[2024-01-25 17:44:35,649] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:35,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:35,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg4051aaa3-f78d-401e-ab6b-c38f6ae27ba3/dqc_reference
[2024-01-25 17:44:36,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:36,805] [INFO] Task started: Prodigal
[2024-01-25 17:44:36,805] [INFO] Running command: gunzip -c /var/lib/cwl/stgf565fcb0-cb9e-4234-848f-c1cfc3af39a4/GCF_003014485.1_ASM301448v1_genomic.fna.gz | prodigal -d GCF_003014485.1_ASM301448v1_genomic.fna/cds.fna -a GCF_003014485.1_ASM301448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:54,926] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:54,927] [INFO] Task started: HMMsearch
[2024-01-25 17:44:54,927] [INFO] Running command: hmmsearch --tblout GCF_003014485.1_ASM301448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4051aaa3-f78d-401e-ab6b-c38f6ae27ba3/dqc_reference/reference_markers.hmm GCF_003014485.1_ASM301448v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:55,213] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:55,215] [INFO] Found 6/6 markers.
[2024-01-25 17:44:55,270] [INFO] Query marker FASTA was written to GCF_003014485.1_ASM301448v1_genomic.fna/markers.fasta
[2024-01-25 17:44:55,270] [INFO] Task started: Blastn
[2024-01-25 17:44:55,270] [INFO] Running command: blastn -query GCF_003014485.1_ASM301448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4051aaa3-f78d-401e-ab6b-c38f6ae27ba3/dqc_reference/reference_markers.fasta -out GCF_003014485.1_ASM301448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:56,415] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:56,417] [INFO] Selected 22 target genomes.
[2024-01-25 17:44:56,418] [INFO] Target genome list was writen to GCF_003014485.1_ASM301448v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:56,422] [INFO] Task started: fastANI
[2024-01-25 17:44:56,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgf565fcb0-cb9e-4234-848f-c1cfc3af39a4/GCF_003014485.1_ASM301448v1_genomic.fna.gz --refList GCF_003014485.1_ASM301448v1_genomic.fna/target_genomes.txt --output GCF_003014485.1_ASM301448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:25,438] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:25,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4051aaa3-f78d-401e-ab6b-c38f6ae27ba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:25,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4051aaa3-f78d-401e-ab6b-c38f6ae27ba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:25,455] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:45:25,455] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:45:25,455] [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 gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	79.8948	890	2425	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	79.8931	820	2425	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	79.6875	990	2425	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.4657	784	2425	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.4466	967	2425	95	below_threshold
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	79.4284	942	2425	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	79.4146	800	2425	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	79.413	809	2425	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	79.3444	1082	2425	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	79.3124	1148	2425	95	below_threshold
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	79.233	896	2425	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	79.1664	922	2425	95	below_threshold
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	79.1077	929	2425	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	79.0562	847	2425	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	79.0485	930	2425	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	78.8903	792	2425	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	78.8058	673	2425	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	78.7851	974	2425	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	78.7482	837	2425	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	78.725	864	2425	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	78.664	921	2425	95	below_threshold
Nocardiopsis coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	78.4602	814	2425	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:25,457] [INFO] DFAST Taxonomy check result was written to GCF_003014485.1_ASM301448v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:25,457] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:25,457] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:25,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4051aaa3-f78d-401e-ab6b-c38f6ae27ba3/dqc_reference/checkm_data
[2024-01-25 17:45:25,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:25,527] [INFO] Task started: CheckM
[2024-01-25 17:45:25,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014485.1_ASM301448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014485.1_ASM301448v1_genomic.fna/checkm_input GCF_003014485.1_ASM301448v1_genomic.fna/checkm_result
[2024-01-25 17:46:28,776] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:28,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.24%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-25 17:46:28,800] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:28,801] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:28,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014485.1_ASM301448v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:28,802] [INFO] Task started: Blastn
[2024-01-25 17:46:28,802] [INFO] Running command: blastn -query GCF_003014485.1_ASM301448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4051aaa3-f78d-401e-ab6b-c38f6ae27ba3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014485.1_ASM301448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:30,684] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:30,689] [INFO] Selected 16 target genomes.
[2024-01-25 17:46:30,689] [INFO] Target genome list was writen to GCF_003014485.1_ASM301448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:30,703] [INFO] Task started: fastANI
[2024-01-25 17:46:30,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgf565fcb0-cb9e-4234-848f-c1cfc3af39a4/GCF_003014485.1_ASM301448v1_genomic.fna.gz --refList GCF_003014485.1_ASM301448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014485.1_ASM301448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:55,757] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:55,767] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:55,768] [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_003014485.1	s__Murinocardiopsis flavida	100.0	2424	2425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Murinocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013408795.1	s__Spinactinospora alkalitolerans	80.8367	1168	2425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	80.5204	1111	2425	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_003336425.1	s__Marinitenerispora sediminis	80.0626	984	2425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	79.954	1126	2425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_002263495.1	s__Nocardiopsis_C gilva	79.8811	892	2425	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_014201195.1	s__Nocardiopsis_C mwathae	79.7136	985	2425	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_001660385.1	s__Thermobifida halotolerans	79.4209	798	2425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.91	99.91	0.97	0.97	2	-
GCF_004323735.1	s__Streptomonospora sp004323735	79.4195	973	2425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	79.3638	1136	2425	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_000341105.1	s__Nocardiopsis_A potens	79.3251	1087	2425	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_000092985.1	s__Nocardiopsis dassonvillei	79.1495	925	2425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
GCF_000341065.1	s__Nocardiopsis halotolerans	78.8933	791	2425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201115.1	s__Nocardiopsis metallicus	78.7136	867	2425	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	78.6459	925	2425	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	78.4788	810	2425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:55,770] [INFO] GTDB search result was written to GCF_003014485.1_ASM301448v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:55,771] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:55,775] [INFO] DFAST_QC result json was written to GCF_003014485.1_ASM301448v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:55,775] [INFO] DFAST_QC completed!
[2024-01-25 17:46:55,775] [INFO] Total running time: 0h2m20s