[2024-01-24 11:27:04,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fca7f20-82e1-4d10-8938-0f18a410e637/dqc_reference
[2024-01-24 11:27:05,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,755] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg007065c2-da9b-40d5-b224-61a801d6cc98/GCF_016863455.1_ASM1686345v1_genomic.fna.gz | prodigal -d GCF_016863455.1_ASM1686345v1_genomic.fna/cds.fna -a GCF_016863455.1_ASM1686345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:14,907] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:14,908] [INFO] Task started: HMMsearch
[2024-01-24 11:27:14,908] [INFO] Running command: hmmsearch --tblout GCF_016863455.1_ASM1686345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fca7f20-82e1-4d10-8938-0f18a410e637/dqc_reference/reference_markers.hmm GCF_016863455.1_ASM1686345v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:15,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:15,159] [INFO] Found 6/6 markers.
[2024-01-24 11:27:15,192] [INFO] Query marker FASTA was written to GCF_016863455.1_ASM1686345v1_genomic.fna/markers.fasta
[2024-01-24 11:27:15,192] [INFO] Task started: Blastn
[2024-01-24 11:27:15,192] [INFO] Running command: blastn -query GCF_016863455.1_ASM1686345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fca7f20-82e1-4d10-8938-0f18a410e637/dqc_reference/reference_markers.fasta -out GCF_016863455.1_ASM1686345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:16,535] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:16,539] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:16,539] [INFO] Target genome list was writen to GCF_016863455.1_ASM1686345v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:16,557] [INFO] Task started: fastANI
[2024-01-24 11:27:16,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg007065c2-da9b-40d5-b224-61a801d6cc98/GCF_016863455.1_ASM1686345v1_genomic.fna.gz --refList GCF_016863455.1_ASM1686345v1_genomic.fna/target_genomes.txt --output GCF_016863455.1_ASM1686345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:31,859] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:31,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fca7f20-82e1-4d10-8938-0f18a410e637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:31,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fca7f20-82e1-4d10-8938-0f18a410e637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:31,877] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:31,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:31,877] [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
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	100.0	1122	1125	95	conclusive
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	99.9995	1125	1125	95	conclusive
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	81.3324	680	1125	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	81.3067	680	1125	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	81.2417	687	1125	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	81.2211	716	1125	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	81.1995	682	1125	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	81.178	695	1125	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	81.1412	704	1125	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	81.1206	681	1125	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	80.6653	659	1125	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.0841	590	1125	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	79.9208	613	1125	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	79.9022	609	1125	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	79.853	641	1125	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.4075	607	1125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:31,879] [INFO] DFAST Taxonomy check result was written to GCF_016863455.1_ASM1686345v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:31,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:31,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:31,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fca7f20-82e1-4d10-8938-0f18a410e637/dqc_reference/checkm_data
[2024-01-24 11:27:31,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:31,919] [INFO] Task started: CheckM
[2024-01-24 11:27:31,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863455.1_ASM1686345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863455.1_ASM1686345v1_genomic.fna/checkm_input GCF_016863455.1_ASM1686345v1_genomic.fna/checkm_result
[2024-01-24 11:28:20,199] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:20,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:20,220] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:20,221] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:20,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863455.1_ASM1686345v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:20,222] [INFO] Task started: Blastn
[2024-01-24 11:28:20,222] [INFO] Running command: blastn -query GCF_016863455.1_ASM1686345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fca7f20-82e1-4d10-8938-0f18a410e637/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863455.1_ASM1686345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:22,356] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:22,359] [INFO] Selected 23 target genomes.
[2024-01-24 11:28:22,359] [INFO] Target genome list was writen to GCF_016863455.1_ASM1686345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:22,401] [INFO] Task started: fastANI
[2024-01-24 11:28:22,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg007065c2-da9b-40d5-b224-61a801d6cc98/GCF_016863455.1_ASM1686345v1_genomic.fna.gz --refList GCF_016863455.1_ASM1686345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863455.1_ASM1686345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:44,309] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:44,332] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:44,333] [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_002797595.1	s__Sediminihabitans luteus	99.9995	1125	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003752595.1	s__Sediminihabitans sp003752595	82.075	686	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	81.5865	696	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	81.5119	609	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005937995.2	s__Oerskovia sp005937995	81.2984	693	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	96.13	96.13	0.91	0.91	2	-
GCF_016907235.1	s__Oerskovia jenensis	81.2883	701	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718325.1	s__Oerskovia turbata	81.2848	682	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.78	99.34	0.96	0.90	4	-
GCF_004519295.1	s__Cellulosimicrobium funkei	81.274	709	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	81.1949	739	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_015142735.1	s__Oerskovia sp015142735	81.182	695	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	81.1432	669	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	81.1356	731	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836755.1	s__Oerskovia sp014836755	81.1186	691	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	81.1132	725	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	81.1035	757	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001692445.1	s__Oerskovia enterophila	81.1014	683	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	81.0418	750	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_000701465.1	s__Paraoerskovia marina	80.7269	607	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Paraoerskovia	95.0	98.25	98.25	0.95	0.95	2	-
GCF_000212695.1	s__Cellulomonas fimi	79.968	608	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_004306155.1	s__Cellulomonas biazotea	79.8426	553	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635665.1	s__Isoptericola cucumis	79.7194	626	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167525.1	s__Isoptericola flava	79.6932	649	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003755175.1	s__Cellulomonas sp003755175	79.6531	576	1125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:44,334] [INFO] GTDB search result was written to GCF_016863455.1_ASM1686345v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:44,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:44,339] [INFO] DFAST_QC result json was written to GCF_016863455.1_ASM1686345v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:44,339] [INFO] DFAST_QC completed!
[2024-01-24 11:28:44,339] [INFO] Total running time: 0h1m40s