[2024-01-25 20:22:21,230] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:21,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:21,232] [INFO] DQC Reference Directory: /var/lib/cwl/stg824c7977-6bd4-44ed-81fd-4708833c717a/dqc_reference
[2024-01-25 20:22:22,392] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:22,392] [INFO] Task started: Prodigal
[2024-01-25 20:22:22,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b53d68c-8f6f-45b2-b66f-c82e2e3cc379/GCF_014200805.1_ASM1420080v1_genomic.fna.gz | prodigal -d GCF_014200805.1_ASM1420080v1_genomic.fna/cds.fna -a GCF_014200805.1_ASM1420080v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:39,556] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:39,556] [INFO] Task started: HMMsearch
[2024-01-25 20:22:39,557] [INFO] Running command: hmmsearch --tblout GCF_014200805.1_ASM1420080v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg824c7977-6bd4-44ed-81fd-4708833c717a/dqc_reference/reference_markers.hmm GCF_014200805.1_ASM1420080v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:39,844] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:39,845] [INFO] Found 6/6 markers.
[2024-01-25 20:22:39,897] [INFO] Query marker FASTA was written to GCF_014200805.1_ASM1420080v1_genomic.fna/markers.fasta
[2024-01-25 20:22:39,898] [INFO] Task started: Blastn
[2024-01-25 20:22:39,898] [INFO] Running command: blastn -query GCF_014200805.1_ASM1420080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg824c7977-6bd4-44ed-81fd-4708833c717a/dqc_reference/reference_markers.fasta -out GCF_014200805.1_ASM1420080v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:41,166] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:41,169] [INFO] Selected 20 target genomes.
[2024-01-25 20:22:41,169] [INFO] Target genome list was writen to GCF_014200805.1_ASM1420080v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:41,198] [INFO] Task started: fastANI
[2024-01-25 20:22:41,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b53d68c-8f6f-45b2-b66f-c82e2e3cc379/GCF_014200805.1_ASM1420080v1_genomic.fna.gz --refList GCF_014200805.1_ASM1420080v1_genomic.fna/target_genomes.txt --output GCF_014200805.1_ASM1420080v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:11,085] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:11,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg824c7977-6bd4-44ed-81fd-4708833c717a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:11,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg824c7977-6bd4-44ed-81fd-4708833c717a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:11,097] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:11,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:11,097] [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 composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	100.0	2463	2464	95	conclusive
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	92.6742	1874	2464	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	82.8735	1348	2464	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	80.9991	1143	2464	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	80.9333	971	2464	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	80.8781	1071	2464	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	80.1768	887	2464	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	80.1407	1071	2464	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	79.9908	1107	2464	95	below_threshold
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	79.9901	1068	2464	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	79.921	1030	2464	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	79.9075	1065	2464	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	79.7618	881	2464	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.6414	995	2464	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	78.9997	738	2464	95	below_threshold
Nocardia araoensis	strain=NBRC 100135	GCA_000308435.1	228600	228600	type	True	76.0623	485	2464	95	below_threshold
Rhodococcus rhodochrous	strain=NCTC10210	GCA_900187265.1	1829	1829	suspected-type	True	76.0438	347	2464	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	76.0431	513	2464	95	below_threshold
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	75.9134	327	2464	95	below_threshold
Rhodococcus rhodochrous	strain=NBRC 16069	GCA_001047055.1	1829	1829	suspected-type	True	75.9042	333	2464	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:11,098] [INFO] DFAST Taxonomy check result was written to GCF_014200805.1_ASM1420080v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:11,099] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:11,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:11,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg824c7977-6bd4-44ed-81fd-4708833c717a/dqc_reference/checkm_data
[2024-01-25 20:23:11,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:11,170] [INFO] Task started: CheckM
[2024-01-25 20:23:11,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014200805.1_ASM1420080v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014200805.1_ASM1420080v1_genomic.fna/checkm_input GCF_014200805.1_ASM1420080v1_genomic.fna/checkm_result
[2024-01-25 20:24:39,988] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:39,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:40,007] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:40,007] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:40,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014200805.1_ASM1420080v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:40,008] [INFO] Task started: Blastn
[2024-01-25 20:24:40,008] [INFO] Running command: blastn -query GCF_014200805.1_ASM1420080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg824c7977-6bd4-44ed-81fd-4708833c717a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014200805.1_ASM1420080v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:42,163] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:42,166] [INFO] Selected 14 target genomes.
[2024-01-25 20:24:42,166] [INFO] Target genome list was writen to GCF_014200805.1_ASM1420080v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:42,179] [INFO] Task started: fastANI
[2024-01-25 20:24:42,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b53d68c-8f6f-45b2-b66f-c82e2e3cc379/GCF_014200805.1_ASM1420080v1_genomic.fna.gz --refList GCF_014200805.1_ASM1420080v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014200805.1_ASM1420080v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:07,486] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:07,496] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:07,496] [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_014200805.1	s__Nocardiopsis_A composta	100.0	2464	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000341105.1	s__Nocardiopsis_A potens	92.6552	1876	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341245.1	s__Nocardiopsis_A halophila	83.0657	1304	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	98.23	98.23	0.90	0.90	2	-
GCF_000341185.1	s__Nocardiopsis_A chromatogenes	82.8942	1345	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	81.0514	1142	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	80.9546	1196	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002263495.1	s__Nocardiopsis_C gilva	80.9171	1065	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	99.97	99.97	1.00	1.00	2	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	80.7965	1244	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_003336425.1	s__Marinitenerispora sediminis	80.0334	1038	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCA_002529455.1	s__Nocardiopsis fusca	79.9987	1092	2464	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	79.9902	1011	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_000341085.1	s__Nocardiopsis ganjiahuensis	79.594	1064	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308435.1	s__Nocardia araoensis	76.0432	491	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187265.1	s__Rhodococcus rhodochrous	76.0112	355	2464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.52	95.51	0.91	0.84	11	-
--------------------------------------------------------------------------------
[2024-01-25 20:25:07,498] [INFO] GTDB search result was written to GCF_014200805.1_ASM1420080v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:07,498] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:07,501] [INFO] DFAST_QC result json was written to GCF_014200805.1_ASM1420080v1_genomic.fna/dqc_result.json
[2024-01-25 20:25:07,502] [INFO] DFAST_QC completed!
[2024-01-25 20:25:07,502] [INFO] Total running time: 0h2m46s