[2023-06-30 17:45:37,823] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:45:37,828] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:45:37,828] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa5e2d53-fd2b-40f7-ad95-e3c0a486f074/dqc_reference
[2023-06-30 17:45:39,371] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:45:39,372] [INFO] Task started: Prodigal
[2023-06-30 17:45:39,372] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9c220a4-92cc-4d03-b092-58d401e13ad7/GCA_019115445.1_ASM1911544v1_genomic.fna.gz | prodigal -d GCA_019115445.1_ASM1911544v1_genomic.fna/cds.fna -a GCA_019115445.1_ASM1911544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:45:49,803] [INFO] Task succeeded: Prodigal
[2023-06-30 17:45:49,803] [INFO] Task started: HMMsearch
[2023-06-30 17:45:49,803] [INFO] Running command: hmmsearch --tblout GCA_019115445.1_ASM1911544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa5e2d53-fd2b-40f7-ad95-e3c0a486f074/dqc_reference/reference_markers.hmm GCA_019115445.1_ASM1911544v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:45:50,029] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:45:50,030] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf9c220a4-92cc-4d03-b092-58d401e13ad7/GCA_019115445.1_ASM1911544v1_genomic.fna.gz]
[2023-06-30 17:45:50,063] [INFO] Query marker FASTA was written to GCA_019115445.1_ASM1911544v1_genomic.fna/markers.fasta
[2023-06-30 17:45:50,063] [INFO] Task started: Blastn
[2023-06-30 17:45:50,063] [INFO] Running command: blastn -query GCA_019115445.1_ASM1911544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5e2d53-fd2b-40f7-ad95-e3c0a486f074/dqc_reference/reference_markers.fasta -out GCA_019115445.1_ASM1911544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:45:50,914] [INFO] Task succeeded: Blastn
[2023-06-30 17:45:50,917] [INFO] Selected 22 target genomes.
[2023-06-30 17:45:50,918] [INFO] Target genome list was writen to GCA_019115445.1_ASM1911544v1_genomic.fna/target_genomes.txt
[2023-06-30 17:45:50,940] [INFO] Task started: fastANI
[2023-06-30 17:45:50,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9c220a4-92cc-4d03-b092-58d401e13ad7/GCA_019115445.1_ASM1911544v1_genomic.fna.gz --refList GCA_019115445.1_ASM1911544v1_genomic.fna/target_genomes.txt --output GCA_019115445.1_ASM1911544v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:46:13,700] [INFO] Task succeeded: fastANI
[2023-06-30 17:46:13,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa5e2d53-fd2b-40f7-ad95-e3c0a486f074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:46:13,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa5e2d53-fd2b-40f7-ad95-e3c0a486f074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:46:13,713] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:46:13,713] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 17:46:13,714] [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 dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	80.8847	700	1127	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	80.8692	671	1127	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	80.8637	699	1127	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	80.8545	737	1127	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	80.8401	672	1127	95	below_threshold
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	80.8327	684	1127	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	80.8283	718	1127	95	below_threshold
Nocardiopsis xinjiangensis	strain=YIM 90004	GCA_000341145.1	124285	124285	type	True	80.8173	683	1127	95	below_threshold
Nocardiopsis coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	80.8059	700	1127	95	below_threshold
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	80.8011	725	1127	95	below_threshold
Nocardiopsis terrae	strain=KCTC 19431	GCA_014651695.1	372655	372655	type	True	80.7983	687	1127	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	80.792	691	1127	95	below_threshold
Nocardiopsis terrae	strain=DSM 45157	GCA_014874035.1	372655	372655	type	True	80.7835	683	1127	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	80.7259	715	1127	95	below_threshold
Nocardiopsis listeri	strain=NBRC 13360	GCA_001570765.1	53440	53440	type	True	80.6604	684	1127	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	80.6156	633	1127	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	80.5186	535	1127	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	80.4092	678	1127	95	below_threshold
Nocardiopsis alkaliphila	strain=YIM 80379	GCA_000341005.1	225762	225762	type	True	80.3127	653	1127	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	78.4804	401	1127	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	78.3926	342	1127	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	78.1935	337	1127	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 17:46:13,715] [INFO] DFAST Taxonomy check result was written to GCA_019115445.1_ASM1911544v1_genomic.fna/tc_result.tsv
