[2024-01-25 18:07:05,523] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:05,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:05,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c959515-981f-4ccc-84dc-4bebb3b1ac17/dqc_reference
[2024-01-25 18:07:06,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:06,675] [INFO] Task started: Prodigal
[2024-01-25 18:07:06,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg98e94440-1644-4012-9de4-df9743f4e660/GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/cds.fna -a GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:13,043] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:13,043] [INFO] Task started: HMMsearch
[2024-01-25 18:07:13,043] [INFO] Running command: hmmsearch --tblout GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c959515-981f-4ccc-84dc-4bebb3b1ac17/dqc_reference/reference_markers.hmm GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:13,226] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:13,227] [INFO] Found 6/6 markers.
[2024-01-25 18:07:13,247] [INFO] Query marker FASTA was written to GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:07:13,248] [INFO] Task started: Blastn
[2024-01-25 18:07:13,248] [INFO] Running command: blastn -query GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c959515-981f-4ccc-84dc-4bebb3b1ac17/dqc_reference/reference_markers.fasta -out GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:14,274] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:14,276] [INFO] Selected 13 target genomes.
[2024-01-25 18:07:14,277] [INFO] Target genome list was writen to GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:07:14,292] [INFO] Task started: fastANI
[2024-01-25 18:07:14,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg98e94440-1644-4012-9de4-df9743f4e660/GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna.gz --refList GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:21,481] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:21,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c959515-981f-4ccc-84dc-4bebb3b1ac17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:21,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c959515-981f-4ccc-84dc-4bebb3b1ac17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:21,492] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:21,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:21,492] [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 mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	100.0	751	755	95	conclusive
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	84.5131	546	755	95	below_threshold
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	84.0722	579	755	95	below_threshold
Corynebacterium qintianiae	strain=MC1420	GCA_011038645.2	2709392	2709392	type	True	83.2122	550	755	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	82.6384	526	755	95	below_threshold
Corynebacterium liangguodongii	strain=2184	GCA_003070865.1	2079535	2079535	type	True	81.4823	494	755	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	81.4617	463	755	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	81.3159	455	755	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	81.2475	417	755	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	81.1708	401	755	95	below_threshold
Corynebacterium gottingense	strain=DSM 103494	GCA_003693265.1	2041036	2041036	type	True	80.2651	379	755	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	79.5241	369	755	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	79.3037	356	755	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:21,493] [INFO] DFAST Taxonomy check result was written to GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:07:21,494] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:21,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:21,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c959515-981f-4ccc-84dc-4bebb3b1ac17/dqc_reference/checkm_data
[2024-01-25 18:07:21,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:21,520] [INFO] Task started: CheckM
[2024-01-25 18:07:21,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/checkm_input GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:07:43,640] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:43,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:43,657] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:43,658] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:43,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:07:43,658] [INFO] Task started: Blastn
[2024-01-25 18:07:43,658] [INFO] Running command: blastn -query GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c959515-981f-4ccc-84dc-4bebb3b1ac17/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:45,207] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:45,211] [INFO] Selected 14 target genomes.
[2024-01-25 18:07:45,211] [INFO] Target genome list was writen to GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:45,222] [INFO] Task started: fastANI
[2024-01-25 18:07:45,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg98e94440-1644-4012-9de4-df9743f4e660/GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna.gz --refList GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:53,256] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:53,266] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:53,266] [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_900103625.1	s__Corynebacterium mycetoides	100.0	753	755	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_000159635.1	s__Corynebacterium lipophiloflavum	84.5131	546	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007641235.1	s__Corynebacterium sanguinis	84.0855	576	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_011038645.2	s__Corynebacterium qintianiae	83.2346	552	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.90	98.90	0.92	0.92	2	-
GCF_900411315.1	s__Corynebacterium senegalense	82.6276	524	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003070865.1	s__Corynebacterium liangguodongii	81.4786	493	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900105305.1	s__Corynebacterium timonense	81.4438	465	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	81.2434	418	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000577555.1	s__Corynebacterium jeddahense	81.1797	400	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339505.1	s__Corynebacterium sp002339505	81.0386	443	755	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	80.8235	404	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_903645305.1	s__Corynebacterium sp001764565	80.592	372	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
GCF_003693265.1	s__Corynebacterium gottingense	80.2762	379	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	-
GCF_000341345.1	s__Corynebacterium halotolerans	79.4636	369	755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:53,267] [INFO] GTDB search result was written to GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:53,268] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:53,270] [INFO] DFAST_QC result json was written to GCF_900103625.1_IMG-taxon_2634166344_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:07:53,271] [INFO] DFAST_QC completed!
[2024-01-25 18:07:53,271] [INFO] Total running time: 0h0m48s