[2024-01-24 14:30:30,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg18f9b9ef-5bf3-4cb5-af4f-b99c9414af8f/dqc_reference
[2024-01-24 14:30:31,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:31,779] [INFO] Task started: Prodigal
[2024-01-24 14:30:31,780] [INFO] Running command: gunzip -c /var/lib/cwl/stg286e56d9-c57b-458d-a664-92ccfdfd4448/GCF_014137965.1_ASM1413796v1_genomic.fna.gz | prodigal -d GCF_014137965.1_ASM1413796v1_genomic.fna/cds.fna -a GCF_014137965.1_ASM1413796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:40,562] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:40,562] [INFO] Task started: HMMsearch
[2024-01-24 14:30:40,562] [INFO] Running command: hmmsearch --tblout GCF_014137965.1_ASM1413796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18f9b9ef-5bf3-4cb5-af4f-b99c9414af8f/dqc_reference/reference_markers.hmm GCF_014137965.1_ASM1413796v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:40,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:40,772] [INFO] Found 6/6 markers.
[2024-01-24 14:30:40,800] [INFO] Query marker FASTA was written to GCF_014137965.1_ASM1413796v1_genomic.fna/markers.fasta
[2024-01-24 14:30:40,800] [INFO] Task started: Blastn
[2024-01-24 14:30:40,800] [INFO] Running command: blastn -query GCF_014137965.1_ASM1413796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18f9b9ef-5bf3-4cb5-af4f-b99c9414af8f/dqc_reference/reference_markers.fasta -out GCF_014137965.1_ASM1413796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:42,057] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:42,060] [INFO] Selected 23 target genomes.
[2024-01-24 14:30:42,061] [INFO] Target genome list was writen to GCF_014137965.1_ASM1413796v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:42,089] [INFO] Task started: fastANI
[2024-01-24 14:30:42,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg286e56d9-c57b-458d-a664-92ccfdfd4448/GCF_014137965.1_ASM1413796v1_genomic.fna.gz --refList GCF_014137965.1_ASM1413796v1_genomic.fna/target_genomes.txt --output GCF_014137965.1_ASM1413796v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:58,090] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:58,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18f9b9ef-5bf3-4cb5-af4f-b99c9414af8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:58,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18f9b9ef-5bf3-4cb5-af4f-b99c9414af8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:58,108] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:30:58,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:58,108] [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	100.0	1128	1132	95	conclusive
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	99.9366	1074	1132	95	conclusive
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.5066	370	1132	95	below_threshold
Curtobacterium luteum	strain=DSM 20542	GCA_016907595.1	33881	33881	type	True	79.3377	486	1132	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.3165	483	1132	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.3034	475	1132	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	79.3028	478	1132	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.2713	478	1132	95	below_threshold
Curtobacterium citreum	strain=DSM 20528	GCA_006715175.1	2036	2036	type	True	79.2576	519	1132	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	79.2568	509	1132	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	79.2405	429	1132	95	below_threshold
Curtobacterium luteum	strain=ATCC 15830	GCA_013359885.1	33881	33881	type	True	79.2382	487	1132	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	79.2324	510	1132	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	79.1655	342	1132	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	79.1243	476	1132	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.071	508	1132	95	below_threshold
Plantibacter flavus	strain=DSM 14012	GCA_003755125.1	150123	150123	type	True	78.8759	430	1132	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	78.7947	413	1132	95	below_threshold
Plantibacter flavus	strain=VKM Ac-2504	GCA_900177615.1	150123	150123	type	True	78.7441	427	1132	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	78.7299	472	1132	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	78.7053	422	1132	95	below_threshold
Agromyces italicus	strain=DSM 16388	GCA_000421545.1	279572	279572	type	True	78.4867	423	1132	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	78.4192	423	1132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:58,110] [INFO] DFAST Taxonomy check result was written to GCF_014137965.1_ASM1413796v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:58,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:58,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:58,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18f9b9ef-5bf3-4cb5-af4f-b99c9414af8f/dqc_reference/checkm_data
[2024-01-24 14:30:58,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:58,147] [INFO] Task started: CheckM
[2024-01-24 14:30:58,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014137965.1_ASM1413796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014137965.1_ASM1413796v1_genomic.fna/checkm_input GCF_014137965.1_ASM1413796v1_genomic.fna/checkm_result
[2024-01-24 14:31:41,606] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:41,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.02%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:41,630] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:41,630] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:41,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014137965.1_ASM1413796v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:41,631] [INFO] Task started: Blastn
[2024-01-24 14:31:41,631] [INFO] Running command: blastn -query GCF_014137965.1_ASM1413796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18f9b9ef-5bf3-4cb5-af4f-b99c9414af8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014137965.1_ASM1413796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:43,652] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:43,656] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:43,656] [INFO] Target genome list was writen to GCF_014137965.1_ASM1413796v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:43,667] [INFO] Task started: fastANI
[2024-01-24 14:31:43,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg286e56d9-c57b-458d-a664-92ccfdfd4448/GCF_014137965.1_ASM1413796v1_genomic.fna.gz --refList GCF_014137965.1_ASM1413796v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014137965.1_ASM1413796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:53,980] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:53,990] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:53,990] [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_007988805.1	s__Frigoribacterium faeni	99.9366	1074	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_014842255.1	s__Frigoribacterium sp014842255	86.7009	844	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422285.1	s__Frigoribacterium sp001422285	86.3648	869	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	99.06	99.06	0.95	0.95	2	-
GCF_001423905.1	s__Frigoribacterium sp001423905	84.7868	786	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	96.23	96.23	0.90	0.90	2	-
GCF_001424645.1	s__Frigoribacterium sp001424645	84.7279	796	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	97.29	95.55	0.92	0.86	4	-
GCF_001421165.1	s__Frigoribacterium sp001421165	84.6036	772	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	98.43	98.29	0.95	0.94	7	-
GCF_003751785.1	s__Frigoribacterium sp003751785	84.5729	783	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761235.1	s__Frigoribacterium faeni_A	84.4507	740	1132	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	84.3436	774	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	97.17	96.59	0.92	0.91	6	-
GCF_017833035.1	s__Frigoribacterium sp017833035	84.2917	759	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248995.1	s__Frigoribacterium sp013248995	84.0667	749	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:53,992] [INFO] GTDB search result was written to GCF_014137965.1_ASM1413796v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:53,992] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:53,996] [INFO] DFAST_QC result json was written to GCF_014137965.1_ASM1413796v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:53,997] [INFO] DFAST_QC completed!
[2024-01-24 14:31:53,997] [INFO] Total running time: 0h1m24s