[2024-01-25 18:56:05,465] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:05,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:05,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg225133cf-6641-4ac2-89a9-7ec3c80e6cf6/dqc_reference
[2024-01-25 18:56:06,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:06,603] [INFO] Task started: Prodigal
[2024-01-25 18:56:06,604] [INFO] Running command: gunzip -c /var/lib/cwl/stgd427764a-abc9-47c5-8ca9-cb1ad5f25b9d/GCF_030296615.1_ASM3029661v1_genomic.fna.gz | prodigal -d GCF_030296615.1_ASM3029661v1_genomic.fna/cds.fna -a GCF_030296615.1_ASM3029661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:17,693] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:17,694] [INFO] Task started: HMMsearch
[2024-01-25 18:56:17,694] [INFO] Running command: hmmsearch --tblout GCF_030296615.1_ASM3029661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg225133cf-6641-4ac2-89a9-7ec3c80e6cf6/dqc_reference/reference_markers.hmm GCF_030296615.1_ASM3029661v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:17,905] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:17,906] [INFO] Found 6/6 markers.
[2024-01-25 18:56:17,949] [INFO] Query marker FASTA was written to GCF_030296615.1_ASM3029661v1_genomic.fna/markers.fasta
[2024-01-25 18:56:17,950] [INFO] Task started: Blastn
[2024-01-25 18:56:17,950] [INFO] Running command: blastn -query GCF_030296615.1_ASM3029661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg225133cf-6641-4ac2-89a9-7ec3c80e6cf6/dqc_reference/reference_markers.fasta -out GCF_030296615.1_ASM3029661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:19,022] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:19,025] [INFO] Selected 33 target genomes.
[2024-01-25 18:56:19,025] [INFO] Target genome list was writen to GCF_030296615.1_ASM3029661v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:19,071] [INFO] Task started: fastANI
[2024-01-25 18:56:19,071] [INFO] Running command: fastANI --query /var/lib/cwl/stgd427764a-abc9-47c5-8ca9-cb1ad5f25b9d/GCF_030296615.1_ASM3029661v1_genomic.fna.gz --refList GCF_030296615.1_ASM3029661v1_genomic.fna/target_genomes.txt --output GCF_030296615.1_ASM3029661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:40,803] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:40,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg225133cf-6641-4ac2-89a9-7ec3c80e6cf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:40,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg225133cf-6641-4ac2-89a9-7ec3c80e6cf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:40,821] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:56:40,821] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:56:40,821] [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
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	80.4053	549	1559	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	80.3638	546	1559	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	78.9463	463	1559	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	78.8934	338	1559	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	78.8608	449	1559	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	78.8535	421	1559	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	78.7849	419	1559	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	78.772	447	1559	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.77	428	1559	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	78.7486	449	1559	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.7142	426	1559	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	78.6812	325	1559	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	78.6429	464	1559	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.6337	420	1559	95	below_threshold
Curtobacterium albidum	strain=DSM 20512	GCA_013359825.1	50728	50728	type	True	78.6317	467	1559	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.5923	395	1559	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	78.572	430	1559	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	78.5682	368	1559	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	78.5673	335	1559	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	78.5372	370	1559	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.4627	320	1559	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	78.4494	402	1559	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	78.4439	316	1559	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	78.3164	413	1559	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.2136	383	1559	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	78.2004	447	1559	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.0049	388	1559	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.0037	363	1559	95	below_threshold
Actinomyces denticolens	strain=NCTC11490	GCA_900445045.1	52767	52767	type	True	76.5638	121	1559	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	76.2217	114	1559	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	76.211	104	1559	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	76.2063	140	1559	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	75.6231	226	1559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:40,823] [INFO] DFAST Taxonomy check result was written to GCF_030296615.1_ASM3029661v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:40,823] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:40,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:40,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg225133cf-6641-4ac2-89a9-7ec3c80e6cf6/dqc_reference/checkm_data
[2024-01-25 18:56:40,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:40,868] [INFO] Task started: CheckM
[2024-01-25 18:56:40,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296615.1_ASM3029661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296615.1_ASM3029661v1_genomic.fna/checkm_input GCF_030296615.1_ASM3029661v1_genomic.fna/checkm_result
[2024-01-25 18:57:31,929] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:31,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:31,962] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:31,962] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:31,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296615.1_ASM3029661v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:31,963] [INFO] Task started: Blastn
[2024-01-25 18:57:31,963] [INFO] Running command: blastn -query GCF_030296615.1_ASM3029661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg225133cf-6641-4ac2-89a9-7ec3c80e6cf6/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296615.1_ASM3029661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:33,789] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:33,791] [INFO] Selected 15 target genomes.
[2024-01-25 18:57:33,791] [INFO] Target genome list was writen to GCF_030296615.1_ASM3029661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:33,824] [INFO] Task started: fastANI
[2024-01-25 18:57:33,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgd427764a-abc9-47c5-8ca9-cb1ad5f25b9d/GCF_030296615.1_ASM3029661v1_genomic.fna.gz --refList GCF_030296615.1_ASM3029661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296615.1_ASM3029661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:44,776] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:44,786] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:57:44,786] [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_003752365.1	s__Frondihabitans sp003752365	82.546	775	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001577365.1	s__Frondihabitans sp001577365	82.2423	826	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002074055.1	s__Frondihabitans sp002074055	82.2321	714	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634555.1	s__Frondihabitans australicus	82.1118	753	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423105.1	s__Frondihabitans sp001423105	81.837	701	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	96.96	96.22	0.91	0.89	4	-
GCF_011761235.1	s__Frigoribacterium faeni_A	80.2813	568	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759585.1	s__Frigoribacterium endophyticum	80.2709	567	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	97.17	96.59	0.92	0.91	6	-
GCF_001422285.1	s__Frigoribacterium sp001422285	80.2203	533	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	99.06	99.06	0.95	0.95	2	-
GCF_001424645.1	s__Frigoribacterium sp001424645	80.2002	567	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	97.29	95.55	0.92	0.86	4	-
GCF_000878135.1	s__Frigoribacterium sp000878135	80.1701	533	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	98.53	98.34	0.92	0.89	4	-
GCF_013177295.1	s__Actinomyces marmotae	76.4871	112	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.20	98.86	0.98	0.97	5	-
GCF_002072185.1	s__Actinomyces denticolens	76.2108	116	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.84	99.40	0.98	0.94	5	-
GCF_000295095.1	s__Actinomyces timonensis	76.1812	142	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546825.1	s__Actinomyces oris	75.9998	127	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.45	95.25	0.91	0.88	16	-
GCF_900102815.1	s__Glycomyces sambucus	75.6086	229	1559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:44,788] [INFO] GTDB search result was written to GCF_030296615.1_ASM3029661v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:44,788] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:44,793] [INFO] DFAST_QC result json was written to GCF_030296615.1_ASM3029661v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:44,793] [INFO] DFAST_QC completed!
[2024-01-25 18:57:44,793] [INFO] Total running time: 0h1m39s