[2024-01-24 13:16:56,127] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:56,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:56,129] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4ac4e65-e08c-4f10-af18-eb36d80ceec6/dqc_reference
[2024-01-24 13:16:57,334] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:16:57,335] [INFO] Task started: Prodigal
[2024-01-24 13:16:57,335] [INFO] Running command: gunzip -c /var/lib/cwl/stgc63f0643-ae3b-456f-82e6-749580ef75df/GCF_000550805.1_ASM55080v1_genomic.fna.gz | prodigal -d GCF_000550805.1_ASM55080v1_genomic.fna/cds.fna -a GCF_000550805.1_ASM55080v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:06,132] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:06,133] [INFO] Task started: HMMsearch
[2024-01-24 13:17:06,133] [INFO] Running command: hmmsearch --tblout GCF_000550805.1_ASM55080v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4ac4e65-e08c-4f10-af18-eb36d80ceec6/dqc_reference/reference_markers.hmm GCF_000550805.1_ASM55080v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:06,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:06,385] [INFO] Found 6/6 markers.
[2024-01-24 13:17:06,416] [INFO] Query marker FASTA was written to GCF_000550805.1_ASM55080v1_genomic.fna/markers.fasta
[2024-01-24 13:17:06,416] [INFO] Task started: Blastn
[2024-01-24 13:17:06,416] [INFO] Running command: blastn -query GCF_000550805.1_ASM55080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4ac4e65-e08c-4f10-af18-eb36d80ceec6/dqc_reference/reference_markers.fasta -out GCF_000550805.1_ASM55080v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:07,583] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:07,586] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:07,586] [INFO] Target genome list was writen to GCF_000550805.1_ASM55080v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:07,591] [INFO] Task started: fastANI
[2024-01-24 13:17:07,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgc63f0643-ae3b-456f-82e6-749580ef75df/GCF_000550805.1_ASM55080v1_genomic.fna.gz --refList GCF_000550805.1_ASM55080v1_genomic.fna/target_genomes.txt --output GCF_000550805.1_ASM55080v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:13,485] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:13,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4ac4e65-e08c-4f10-af18-eb36d80ceec6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:13,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4ac4e65-e08c-4f10-af18-eb36d80ceec6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:13,501] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:13,501] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:13,501] [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 vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	100.0	977	977	95	conclusive
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	80.6327	457	977	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	80.583	429	977	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	80.5111	434	977	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	80.4675	439	977	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	80.2584	427	977	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	80.2505	454	977	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	78.9978	320	977	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	78.9083	337	977	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	78.6557	232	977	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.6395	248	977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:13,504] [INFO] DFAST Taxonomy check result was written to GCF_000550805.1_ASM55080v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:13,505] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:13,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:13,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4ac4e65-e08c-4f10-af18-eb36d80ceec6/dqc_reference/checkm_data
[2024-01-24 13:17:13,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:13,536] [INFO] Task started: CheckM
[2024-01-24 13:17:13,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000550805.1_ASM55080v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000550805.1_ASM55080v1_genomic.fna/checkm_input GCF_000550805.1_ASM55080v1_genomic.fna/checkm_result
[2024-01-24 13:17:44,173] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:44,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:44,191] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:44,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:44,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000550805.1_ASM55080v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:44,192] [INFO] Task started: Blastn
[2024-01-24 13:17:44,193] [INFO] Running command: blastn -query GCF_000550805.1_ASM55080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4ac4e65-e08c-4f10-af18-eb36d80ceec6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000550805.1_ASM55080v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:45,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:45,981] [INFO] Selected 12 target genomes.
[2024-01-24 13:17:45,981] [INFO] Target genome list was writen to GCF_000550805.1_ASM55080v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:45,992] [INFO] Task started: fastANI
[2024-01-24 13:17:45,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgc63f0643-ae3b-456f-82e6-749580ef75df/GCF_000550805.1_ASM55080v1_genomic.fna.gz --refList GCF_000550805.1_ASM55080v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000550805.1_ASM55080v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:52,534] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:52,546] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:52,546] [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_000550805.1	s__Corynebacterium vitaeruminis	100.0	977	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	conclusive
GCF_000819445.1	s__Corynebacterium humireducens	80.5797	435	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000341345.1	s__Corynebacterium halotolerans	80.5726	457	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177745.1	s__Corynebacterium pollutisoli	80.4975	435	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_001941485.1	s__Corynebacterium frankenforstense	80.4356	438	977	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	80.0911	421	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCA_012838985.1	s__Corynebacterium sp012838985	79.8354	355	977	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	79.7945	382	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375365.1	s__Corynebacterium mastitidis	78.9352	335	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	78.9321	318	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001815985.1	s__Corynebacterium sp001815985	78.7558	221	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.95	96.87	0.95	0.94	3	-
GCF_000159135.1	s__Corynebacterium striatum	78.3529	244	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:52,548] [INFO] GTDB search result was written to GCF_000550805.1_ASM55080v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:52,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:52,552] [INFO] DFAST_QC result json was written to GCF_000550805.1_ASM55080v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:52,553] [INFO] DFAST_QC completed!
[2024-01-24 13:17:52,553] [INFO] Total running time: 0h0m56s