[2023-06-30 17:46:13,716] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:46:13,716] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:46:13,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa5e2d53-fd2b-40f7-ad95-e3c0a486f074/dqc_reference/checkm_data
[2023-06-30 17:46:13,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:46:13,757] [INFO] Task started: CheckM
[2023-06-30 17:46:13,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019115445.1_ASM1911544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019115445.1_ASM1911544v1_genomic.fna/checkm_input GCA_019115445.1_ASM1911544v1_genomic.fna/checkm_result
[2023-06-30 17:47:08,550] [INFO] Task succeeded: CheckM
[2023-06-30 17:47:08,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:47:08,567] [INFO] ===== Completeness check finished =====
[2023-06-30 17:47:08,567] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:47:08,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019115445.1_ASM1911544v1_genomic.fna/markers.fasta)
[2023-06-30 17:47:08,567] [INFO] Task started: Blastn
[2023-06-30 17:47:08,567] [INFO] Running command: blastn -query GCA_019115445.1_ASM1911544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5e2d53-fd2b-40f7-ad95-e3c0a486f074/dqc_reference/reference_markers_gtdb.fasta -out GCA_019115445.1_ASM1911544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:47:09,805] [INFO] Task succeeded: Blastn
[2023-06-30 17:47:09,808] [INFO] Selected 20 target genomes.
[2023-06-30 17:47:09,808] [INFO] Target genome list was writen to GCA_019115445.1_ASM1911544v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:47:09,819] [INFO] Task started: fastANI
[2023-06-30 17:47:09,819] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9c220a4-92cc-4d03-b092-58d401e13ad7/GCA_019115445.1_ASM1911544v1_genomic.fna.gz --refList GCA_019115445.1_ASM1911544v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019115445.1_ASM1911544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:47:30,113] [INFO] Task succeeded: fastANI
[2023-06-30 17:47:30,125] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:47:30,125] [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
GCA_019115445.1	s__Nocardiopsis merdipullorum	100.0	1106	1127	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_001905145.1	s__Nocardiopsis sp001905145	81.0219	696	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340965.1	s__Nocardiopsis kunsanensis	80.873	671	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.42	99.42	0.93	0.93	2	-
GCF_000092985.1	s__Nocardiopsis dassonvillei	80.8427	702	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
GCF_000341145.1	s__Nocardiopsis xinjiangensis	80.8359	681	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341065.1	s__Nocardiopsis halotolerans	80.8342	672	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014892575.1	s__Nocardiopsis coralli	80.8141	699	1127	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	80.7983	687	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000341085.1	s__Nocardiopsis ganjiahuensis	80.7892	726	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830945.1	s__Nocardiopsis sp009830945	80.7267	691	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_012396365.1	s__Nocardiopsis alborubida	80.7086	717	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCF_003386285.1	s__Nocardiopsis sp003386285	80.6977	627	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341265.1	s__Nocardiopsis prasina	80.606	634	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.74	95.74	0.91	0.87	4	-
GCF_000341125.1	s__Nocardiopsis lucentensis	80.5412	533	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018388625.1	s__Nocardiopsis sp018388625	80.5014	659	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279585.1	s__Nocardiopsis sp001279585	80.474	666	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410755.1	s__Nocardiopsis aegyptia	80.4443	674	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018316655.1	s__Nocardiopsis sp018316655	80.3546	664	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341005.1	s__Nocardiopsis alkaliphila	80.3023	655	1127	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	80.1563	539	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 17:47:30,127] [INFO] GTDB search result was written to GCA_019115445.1_ASM1911544v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:47:30,127] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:47:30,131] [INFO] DFAST_QC result json was written to GCA_019115445.1_ASM1911544v1_genomic.fna/dqc_result.json
[2023-06-30 17:47:30,131] [INFO] DFAST_QC completed!
[2023-06-30 17:47:30,131] [INFO] Total running time: 0h1m52s