[2024-01-24 13:17:46,370] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:46,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:46,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg38ce3d09-c276-44af-9412-da5e0063fc67/dqc_reference
[2024-01-24 13:17:47,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:47,650] [INFO] Task started: Prodigal
[2024-01-24 13:17:47,651] [INFO] Running command: gunzip -c /var/lib/cwl/stgad5b3246-8622-42c6-8190-9c81b7a0e8cb/GCF_022568835.1_ASM2256883v1_genomic.fna.gz | prodigal -d GCF_022568835.1_ASM2256883v1_genomic.fna/cds.fna -a GCF_022568835.1_ASM2256883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:58,376] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:58,377] [INFO] Task started: HMMsearch
[2024-01-24 13:17:58,377] [INFO] Running command: hmmsearch --tblout GCF_022568835.1_ASM2256883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38ce3d09-c276-44af-9412-da5e0063fc67/dqc_reference/reference_markers.hmm GCF_022568835.1_ASM2256883v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:58,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:58,761] [INFO] Found 6/6 markers.
[2024-01-24 13:17:58,798] [INFO] Query marker FASTA was written to GCF_022568835.1_ASM2256883v1_genomic.fna/markers.fasta
[2024-01-24 13:17:58,799] [INFO] Task started: Blastn
[2024-01-24 13:17:58,799] [INFO] Running command: blastn -query GCF_022568835.1_ASM2256883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38ce3d09-c276-44af-9412-da5e0063fc67/dqc_reference/reference_markers.fasta -out GCF_022568835.1_ASM2256883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:00,311] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:00,314] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:00,315] [INFO] Target genome list was writen to GCF_022568835.1_ASM2256883v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:00,325] [INFO] Task started: fastANI
[2024-01-24 13:18:00,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgad5b3246-8622-42c6-8190-9c81b7a0e8cb/GCF_022568835.1_ASM2256883v1_genomic.fna.gz --refList GCF_022568835.1_ASM2256883v1_genomic.fna/target_genomes.txt --output GCF_022568835.1_ASM2256883v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:15,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:15,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38ce3d09-c276-44af-9412-da5e0063fc67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:15,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38ce3d09-c276-44af-9412-da5e0063fc67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:15,332] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:15,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:15,333] [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
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	100.0	1193	1195	95	conclusive
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	80.5294	592	1195	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	80.4732	623	1195	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	80.2048	538	1195	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.1912	492	1195	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.0645	443	1195	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	78.9999	391	1195	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.7256	441	1195	95	below_threshold
Flexivirga endophytica	strain=KCTC 39536	GCA_014652735.1	1849103	1849103	type	True	78.1681	331	1195	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	78.147	377	1195	95	below_threshold
Flexivirga endophytica	strain=CGMCC 1.15085	GCA_014640635.1	1849103	1849103	type	True	78.1322	339	1195	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	77.6236	328	1195	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.5487	248	1195	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	77.1329	336	1195	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	77.1141	362	1195	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	77.0973	336	1195	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	76.8296	388	1195	95	below_threshold
Actinomadura flavalba	strain=DSM 45200	GCA_000374305.1	1120938	1120938	type	True	76.6476	340	1195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:15,334] [INFO] DFAST Taxonomy check result was written to GCF_022568835.1_ASM2256883v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:15,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:15,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:15,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38ce3d09-c276-44af-9412-da5e0063fc67/dqc_reference/checkm_data
[2024-01-24 13:18:15,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:15,390] [INFO] Task started: CheckM
[2024-01-24 13:18:15,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022568835.1_ASM2256883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022568835.1_ASM2256883v1_genomic.fna/checkm_input GCF_022568835.1_ASM2256883v1_genomic.fna/checkm_result
[2024-01-24 13:18:52,035] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:52,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:52,057] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:52,057] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:52,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022568835.1_ASM2256883v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:52,058] [INFO] Task started: Blastn
[2024-01-24 13:18:52,058] [INFO] Running command: blastn -query GCF_022568835.1_ASM2256883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38ce3d09-c276-44af-9412-da5e0063fc67/dqc_reference/reference_markers_gtdb.fasta -out GCF_022568835.1_ASM2256883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:54,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:54,397] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:54,398] [INFO] Target genome list was writen to GCF_022568835.1_ASM2256883v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:54,689] [INFO] Task started: fastANI
[2024-01-24 13:18:54,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgad5b3246-8622-42c6-8190-9c81b7a0e8cb/GCF_022568835.1_ASM2256883v1_genomic.fna.gz --refList GCF_022568835.1_ASM2256883v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022568835.1_ASM2256883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:09,536] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:09,551] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:19:09,552] [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_001189535.1	s__Arsenicicoccus sp001189535	80.7227	622	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707125.1	s__Arsenicicoccus sp009707125	80.5232	592	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426385.1	s__Arsenicicoccus bolidensis	80.4339	627	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	98.16	98.06	0.89	0.88	4	-
GCF_006716205.1	s__Oryzihumus leptocrescens	79.7301	473	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	79.2453	489	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_001428025.1	s__Pedococcus sp001428025	79.1361	444	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591405.1	s__Janibacter terrae	78.9867	415	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	98.98	98.88	0.95	0.93	4	-
GCF_016888335.1	s__Marihabitans sp016888335	78.9787	392	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428505.1	s__Terrabacter sp001428505	78.8456	485	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.23	99.23	0.97	0.97	2	-
GCF_001426245.1	s__Pedococcus sp001426245	78.8126	461	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.80	98.80	0.95	0.95	2	-
GCF_006715055.1	s__Lapillicoccus jejuensis	78.8056	504	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763705.1	s__Phycicoccus sp014763705	78.702	353	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361975.1	s__Terrabacter sp013361975	78.3232	311	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	98.22	98.02	0.74	0.70	4	-
GCF_001046855.1	s__Tetrasphaera japonica	78.2355	426	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Tetrasphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640635.1	s__Flexivirga endophytica	78.1422	338	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003194625.1	s__Nocardioides solisilvae	77.6446	326	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552375.1	s__Cellulomonas iranensis	77.051	342	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_006386485.1	s__Cellulomonas oligotrophica	77.0426	349	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:09,554] [INFO] GTDB search result was written to GCF_022568835.1_ASM2256883v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:09,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:09,561] [INFO] DFAST_QC result json was written to GCF_022568835.1_ASM2256883v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:09,562] [INFO] DFAST_QC completed!
[2024-01-24 13:19:09,562] [INFO] Total running time: 0h1m23s