[2024-01-24 14:28:15,723] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg27a16079-0546-4bd3-bcc0-ebc134f7e489/dqc_reference
[2024-01-24 14:28:17,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,938] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,938] [INFO] Running command: gunzip -c /var/lib/cwl/stge6f4aba1-58d6-4b4a-988d-43031cb4a7df/GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna.gz | prodigal -d GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/cds.fna -a GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:34,524] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:34,524] [INFO] Task started: HMMsearch
[2024-01-24 14:28:34,524] [INFO] Running command: hmmsearch --tblout GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27a16079-0546-4bd3-bcc0-ebc134f7e489/dqc_reference/reference_markers.hmm GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:34,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:34,813] [INFO] Found 6/6 markers.
[2024-01-24 14:28:34,859] [INFO] Query marker FASTA was written to GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta
[2024-01-24 14:28:34,859] [INFO] Task started: Blastn
[2024-01-24 14:28:34,859] [INFO] Running command: blastn -query GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta -db /var/lib/cwl/stg27a16079-0546-4bd3-bcc0-ebc134f7e489/dqc_reference/reference_markers.fasta -out GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:35,938] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:35,942] [INFO] Selected 17 target genomes.
[2024-01-24 14:28:35,942] [INFO] Target genome list was writen to GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/target_genomes.txt
[2024-01-24 14:28:35,952] [INFO] Task started: fastANI
[2024-01-24 14:28:35,952] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f4aba1-58d6-4b4a-988d-43031cb4a7df/GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna.gz --refList GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/target_genomes.txt --output GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:56,968] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:56,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27a16079-0546-4bd3-bcc0-ebc134f7e489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:56,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27a16079-0546-4bd3-bcc0-ebc134f7e489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:56,982] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:56,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:56,982] [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
Nocardiopsis alkaliphila	strain=YIM 80379	GCA_000341005.1	225762	225762	type	True	100.0	1624	1633	95	conclusive
Nocardiopsis listeri	strain=NBRC 13360	GCA_001570765.1	53440	53440	type	True	85.0528	1210	1633	95	below_threshold
Nocardiopsis alba	strain=DSM 43377	GCA_000341225.1	53437	53437	type	True	84.1389	1109	1633	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	83.835	1191	1633	95	below_threshold
Nocardiopsis terrae	strain=KCTC 19431	GCA_014651695.1	372655	372655	type	True	83.7488	1168	1633	95	below_threshold
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	83.7363	1208	1633	95	below_threshold
Nocardiopsis terrae	strain=DSM 45157	GCA_014874035.1	372655	372655	type	True	83.708	1171	1633	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	83.6646	1203	1633	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	83.2771	1078	1633	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	82.1183	1023	1633	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	81.6944	786	1633	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	81.6151	987	1633	95	below_threshold
Nocardiopsis xinjiangensis	strain=YIM 90004	GCA_000341145.1	124285	124285	type	True	81.068	849	1633	95	below_threshold
Nocardiopsis salina	strain=YIM 90010	GCA_000341025.1	245836	245836	type	True	81.0144	806	1633	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	80.8853	831	1633	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.1614	533	1633	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	78.7026	523	1633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:56,984] [INFO] DFAST Taxonomy check result was written to GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/tc_result.tsv
[2024-01-24 14:28:56,984] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:56,984] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:56,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27a16079-0546-4bd3-bcc0-ebc134f7e489/dqc_reference/checkm_data
[2024-01-24 14:28:56,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:57,033] [INFO] Task started: CheckM
[2024-01-24 14:28:57,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/checkm_input GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/checkm_result
[2024-01-24 14:29:47,044] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:47,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:47,067] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:47,067] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:47,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta)
[2024-01-24 14:29:47,067] [INFO] Task started: Blastn
[2024-01-24 14:29:47,068] [INFO] Running command: blastn -query GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta -db /var/lib/cwl/stg27a16079-0546-4bd3-bcc0-ebc134f7e489/dqc_reference/reference_markers_gtdb.fasta -out GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:48,710] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:48,713] [INFO] Selected 12 target genomes.
[2024-01-24 14:29:48,713] [INFO] Target genome list was writen to GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:48,724] [INFO] Task started: fastANI
[2024-01-24 14:29:48,725] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f4aba1-58d6-4b4a-988d-43031cb4a7df/GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna.gz --refList GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/target_genomes_gtdb.txt --output GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:03,919] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:03,931] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:03,931] [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_000341005.1	s__Nocardiopsis alkaliphila	100.0	1624	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900143625.1	s__Nocardiopsis sp900143625	85.2047	1274	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570765.1	s__Nocardiopsis listeri	85.0661	1208	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018207095.1	s__Nocardiopsis sp018207095	84.7198	1133	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341225.1	s__Nocardiopsis alba	84.1308	1110	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	98.86	98.56	0.95	0.95	4	-
GCF_000341085.1	s__Nocardiopsis ganjiahuensis	83.7483	1206	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651695.1	s__Nocardiopsis terrae	83.7394	1169	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014201115.1	s__Nocardiopsis metallicus	83.6622	1203	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341125.1	s__Nocardiopsis lucentensis	81.7131	785	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515115.1	s__Nocardiopsis sp000515115	81.1722	762	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341145.1	s__Nocardiopsis xinjiangensis	81.045	852	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115445.1	s__Nocardiopsis merdipullorum	80.3956	642	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:03,937] [INFO] GTDB search result was written to GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:03,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:03,943] [INFO] DFAST_QC result json was written to GCF_000341005.1_SOAPdenovo_v1.06_genomic.fna/dqc_result.json
[2024-01-24 14:30:03,943] [INFO] DFAST_QC completed!
[2024-01-24 14:30:03,943] [INFO] Total running time: 0h1m48s