51,887] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:51,887] [INFO] Task started: Prodigal
[2024-01-25 18:46:51,887] [INFO] Running command: gunzip -c /var/lib/cwl/stg05f9d239-b647-4494-8d96-f838802d9395/GCF_028609845.1_ASM2860984v1_genomic.fna.gz | prodigal -d GCF_028609845.1_ASM2860984v1_genomic.fna/cds.fna -a GCF_028609845.1_ASM2860984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:58,553] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:58,554] [INFO] Task started: HMMsearch
[2024-01-25 18:46:58,554] [INFO] Running command: hmmsearch --tblout GCF_028609845.1_ASM2860984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a821e28-b73e-4e85-a469-a8f04def4295/dqc_reference/reference_markers.hmm GCF_028609845.1_ASM2860984v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:58,816] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:58,817] [INFO] Found 6/6 markers.
[2024-01-25 18:46:58,845] [INFO] Query marker FASTA was written to GCF_028609845.1_ASM2860984v1_genomic.fna/markers.fasta
[2024-01-25 18:46:58,845] [INFO] Task started: Blastn
[2024-01-25 18:46:58,845] [INFO] Running command: blastn -query GCF_028609845.1_ASM2860984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a821e28-b73e-4e85-a469-a8f04def4295/dqc_reference/reference_markers.fasta -out GCF_028609845.1_ASM2860984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:59,696] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:59,699] [INFO] Selected 17 target genomes.
[2024-01-25 18:46:59,699] [INFO] Target genome list was writen to GCF_028609845.1_ASM2860984v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:59,706] [INFO] Task started: fastANI
[2024-01-25 18:46:59,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg05f9d239-b647-4494-8d96-f838802d9395/GCF_028609845.1_ASM2860984v1_genomic.fna.gz --refList GCF_028609845.1_ASM2860984v1_genomic.fna/target_genomes.txt --output GCF_028609845.1_ASM2860984v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:07,477] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:07,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a821e28-b73e-4e85-a469-a8f04def4295/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:07,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a821e28-b73e-4e85-a469-a8f04def4295/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:07,488] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:47:07,488] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:07,488] [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 heidelbergense	strain=DSM 104638	GCA_003285565.1	2055947	2055947	type	True	99.8357	671	776	95	conclusive
Corynebacterium jeikeium	strain=NCTC11913	GCA_900461185.1	38289	38289	suspected-type	True	78.5533	207	776	95	below_threshold
Corynebacterium urogenitale	strain=LMM-1652	GCA_009026825.1	2487892	2487892	type	True	78.5151	146	776	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	78.5068	213	776	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	78.462	216	776	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_000183325.2	36808	36808	type	True	78.3399	181	776	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	78.2882	211	776	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_001999385.1	38289	38289	suspected-type	True	78.2575	203	776	95	below_threshold
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	78.244	205	776	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	78.2217	204	776	95	below_threshold
Corynebacterium urealyticum	strain=DSM 7109	GCA_000069945.1	43771	43771	type	True	78.1723	201	776	95	below_threshold
Corynebacterium suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	77.9218	165	776	95	below_threshold
Corynebacterium otitidis	strain=ATCC 51513	GCA_000296405.1	29321	29321	type	True	77.4224	117	776	95	below_threshold
Corynebacterium otitidis	strain=ATCC 51513	GCA_000297795.2	29321	29321	type	True	77.3626	115	776	95	below_threshold
Amycolatopsis jiangsuensis	strain=DSM 45859	GCA_014204865.1	1181879	1181879	type	True	77.0111	80	776	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	76.8103	66	776	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:07,490] [INFO] DFAST Taxonomy check result was written to GCF_028609845.1_ASM2860984v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:07,490] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:07,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:07,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a821e28-b73e-4e85-a469-a8f04def4295/dqc_reference/checkm_data
[2024-01-25 18:47:07,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:07,517] [INFO] Task started: CheckM
[2024-01-25 18:47:07,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028609845.1_ASM2860984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028609845.1_ASM2860984v1_genomic.fna/checkm_input GCF_028609845.1_ASM2860984v1_genomic.fna/checkm_result
[2024-01-25 18:47:30,126] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:30,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:30,142] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:30,143] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:30,143] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028609845.1_ASM2860984v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:30,143] [INFO] Task started: Blastn
[2024-01-25 18:47:30,143] [INFO] Running command: blastn -query GCF_028609845.1_ASM2860984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a821e28-b73e-4e85-a469-a8f04def4295/dqc_reference/reference_markers_gtdb.fasta -out GCF_028609845.1_ASM2860984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:31,364] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:31,367] [INFO] Selected 22 target genomes.
[2024-01-25 18:47:31,367] [INFO] Target genome list was writen to GCF_028609845.1_ASM2860984v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:31,396] [INFO] Task started: fastANI
[2024-01-25 18:47:31,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg05f9d239-b647-4494-8d96-f838802d9395/GCF_028609845.1_ASM2860984v1_genomic.fna.gz --refList GCF_028609845.1_ASM2860984v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028609845.1_ASM2860984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:41,236] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:41,246] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:41,246] [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_003285565.1	s__Corynebacterium heidelbergense	99.8357	671	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.29	96.29	0.86	0.86	2	conclusive
GCF_000738265.1	s__Corynebacterium jeikeium_A	79.053	203	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCF_000738175.1	s__Corynebacterium jeikeium_C	78.6681	221	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001054945.1	s__Corynebacterium falsenii_A	78.6311	181	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807485.1	s__Corynebacterium sp001807485	78.4149	219	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_000183325.1	s__Corynebacterium bovis	78.3484	180	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.01	98.42	0.92	0.83	23	-
GCF_000163435.1	s__Corynebacterium jeikeium	78.2882	211	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.68	96.00	0.93	0.90	9	-
GCF_000069945.1	s__Corynebacterium urealyticum	78.2294	203	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	-
GCA_019114175.1	s__Corynebacterium gallistercoris	78.2164	204	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120635.1	s__Corynebacterium intestinavium	78.2144	183	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001815985.1	s__Corynebacterium sp001815985	78.0972	207	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.95	96.87	0.95	0.94	3	-
GCF_000819445.1	s__Corynebacterium humireducens	77.932	165	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_015351405.1	s__Corynebacterium sp015351405	77.9218	165	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941505.1	s__Corynebacterium sphenisci	77.6655	194	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296405.1	s__Corynebacterium otitidis	77.5196	118	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.41	98.97	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:41,248] [INFO] GTDB search result was written to GCF_028609845.1_ASM2860984v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:41,249] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:41,252] [INFO] DFAST_QC result json was written to GCF_028609845.1_ASM2860984v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:41,252] [INFO] DFAST_QC completed!
[2024-01-25 18:47:41,253] [INFO] Total running time: 0h0m50s