[2024-01-24 14:12:47,540] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg8294927d-4fbf-410a-aba0-4d0656b2e409/dqc_reference
[2024-01-24 14:12:48,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,750] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,750] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d17d180-0c06-4362-963c-e93918375e54/GCF_008642235.1_ASM864223v1_genomic.fna.gz | prodigal -d GCF_008642235.1_ASM864223v1_genomic.fna/cds.fna -a GCF_008642235.1_ASM864223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:58,710] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:58,711] [INFO] Task started: HMMsearch
[2024-01-24 14:12:58,711] [INFO] Running command: hmmsearch --tblout GCF_008642235.1_ASM864223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8294927d-4fbf-410a-aba0-4d0656b2e409/dqc_reference/reference_markers.hmm GCF_008642235.1_ASM864223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:58,952] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:58,954] [INFO] Found 6/6 markers.
[2024-01-24 14:12:58,999] [INFO] Query marker FASTA was written to GCF_008642235.1_ASM864223v1_genomic.fna/markers.fasta
[2024-01-24 14:12:59,000] [INFO] Task started: Blastn
[2024-01-24 14:12:59,000] [INFO] Running command: blastn -query GCF_008642235.1_ASM864223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8294927d-4fbf-410a-aba0-4d0656b2e409/dqc_reference/reference_markers.fasta -out GCF_008642235.1_ASM864223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:00,133] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:00,136] [INFO] Selected 24 target genomes.
[2024-01-24 14:13:00,137] [INFO] Target genome list was writen to GCF_008642235.1_ASM864223v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:00,142] [INFO] Task started: fastANI
[2024-01-24 14:13:00,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d17d180-0c06-4362-963c-e93918375e54/GCF_008642235.1_ASM864223v1_genomic.fna.gz --refList GCF_008642235.1_ASM864223v1_genomic.fna/target_genomes.txt --output GCF_008642235.1_ASM864223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:14,148] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:14,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8294927d-4fbf-410a-aba0-4d0656b2e409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:14,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8294927d-4fbf-410a-aba0-4d0656b2e409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:14,171] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:14,171] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:14,171] [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
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	80.0942	346	1096	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.8646	432	1096	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	79.8328	447	1096	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	79.7366	433	1096	95	below_threshold
Clavibacter michiganensis	strain=VKM Ac-1403	GCA_900168345.1	28447	28447	suspected-type	True	79.7282	426	1096	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.6917	436	1096	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.6822	458	1096	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=LMG 3663	GCA_002240565.1	33014	28447	type	True	79.6778	430	1096	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	79.6757	448	1096	95	below_threshold
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	79.6644	437	1096	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.6477	462	1096	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	79.6408	428	1096	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.1974	399	1096	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	79.0385	386	1096	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.967	380	1096	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	78.891	424	1096	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.8375	409	1096	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	78.7856	352	1096	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	78.7685	363	1096	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	78.7009	389	1096	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	78.6993	362	1096	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.6319	385	1096	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.55	355	1096	95	below_threshold
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	78.2181	298	1096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:14,173] [INFO] DFAST Taxonomy check result was written to GCF_008642235.1_ASM864223v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:14,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:14,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:14,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8294927d-4fbf-410a-aba0-4d0656b2e409/dqc_reference/checkm_data
[2024-01-24 14:13:14,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:14,213] [INFO] Task started: CheckM
[2024-01-24 14:13:14,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008642235.1_ASM864223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008642235.1_ASM864223v1_genomic.fna/checkm_input GCF_008642235.1_ASM864223v1_genomic.fna/checkm_result
[2024-01-24 14:13:50,320] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:50,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:50,348] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:50,349] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:50,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008642235.1_ASM864223v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:50,349] [INFO] Task started: Blastn
[2024-01-24 14:13:50,350] [INFO] Running command: blastn -query GCF_008642235.1_ASM864223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8294927d-4fbf-410a-aba0-4d0656b2e409/dqc_reference/reference_markers_gtdb.fasta -out GCF_008642235.1_ASM864223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:52,161] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:52,166] [INFO] Selected 20 target genomes.
[2024-01-24 14:13:52,166] [INFO] Target genome list was writen to GCF_008642235.1_ASM864223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:52,201] [INFO] Task started: fastANI
[2024-01-24 14:13:52,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d17d180-0c06-4362-963c-e93918375e54/GCF_008642235.1_ASM864223v1_genomic.fna.gz --refList GCF_008642235.1_ASM864223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008642235.1_ASM864223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:06,204] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:06,221] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:06,222] [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
GCA_008642235.1	s__Planctomonas sp008642235	100.0	1096	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Planctomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003067705.1	s__Planctomonas deserti	81.1316	615	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Planctomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280205.1	s__Clavibacter capsici	79.9789	442	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
GCF_002151125.1	s__Clavibacter michiganensis_C	79.8616	442	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014775655.1	s__Clavibacter zhangzhiyongii	79.8093	449	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.40	98.40	0.96	0.96	2	-
GCF_016907085.1	s__Clavibacter michiganensis_O	79.7989	436	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168345.1	s__Clavibacter michiganensis	79.728	426	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.05	95.09	0.97	0.88	49	-
GCF_015351075.1	s__Clavibacter sp015351075	79.669	425	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002240635.1	s__Clavibacter tessellarius	79.6471	462	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.95	95.37	0.96	0.94	3	-
GCF_003384945.1	s__Clavibacter sp003384945	79.6048	466	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002150995.1	s__Clavibacter michiganensis_K	79.424	455	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.44	98.42	0.92	0.92	3	-
GCF_001422325.1	s__Leifsonia_A sp001422325	78.9952	360	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	96.12	96.12	0.77	0.77	2	-
GCF_002797855.1	s__Compostimonas suwonensis	78.94	396	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Compostimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	78.8579	407	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640535.1	s__Cnuibacter physcomitrellae	78.6881	363	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cnuibacter	95.0	98.64	97.29	0.95	0.90	3	-
GCF_003751785.1	s__Frigoribacterium sp003751785	78.6757	408	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	78.6429	384	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	78.5991	392	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402485.1	s__Cryobacterium sp004402485	78.5744	338	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002404115.1	s__Cryobacterium sp002404115	78.3509	218	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:06,223] [INFO] GTDB search result was written to GCF_008642235.1_ASM864223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:06,224] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:06,229] [INFO] DFAST_QC result json was written to GCF_008642235.1_ASM864223v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:06,229] [INFO] DFAST_QC completed!
[2024-01-24 14:14:06,229] [INFO] Total running time: 0h1m19s