[2024-01-24 13:48:42,819] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:42,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:42,821] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6ccfbfb-3c10-47ee-b5f1-e68fd878ef40/dqc_reference
[2024-01-24 13:48:44,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,096] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cf34328-b827-4db9-9cb9-d061bb27c6d3/GCF_003752405.1_ASM375240v1_genomic.fna.gz | prodigal -d GCF_003752405.1_ASM375240v1_genomic.fna/cds.fna -a GCF_003752405.1_ASM375240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:54,158] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:54,159] [INFO] Task started: HMMsearch
[2024-01-24 13:48:54,159] [INFO] Running command: hmmsearch --tblout GCF_003752405.1_ASM375240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6ccfbfb-3c10-47ee-b5f1-e68fd878ef40/dqc_reference/reference_markers.hmm GCF_003752405.1_ASM375240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:54,434] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:54,436] [INFO] Found 6/6 markers.
[2024-01-24 13:48:54,469] [INFO] Query marker FASTA was written to GCF_003752405.1_ASM375240v1_genomic.fna/markers.fasta
[2024-01-24 13:48:54,470] [INFO] Task started: Blastn
[2024-01-24 13:48:54,470] [INFO] Running command: blastn -query GCF_003752405.1_ASM375240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6ccfbfb-3c10-47ee-b5f1-e68fd878ef40/dqc_reference/reference_markers.fasta -out GCF_003752405.1_ASM375240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:55,522] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:55,526] [INFO] Selected 19 target genomes.
[2024-01-24 13:48:55,526] [INFO] Target genome list was writen to GCF_003752405.1_ASM375240v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:55,541] [INFO] Task started: fastANI
[2024-01-24 13:48:55,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cf34328-b827-4db9-9cb9-d061bb27c6d3/GCF_003752405.1_ASM375240v1_genomic.fna.gz --refList GCF_003752405.1_ASM375240v1_genomic.fna/target_genomes.txt --output GCF_003752405.1_ASM375240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:08,316] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:08,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6ccfbfb-3c10-47ee-b5f1-e68fd878ef40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:08,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6ccfbfb-3c10-47ee-b5f1-e68fd878ef40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:08,335] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:08,335] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:08,335] [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
Bogoriella caseilytica	strain=DSM 11294	GCA_003752405.1	56055	56055	type	True	100.0	1077	1078	95	conclusive
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	78.5469	304	1078	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	78.5079	335	1078	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	78.4445	325	1078	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	78.4057	342	1078	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	78.4011	339	1078	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	78.3896	360	1078	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	78.3596	324	1078	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	78.3524	347	1078	95	below_threshold
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	78.1603	271	1078	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	78.0782	286	1078	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	77.923	262	1078	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.8509	309	1078	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	77.4488	238	1078	95	below_threshold
Actinomyces respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	77.4088	169	1078	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	77.4085	253	1078	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	77.3735	247	1078	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	76.3429	172	1078	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	76.1539	170	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:08,337] [INFO] DFAST Taxonomy check result was written to GCF_003752405.1_ASM375240v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:08,337] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:08,337] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:08,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6ccfbfb-3c10-47ee-b5f1-e68fd878ef40/dqc_reference/checkm_data
[2024-01-24 13:49:08,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:08,374] [INFO] Task started: CheckM
[2024-01-24 13:49:08,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003752405.1_ASM375240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003752405.1_ASM375240v1_genomic.fna/checkm_input GCF_003752405.1_ASM375240v1_genomic.fna/checkm_result
[2024-01-24 13:49:45,813] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:45,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:45,851] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:45,851] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:45,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003752405.1_ASM375240v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:45,852] [INFO] Task started: Blastn
[2024-01-24 13:49:45,853] [INFO] Running command: blastn -query GCF_003752405.1_ASM375240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6ccfbfb-3c10-47ee-b5f1-e68fd878ef40/dqc_reference/reference_markers_gtdb.fasta -out GCF_003752405.1_ASM375240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:47,539] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:47,543] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:47,543] [INFO] Target genome list was writen to GCF_003752405.1_ASM375240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:47,554] [INFO] Task started: fastANI
[2024-01-24 13:49:47,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cf34328-b827-4db9-9cb9-d061bb27c6d3/GCF_003752405.1_ASM375240v1_genomic.fna.gz --refList GCF_003752405.1_ASM375240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003752405.1_ASM375240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:00,414] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,427] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:00,427] [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_003752405.1	s__Bogoriella caseilytica	100.0	1077	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Bogoriella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002563695.1	s__Georgenia soli	78.5639	335	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006352065.1	s__Georgenia sp006352065	78.5386	303	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	-
GCF_009193185.1	s__Georgenia thermotolerans	78.4223	357	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009193155.1	s__Georgenia subflava	78.4214	340	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003814705.1	s__Georgenia muralis	78.384	322	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193175.1	s__Georgenia ruanii	78.3753	345	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991205.1	s__Georgenia sp003991205	78.1568	306	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006349365.1	s__Oceanitalea sp006349365	78.1308	285	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	99.20	99.20	0.95	0.95	2	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	78.0181	307	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009193135.1	s__Oceanitalea satyanarayanai	77.8624	292	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014837105.1	s__Oceanitalea sp014837105	77.8299	311	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	77.4206	224	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_004353825.1	s__Occultella glacieicola	77.3734	247	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752595.1	s__Sediminihabitans sp003752595	77.3136	200	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716785.1	s__Thermopolyspora flexuosa	76.2487	173	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,429] [INFO] GTDB search result was written to GCF_003752405.1_ASM375240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:00,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:00,434] [INFO] DFAST_QC result json was written to GCF_003752405.1_ASM375240v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:00,434] [INFO] DFAST_QC completed!
[2024-01-24 13:50:00,434] [INFO] Total running time: 0h1m18s