[2024-01-24 10:47:06,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,596] [INFO] DQC Reference Directory: /var/lib/cwl/stgb78f8c70-4b37-41c6-a5a7-62ffec188544/dqc_reference
[2024-01-24 10:47:12,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,810] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg68a4c5f0-eb7f-4557-9392-57da6b24b32f/GCF_008931025.1_ASM893102v1_genomic.fna.gz | prodigal -d GCF_008931025.1_ASM893102v1_genomic.fna/cds.fna -a GCF_008931025.1_ASM893102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,084] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,084] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,084] [INFO] Running command: hmmsearch --tblout GCF_008931025.1_ASM893102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb78f8c70-4b37-41c6-a5a7-62ffec188544/dqc_reference/reference_markers.hmm GCF_008931025.1_ASM893102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:21,333] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:21,334] [INFO] Found 6/6 markers.
[2024-01-24 10:47:21,359] [INFO] Query marker FASTA was written to GCF_008931025.1_ASM893102v1_genomic.fna/markers.fasta
[2024-01-24 10:47:21,359] [INFO] Task started: Blastn
[2024-01-24 10:47:21,359] [INFO] Running command: blastn -query GCF_008931025.1_ASM893102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb78f8c70-4b37-41c6-a5a7-62ffec188544/dqc_reference/reference_markers.fasta -out GCF_008931025.1_ASM893102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,295] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,298] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:22,299] [INFO] Target genome list was writen to GCF_008931025.1_ASM893102v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,423] [INFO] Task started: fastANI
[2024-01-24 10:47:23,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg68a4c5f0-eb7f-4557-9392-57da6b24b32f/GCF_008931025.1_ASM893102v1_genomic.fna.gz --refList GCF_008931025.1_ASM893102v1_genomic.fna/target_genomes.txt --output GCF_008931025.1_ASM893102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:33,572] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:33,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb78f8c70-4b37-41c6-a5a7-62ffec188544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:33,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb78f8c70-4b37-41c6-a5a7-62ffec188544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:33,590] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:33,591] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:33,591] [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 ciconiae	strain=DSM 44920	GCA_000372385.1	227319	227319	type	True	84.6289	687	808	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.2837	229	808	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	78.1518	165	808	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.1302	216	808	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.1008	226	808	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	78.0989	170	808	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	78.019	190	808	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.0087	230	808	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	77.985	182	808	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	77.9632	215	808	95	below_threshold
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	77.9348	132	808	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	77.8949	165	808	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.8461	212	808	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	77.7756	190	808	95	below_threshold
Corynebacterium maris	strain=DSM 45190	GCA_000442645.1	575200	575200	type	True	77.7603	154	808	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	77.7372	193	808	95	below_threshold
Corynebacterium lowii	strain=NML 130206	GCA_001412085.1	1544413	1544413	type	True	77.6784	161	808	95	below_threshold
Corynebacterium canis	strain=CCUG 58627	GCA_007859215.1	679663	679663	type	True	77.6264	142	808	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	77.5931	160	808	95	below_threshold
Corynebacterium oculi	strain=NML 130210	GCA_001412105.1	1544416	1544416	type	True	77.4896	172	808	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	77.4407	190	808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:33,593] [INFO] DFAST Taxonomy check result was written to GCF_008931025.1_ASM893102v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:33,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:33,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:33,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb78f8c70-4b37-41c6-a5a7-62ffec188544/dqc_reference/checkm_data
[2024-01-24 10:47:33,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:33,622] [INFO] Task started: CheckM
[2024-01-24 10:47:33,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008931025.1_ASM893102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008931025.1_ASM893102v1_genomic.fna/checkm_input GCF_008931025.1_ASM893102v1_genomic.fna/checkm_result
[2024-01-24 10:48:02,383] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:02,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:02,409] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:02,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:02,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008931025.1_ASM893102v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:02,410] [INFO] Task started: Blastn
[2024-01-24 10:48:02,411] [INFO] Running command: blastn -query GCF_008931025.1_ASM893102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb78f8c70-4b37-41c6-a5a7-62ffec188544/dqc_reference/reference_markers_gtdb.fasta -out GCF_008931025.1_ASM893102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:03,818] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:03,830] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:03,831] [INFO] Target genome list was writen to GCF_008931025.1_ASM893102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:03,914] [INFO] Task started: fastANI
[2024-01-24 10:48:03,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg68a4c5f0-eb7f-4557-9392-57da6b24b32f/GCF_008931025.1_ASM893102v1_genomic.fna.gz --refList GCF_008931025.1_ASM893102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008931025.1_ASM893102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:12,083] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:12,096] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:12,097] [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_008930665.1	s__Corynebacterium sp008930665	96.1192	765	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.86	95.30	0.97	0.95	18	conclusive
GCF_000372385.1	s__Corynebacterium ciconiae	84.6435	686	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.1302	216	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.1008	226	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000375365.1	s__Corynebacterium mastitidis	78.019	190	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCF_009734425.1	s__Corynebacterium sp009734425	77.985	182	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819445.1	s__Corynebacterium humireducens	77.9632	215	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_014267345.1	s__Corynebacterium sp014267345	77.962	160	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	77.7773	157	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_000442645.1	s__Corynebacterium maris	77.7603	154	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000835165.1	s__Corynebacterium marinum	77.7372	193	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_001412085.1	s__Corynebacterium lowii	77.6784	161	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859215.1	s__Corynebacterium canis	77.6264	142	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176865.1	s__Corynebacterium fournieri	77.5732	161	808	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	77.4562	189	808	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	77.3629	173	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114135.1	s__Corynebacterium avicola	77.3497	125	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:12,098] [INFO] GTDB search result was written to GCF_008931025.1_ASM893102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:12,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:12,103] [INFO] DFAST_QC result json was written to GCF_008931025.1_ASM893102v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:12,103] [INFO] DFAST_QC completed!
[2024-01-24 10:48:12,104] [INFO] Total running time: 0h1m6s