[2024-01-24 14:55:08,249] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,252] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,252] [INFO] DQC Reference Directory: /var/lib/cwl/stg01f976cc-8cc5-4e87-81c6-1f481488ab65/dqc_reference
[2024-01-24 14:55:09,919] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,920] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg528dc6ad-c774-42fc-8e4e-5bbec9816526/GCF_900092335.1_PRJEB14666_genomic.fna.gz | prodigal -d GCF_900092335.1_PRJEB14666_genomic.fna/cds.fna -a GCF_900092335.1_PRJEB14666_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:18,544] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:18,544] [INFO] Task started: HMMsearch
[2024-01-24 14:55:18,545] [INFO] Running command: hmmsearch --tblout GCF_900092335.1_PRJEB14666_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01f976cc-8cc5-4e87-81c6-1f481488ab65/dqc_reference/reference_markers.hmm GCF_900092335.1_PRJEB14666_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:18,774] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:18,775] [INFO] Found 6/6 markers.
[2024-01-24 14:55:18,800] [INFO] Query marker FASTA was written to GCF_900092335.1_PRJEB14666_genomic.fna/markers.fasta
[2024-01-24 14:55:18,801] [INFO] Task started: Blastn
[2024-01-24 14:55:18,801] [INFO] Running command: blastn -query GCF_900092335.1_PRJEB14666_genomic.fna/markers.fasta -db /var/lib/cwl/stg01f976cc-8cc5-4e87-81c6-1f481488ab65/dqc_reference/reference_markers.fasta -out GCF_900092335.1_PRJEB14666_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:19,818] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:19,822] [INFO] Selected 22 target genomes.
[2024-01-24 14:55:19,823] [INFO] Target genome list was writen to GCF_900092335.1_PRJEB14666_genomic.fna/target_genomes.txt
[2024-01-24 14:55:19,833] [INFO] Task started: fastANI
[2024-01-24 14:55:19,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg528dc6ad-c774-42fc-8e4e-5bbec9816526/GCF_900092335.1_PRJEB14666_genomic.fna.gz --refList GCF_900092335.1_PRJEB14666_genomic.fna/target_genomes.txt --output GCF_900092335.1_PRJEB14666_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:31,444] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:31,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01f976cc-8cc5-4e87-81c6-1f481488ab65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:31,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01f976cc-8cc5-4e87-81c6-1f481488ab65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:31,462] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:31,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:31,462] [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 phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	99.9999	923	924	95	conclusive
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	80.922	388	924	95	below_threshold
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	80.9086	387	924	95	below_threshold
Corynebacterium striatum	strain=ATCC 6940	GCA_000159135.1	43770	43770	type	True	80.876	388	924	95	below_threshold
Corynebacterium striatum	strain=NCTC764	GCA_900447675.1	43770	43770	type	True	80.8234	393	924	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	79.8122	358	924	95	below_threshold
Corynebacterium aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	79.5864	364	924	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	79.5735	313	924	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	79.5664	309	924	95	below_threshold
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	79.5311	336	924	95	below_threshold
Corynebacterium minutissimum	strain=ATCC 23348	GCA_000805675.1	38301	38301	type	True	79.4804	326	924	95	below_threshold
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	79.1618	310	924	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	79.1396	314	924	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.8545	337	924	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.8247	322	924	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.7526	330	924	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.7081	324	924	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	78.4163	271	924	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_000183325.2	36808	36808	type	True	77.2487	156	924	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	77.1898	187	924	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	77.1873	187	924	95	below_threshold
Nocardia yunnanensis	strain=CFH S0054	GCA_003626895.1	2382165	2382165	type	True	76.6121	124	924	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:31,464] [INFO] DFAST Taxonomy check result was written to GCF_900092335.1_PRJEB14666_genomic.fna/tc_result.tsv
[2024-01-24 14:55:31,465] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:31,465] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:31,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01f976cc-8cc5-4e87-81c6-1f481488ab65/dqc_reference/checkm_data
[2024-01-24 14:55:31,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:31,494] [INFO] Task started: CheckM
[2024-01-24 14:55:31,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900092335.1_PRJEB14666_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900092335.1_PRJEB14666_genomic.fna/checkm_input GCF_900092335.1_PRJEB14666_genomic.fna/checkm_result
[2024-01-24 14:56:01,018] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:01,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:01,038] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:01,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:01,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900092335.1_PRJEB14666_genomic.fna/markers.fasta)
[2024-01-24 14:56:01,039] [INFO] Task started: Blastn
[2024-01-24 14:56:01,040] [INFO] Running command: blastn -query GCF_900092335.1_PRJEB14666_genomic.fna/markers.fasta -db /var/lib/cwl/stg01f976cc-8cc5-4e87-81c6-1f481488ab65/dqc_reference/reference_markers_gtdb.fasta -out GCF_900092335.1_PRJEB14666_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:02,460] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:02,463] [INFO] Selected 18 target genomes.
[2024-01-24 14:56:02,463] [INFO] Target genome list was writen to GCF_900092335.1_PRJEB14666_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:02,477] [INFO] Task started: fastANI
[2024-01-24 14:56:02,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg528dc6ad-c774-42fc-8e4e-5bbec9816526/GCF_900092335.1_PRJEB14666_genomic.fna.gz --refList GCF_900092335.1_PRJEB14666_genomic.fna/target_genomes_gtdb.txt --output GCF_900092335.1_PRJEB14666_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:13,205] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:13,219] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:13,220] [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_900092335.1	s__Corynebacterium phoceense	99.9999	923	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	conclusive
GCF_000159135.1	s__Corynebacterium striatum	80.8906	387	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_001586215.1	s__Corynebacterium simulans	80.7456	357	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	79.9582	365	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_001812805.1	s__Corynebacterium sp001812805	79.6903	332	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001815935.1	s__Corynebacterium sp001815935	79.688	395	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016889765.1	s__Corynebacterium minutissimum_B	79.658	329	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	96.19	0.95	0.91	3	-
GCF_000988205.1	s__Corynebacterium minutissimum_A	79.5926	367	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.53	96.09	0.91	0.89	16	-
GCF_000805675.1	s__Corynebacterium minutissimum	79.4955	325	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	6	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	79.1427	309	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_000980815.1	s__Corynebacterium camporealensis	79.127	314	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000819445.1	s__Corynebacterium humireducens	78.8608	336	924	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	78.7759	328	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900411315.1	s__Corynebacterium senegalense	78.4161	271	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183325.1	s__Corynebacterium bovis	77.2487	156	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.01	98.42	0.92	0.83	23	-
GCF_003626895.1	s__Nocardia yunnanensis	76.6192	122	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	76.4151	101	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139625.1	s__Actinospica sp018139625	75.7234	118	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:13,221] [INFO] GTDB search result was written to GCF_900092335.1_PRJEB14666_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:13,222] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:13,227] [INFO] DFAST_QC result json was written to GCF_900092335.1_PRJEB14666_genomic.fna/dqc_result.json
[2024-01-24 14:56:13,227] [INFO] DFAST_QC completed!
[2024-01-24 14:56:13,227] [INFO] Total running time: 0h1m5s