[2024-01-24 12:37:09,471] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,484] [INFO] DQC Reference Directory: /var/lib/cwl/stg79890819-888f-4a99-a099-b37bbadf822b/dqc_reference
[2024-01-24 12:37:10,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:10,873] [INFO] Task started: Prodigal
[2024-01-24 12:37:10,873] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb81c7e4-4910-41e3-b457-06580c59c24c/GCF_006716695.1_ASM671669v1_genomic.fna.gz | prodigal -d GCF_006716695.1_ASM671669v1_genomic.fna/cds.fna -a GCF_006716695.1_ASM671669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:21,000] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:21,001] [INFO] Task started: HMMsearch
[2024-01-24 12:37:21,001] [INFO] Running command: hmmsearch --tblout GCF_006716695.1_ASM671669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79890819-888f-4a99-a099-b37bbadf822b/dqc_reference/reference_markers.hmm GCF_006716695.1_ASM671669v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:21,242] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:21,244] [INFO] Found 6/6 markers.
[2024-01-24 12:37:21,271] [INFO] Query marker FASTA was written to GCF_006716695.1_ASM671669v1_genomic.fna/markers.fasta
[2024-01-24 12:37:21,271] [INFO] Task started: Blastn
[2024-01-24 12:37:21,271] [INFO] Running command: blastn -query GCF_006716695.1_ASM671669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79890819-888f-4a99-a099-b37bbadf822b/dqc_reference/reference_markers.fasta -out GCF_006716695.1_ASM671669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:21,985] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:21,992] [INFO] Selected 31 target genomes.
[2024-01-24 12:37:21,993] [INFO] Target genome list was writen to GCF_006716695.1_ASM671669v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:22,008] [INFO] Task started: fastANI
[2024-01-24 12:37:22,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb81c7e4-4910-41e3-b457-06580c59c24c/GCF_006716695.1_ASM671669v1_genomic.fna.gz --refList GCF_006716695.1_ASM671669v1_genomic.fna/target_genomes.txt --output GCF_006716695.1_ASM671669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:41,029] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:41,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79890819-888f-4a99-a099-b37bbadf822b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:41,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79890819-888f-4a99-a099-b37bbadf822b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:41,051] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:41,051] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:41,051] [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
Klugiella xanthotipulae	strain=DSM 18031	GCA_006716695.1	244735	244735	type	True	100.0	987	993	95	conclusive
Lysinibacter cavernae	strain=DSM 27960	GCA_011758565.1	1640652	1640652	type	True	78.1878	198	993	95	below_threshold
Cryobacterium roopkundense	strain=DSM 21065	GCA_014200405.1	1001240	1001240	type	True	77.6942	87	993	95	below_threshold
Leucobacter komagatae	strain=DSM 8803	GCA_006716085.1	55969	55969	type	True	77.5194	87	993	95	below_threshold
Mycetocola saprophilus	strain=NRRL B-24119	GCA_000718085.1	76636	76636	type	True	77.4875	110	993	95	below_threshold
Mycetocola spongiae	strain=MSC19	GCA_020424085.1	2859226	2859226	type	True	77.449	110	993	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	77.4024	96	993	95	below_threshold
Salinibacterium amurskyense	strain=KCTC 9931	GCA_014652955.1	205941	205941	type	True	77.386	73	993	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	77.3814	91	993	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	77.3791	118	993	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	77.3597	106	993	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	77.3213	113	993	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.2896	77	993	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	77.287	107	993	95	below_threshold
Salinibacterium amurskyense	strain=JCM 12362	GCA_003668745.1	205941	205941	type	True	77.1366	74	993	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	77.0839	123	993	95	below_threshold
Cryobacterium roopkundense	strain=RuG17	GCA_000764165.1	1001240	1001240	type	True	77.0543	84	993	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.0193	55	993	95	below_threshold
Salinibacterium amurskyense	strain=DSM 16400	GCA_002797685.1	205941	205941	type	True	76.9043	71	993	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	76.9024	93	993	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	76.8114	114	993	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	76.6639	94	993	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	76.5461	98	993	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	76.5382	95	993	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:41,053] [INFO] DFAST Taxonomy check result was written to GCF_006716695.1_ASM671669v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:41,053] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:41,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:41,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79890819-888f-4a99-a099-b37bbadf822b/dqc_reference/checkm_data
[2024-01-24 12:37:41,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:41,088] [INFO] Task started: CheckM
[2024-01-24 12:37:41,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716695.1_ASM671669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716695.1_ASM671669v1_genomic.fna/checkm_input GCF_006716695.1_ASM671669v1_genomic.fna/checkm_result
[2024-01-24 12:38:14,369] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:14,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:14,396] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:14,396] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:14,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716695.1_ASM671669v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:14,397] [INFO] Task started: Blastn
[2024-01-24 12:38:14,397] [INFO] Running command: blastn -query GCF_006716695.1_ASM671669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79890819-888f-4a99-a099-b37bbadf822b/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716695.1_ASM671669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:15,480] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:15,485] [INFO] Selected 31 target genomes.
[2024-01-24 12:38:15,485] [INFO] Target genome list was writen to GCF_006716695.1_ASM671669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:15,514] [INFO] Task started: fastANI
[2024-01-24 12:38:15,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb81c7e4-4910-41e3-b457-06580c59c24c/GCF_006716695.1_ASM671669v1_genomic.fna.gz --refList GCF_006716695.1_ASM671669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716695.1_ASM671669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:31,553] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:31,583] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:31,584] [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_006716695.1	s__Klugiella xanthotipulae	100.0	988	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Klugiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011758565.1	s__Lysinibacter cavernae	78.1902	199	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lysinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015864955.1	s__Rhodoglobus sp015864955	77.7519	58	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718085.1	s__Mycetocola saprophilus	77.4875	110	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	98.52	97.04	0.95	0.91	3	-
GCF_013409865.1	s__Herbiconiux flava	77.4805	114	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	95.35	95.35	0.90	0.90	2	-
GCF_015752155.1	s__Cryobacterium sp015752155	77.3892	118	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610585.1	s__Microterricola sp003610585	77.3508	114	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	77.329	91	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716085.1	s__Leucobacter komagatae	77.3003	87	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277815.1	s__Microbacterium sp015277815	77.2896	77	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190775.1	s__Leifsonia aquatica	77.287	107	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCA_013823625.1	s__Chryseoglobus sp013823625	77.2019	65	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003667575.1	s__Mycetocola lacteus	77.1757	111	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167575.1	s__Okibacterium fritillariae	77.1367	111	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	77.1263	93	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012317045.1	s__Leifsonia sp002105485	77.1034	114	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.03	98.03	0.91	0.91	2	-
GCF_002797685.1	s__Rhodoglobus amurskyensis	76.9043	71	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004402595.1	s__Cryobacterium sp004402595	76.8735	128	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
GCF_001571005.1	s__Herbiconiux solani	76.8114	114	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	76.7851	95	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016771945.1	s__Leucobacter sulfamidivorax	76.7281	104	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929555.1	s__Cryobacterium sp002929555	76.6681	122	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403945.1	s__Cryobacterium sp004403945	76.6449	133	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297935.1	s__SCRE01 sp004297935	76.5612	77	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__SCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565705.1	s__Leucobacter ruminantium	76.5461	98	993	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:31,586] [INFO] GTDB search result was written to GCF_006716695.1_ASM671669v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:31,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:31,591] [INFO] DFAST_QC result json was written to GCF_006716695.1_ASM671669v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:31,591] [INFO] DFAST_QC completed!
[2024-01-24 12:38:31,591] [INFO] Total running time: 0h1m22s