[2024-01-24 12:46:56,028] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:56,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:56,030] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0422256-0240-4305-98c5-c94640ed296c/dqc_reference
[2024-01-24 12:46:57,333] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:57,334] [INFO] Task started: Prodigal
[2024-01-24 12:46:57,335] [INFO] Running command: gunzip -c /var/lib/cwl/stge02ee8b0-fedf-4c6e-bbb1-9e7f2b8b997a/GCF_003070865.1_ASM307086v1_genomic.fna.gz | prodigal -d GCF_003070865.1_ASM307086v1_genomic.fna/cds.fna -a GCF_003070865.1_ASM307086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:04,531] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:04,531] [INFO] Task started: HMMsearch
[2024-01-24 12:47:04,532] [INFO] Running command: hmmsearch --tblout GCF_003070865.1_ASM307086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0422256-0240-4305-98c5-c94640ed296c/dqc_reference/reference_markers.hmm GCF_003070865.1_ASM307086v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:04,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:04,772] [INFO] Found 6/6 markers.
[2024-01-24 12:47:04,804] [INFO] Query marker FASTA was written to GCF_003070865.1_ASM307086v1_genomic.fna/markers.fasta
[2024-01-24 12:47:04,804] [INFO] Task started: Blastn
[2024-01-24 12:47:04,804] [INFO] Running command: blastn -query GCF_003070865.1_ASM307086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0422256-0240-4305-98c5-c94640ed296c/dqc_reference/reference_markers.fasta -out GCF_003070865.1_ASM307086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:05,890] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:05,895] [INFO] Selected 13 target genomes.
[2024-01-24 12:47:05,895] [INFO] Target genome list was writen to GCF_003070865.1_ASM307086v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:05,904] [INFO] Task started: fastANI
[2024-01-24 12:47:05,904] [INFO] Running command: fastANI --query /var/lib/cwl/stge02ee8b0-fedf-4c6e-bbb1-9e7f2b8b997a/GCF_003070865.1_ASM307086v1_genomic.fna.gz --refList GCF_003070865.1_ASM307086v1_genomic.fna/target_genomes.txt --output GCF_003070865.1_ASM307086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:12,262] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:12,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0422256-0240-4305-98c5-c94640ed296c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:12,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0422256-0240-4305-98c5-c94640ed296c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:12,280] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:12,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:12,281] [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 liangguodongii	strain=2184	GCA_003070865.1	2079535	2079535	type	True	100.0	785	785	95	conclusive
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	81.7678	538	785	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	81.5875	495	785	95	below_threshold
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	81.4049	491	785	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	81.3657	485	785	95	below_threshold
Corynebacterium qintianiae	strain=MC1420	GCA_011038645.2	2709392	2709392	type	True	81.0201	476	785	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	80.5208	443	785	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	80.3913	449	785	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	80.2473	384	785	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	79.9296	347	785	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	79.8475	352	785	95	below_threshold
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	79.5843	335	785	95	below_threshold
Corynebacterium mucifaciens	strain=ATCC 700355	GCA_012396315.1	57171	57171	type	True	79.5717	324	785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:12,285] [INFO] DFAST Taxonomy check result was written to GCF_003070865.1_ASM307086v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:12,286] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:12,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:12,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0422256-0240-4305-98c5-c94640ed296c/dqc_reference/checkm_data
[2024-01-24 12:47:12,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:12,321] [INFO] Task started: CheckM
[2024-01-24 12:47:12,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003070865.1_ASM307086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003070865.1_ASM307086v1_genomic.fna/checkm_input GCF_003070865.1_ASM307086v1_genomic.fna/checkm_result
[2024-01-24 12:47:38,379] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:38,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:38,398] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:38,398] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:38,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003070865.1_ASM307086v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:38,399] [INFO] Task started: Blastn
[2024-01-24 12:47:38,399] [INFO] Running command: blastn -query GCF_003070865.1_ASM307086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0422256-0240-4305-98c5-c94640ed296c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003070865.1_ASM307086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:40,120] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:40,124] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:40,124] [INFO] Target genome list was writen to GCF_003070865.1_ASM307086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:40,134] [INFO] Task started: fastANI
[2024-01-24 12:47:40,134] [INFO] Running command: fastANI --query /var/lib/cwl/stge02ee8b0-fedf-4c6e-bbb1-9e7f2b8b997a/GCF_003070865.1_ASM307086v1_genomic.fna.gz --refList GCF_003070865.1_ASM307086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003070865.1_ASM307086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:46,408] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:46,418] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:46,418] [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_003070865.1	s__Corynebacterium liangguodongii	100.0	785	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_007641235.1	s__Corynebacterium sanguinis	81.8019	540	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_900103625.1	s__Corynebacterium mycetoides	81.6186	496	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159635.1	s__Corynebacterium lipophiloflavum	81.4332	489	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900411315.1	s__Corynebacterium senegalense	81.3376	487	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011038645.2	s__Corynebacterium qintianiae	80.988	477	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.90	98.90	0.92	0.92	2	-
GCF_900105305.1	s__Corynebacterium timonense	80.5405	442	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000577555.1	s__Corynebacterium jeddahense	80.2777	382	785	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	80.0861	419	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351335.1	s__Corynebacterium lipophilum	79.921	348	785	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	79.7013	359	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_012396315.1	s__Corynebacterium mucifaciens	79.5556	325	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:46,420] [INFO] GTDB search result was written to GCF_003070865.1_ASM307086v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:46,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:46,424] [INFO] DFAST_QC result json was written to GCF_003070865.1_ASM307086v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:46,425] [INFO] DFAST_QC completed!
[2024-01-24 12:47:46,425] [INFO] Total running time: 0h0m50s