[2024-01-24 14:30:29,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:29,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:29,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc570a2b-33e5-459e-8302-94905b50d079/dqc_reference
[2024-01-24 14:30:31,328] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:31,329] [INFO] Task started: Prodigal
[2024-01-24 14:30:31,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg576fac69-fefa-42ae-89c5-0eef1d7f3e54/GCF_006334925.1_ASM633492v1_genomic.fna.gz | prodigal -d GCF_006334925.1_ASM633492v1_genomic.fna/cds.fna -a GCF_006334925.1_ASM633492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:38,605] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:38,605] [INFO] Task started: HMMsearch
[2024-01-24 14:30:38,606] [INFO] Running command: hmmsearch --tblout GCF_006334925.1_ASM633492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc570a2b-33e5-459e-8302-94905b50d079/dqc_reference/reference_markers.hmm GCF_006334925.1_ASM633492v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:38,802] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:38,803] [INFO] Found 6/6 markers.
[2024-01-24 14:30:38,834] [INFO] Query marker FASTA was written to GCF_006334925.1_ASM633492v1_genomic.fna/markers.fasta
[2024-01-24 14:30:38,835] [INFO] Task started: Blastn
[2024-01-24 14:30:38,835] [INFO] Running command: blastn -query GCF_006334925.1_ASM633492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc570a2b-33e5-459e-8302-94905b50d079/dqc_reference/reference_markers.fasta -out GCF_006334925.1_ASM633492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:39,934] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:39,937] [INFO] Selected 17 target genomes.
[2024-01-24 14:30:39,937] [INFO] Target genome list was writen to GCF_006334925.1_ASM633492v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:39,955] [INFO] Task started: fastANI
[2024-01-24 14:30:39,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg576fac69-fefa-42ae-89c5-0eef1d7f3e54/GCF_006334925.1_ASM633492v1_genomic.fna.gz --refList GCF_006334925.1_ASM633492v1_genomic.fna/target_genomes.txt --output GCF_006334925.1_ASM633492v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:48,672] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:48,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc570a2b-33e5-459e-8302-94905b50d079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:48,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc570a2b-33e5-459e-8302-94905b50d079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:48,688] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:30:48,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:48,689] [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 tapiri	strain=LMG 28165	GCA_006334925.1	1448266	1448266	type	True	100.0	731	732	95	conclusive
Corynebacterium doosanense	strain=DSM 45436	GCA_000372245.1	1121358	1121358	type	True	78.7224	317	732	95	below_threshold
Corynebacterium doosanense	strain=CAU 212	GCA_000767055.1	1121358	1121358	type	True	78.6833	318	732	95	below_threshold
Corynebacterium uterequi	strain=DSM 45634	GCA_001021065.1	1072256	1072256	type	True	78.664	236	732	95	below_threshold
Corynebacterium maris	strain=DSM 45190	GCA_000442645.1	575200	575200	type	True	78.6393	246	732	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.6043	230	732	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.5342	272	732	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	78.4928	187	732	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	78.3168	189	732	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	78.2788	196	732	95	below_threshold
Corynebacterium testudinoris	strain=DSM 44614	GCA_001021045.1	136857	136857	type	True	78.1789	183	732	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	78.0291	156	732	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	78.0071	155	732	95	below_threshold
Corynebacterium lowii	strain=NML 130206	GCA_001412085.1	1544413	1544413	type	True	77.881	146	732	95	below_threshold
Corynebacterium aquatimens	strain=DSM 45632	GCA_015752125.1	1190508	1190508	type	True	77.532	138	732	95	below_threshold
Corynebacterium crudilactis	strain=JZ16	GCA_001643015.1	1652495	1652495	type	True	77.2933	69	732	95	below_threshold
Amycolatopsis lurida	strain=DSM 43134	GCA_900105055.1	31959	31959	type	True	76.2749	63	732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:48,691] [INFO] DFAST Taxonomy check result was written to GCF_006334925.1_ASM633492v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:48,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:48,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:48,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc570a2b-33e5-459e-8302-94905b50d079/dqc_reference/checkm_data
[2024-01-24 14:30:48,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:48,717] [INFO] Task started: CheckM
[2024-01-24 14:30:48,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006334925.1_ASM633492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006334925.1_ASM633492v1_genomic.fna/checkm_input GCF_006334925.1_ASM633492v1_genomic.fna/checkm_result
[2024-01-24 14:31:14,867] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:14,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:14,885] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:14,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:14,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006334925.1_ASM633492v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:14,886] [INFO] Task started: Blastn
[2024-01-24 14:31:14,886] [INFO] Running command: blastn -query GCF_006334925.1_ASM633492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc570a2b-33e5-459e-8302-94905b50d079/dqc_reference/reference_markers_gtdb.fasta -out GCF_006334925.1_ASM633492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:16,451] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:16,457] [INFO] Selected 18 target genomes.
[2024-01-24 14:31:16,458] [INFO] Target genome list was writen to GCF_006334925.1_ASM633492v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:16,481] [INFO] Task started: fastANI
[2024-01-24 14:31:16,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg576fac69-fefa-42ae-89c5-0eef1d7f3e54/GCF_006334925.1_ASM633492v1_genomic.fna.gz --refList GCF_006334925.1_ASM633492v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006334925.1_ASM633492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:26,132] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:26,147] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:26,147] [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_006334925.1	s__Corynebacterium tapiri	100.0	731	732	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_003065405.1	s__Corynebacterium yudongzhengii	78.7652	271	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001021065.1	s__Corynebacterium uterequi	78.7006	234	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767055.1	s__Corynebacterium doosanense	78.6833	318	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000442645.1	s__Corynebacterium maris	78.6226	247	732	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	78.5547	197	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.5488	271	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000819445.1	s__Corynebacterium humireducens	78.4987	235	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000420605.1	s__Corynebacterium massiliense	78.4928	187	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577555.1	s__Corynebacterium jeddahense	78.3379	189	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103625.1	s__Corynebacterium mycetoides	78.2788	196	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021045.1	s__Corynebacterium testudinoris	78.1789	183	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408445.1	s__Corynebacterium tuberculostearicum	78.0071	157	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCF_001412085.1	s__Corynebacterium lowii	77.9294	144	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838985.1	s__Corynebacterium sp012838985	77.7537	186	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539985.1	s__Corynebacterium sp900539985	77.6791	143	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_001643015.1	s__Corynebacterium crudilactis	77.3293	68	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105055.1	s__Amycolatopsis lurida	76.2749	63	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.56	95.13	0.93	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:26,149] [INFO] GTDB search result was written to GCF_006334925.1_ASM633492v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:26,149] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:26,153] [INFO] DFAST_QC result json was written to GCF_006334925.1_ASM633492v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:26,153] [INFO] DFAST_QC completed!
[2024-01-24 14:31:26,153] [INFO] Total running time: 0h0m56s