[2024-01-25 17:34:50,890] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:50,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:50,892] [INFO] DQC Reference Directory: /var/lib/cwl/stgf09574a3-c7c1-45aa-b849-284cf40ba67e/dqc_reference
[2024-01-25 17:34:52,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:52,021] [INFO] Task started: Prodigal
[2024-01-25 17:34:52,021] [INFO] Running command: gunzip -c /var/lib/cwl/stg96d9f5ca-24ed-4638-b241-bfd075e860e0/GCF_014648675.1_ASM1464867v1_genomic.fna.gz | prodigal -d GCF_014648675.1_ASM1464867v1_genomic.fna/cds.fna -a GCF_014648675.1_ASM1464867v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:11,759] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:11,760] [INFO] Task started: HMMsearch
[2024-01-25 17:35:11,760] [INFO] Running command: hmmsearch --tblout GCF_014648675.1_ASM1464867v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf09574a3-c7c1-45aa-b849-284cf40ba67e/dqc_reference/reference_markers.hmm GCF_014648675.1_ASM1464867v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:12,189] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:12,190] [INFO] Found 6/6 markers.
[2024-01-25 17:35:12,255] [INFO] Query marker FASTA was written to GCF_014648675.1_ASM1464867v1_genomic.fna/markers.fasta
[2024-01-25 17:35:12,255] [INFO] Task started: Blastn
[2024-01-25 17:35:12,255] [INFO] Running command: blastn -query GCF_014648675.1_ASM1464867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf09574a3-c7c1-45aa-b849-284cf40ba67e/dqc_reference/reference_markers.fasta -out GCF_014648675.1_ASM1464867v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:13,496] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:13,500] [INFO] Selected 21 target genomes.
[2024-01-25 17:35:13,500] [INFO] Target genome list was writen to GCF_014648675.1_ASM1464867v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:13,507] [INFO] Task started: fastANI
[2024-01-25 17:35:13,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d9f5ca-24ed-4638-b241-bfd075e860e0/GCF_014648675.1_ASM1464867v1_genomic.fna.gz --refList GCF_014648675.1_ASM1464867v1_genomic.fna/target_genomes.txt --output GCF_014648675.1_ASM1464867v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:02,177] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:02,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf09574a3-c7c1-45aa-b849-284cf40ba67e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:02,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf09574a3-c7c1-45aa-b849-284cf40ba67e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:02,191] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:36:02,191] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:36:02,191] [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
Actinomadura hallensis	strain=DSM 45043	GCA_006716765.1	337895	337895	type	True	89.0581	1870	2691	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	86.5328	1787	2691	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	86.5152	1833	2691	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	86.1768	1718	2691	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	86.1594	1890	2691	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	85.9979	1464	2691	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	85.9024	1736	2691	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	85.7767	1815	2691	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	85.715	1627	2691	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	85.7049	1808	2691	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	85.6722	1834	2691	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	84.8925	1704	2691	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	84.8651	1727	2691	95	below_threshold
Actinomadura chibensis	strain=JCM 14158	GCA_008085895.1	392828	392828	type	True	84.8557	1733	2691	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	84.8469	1722	2691	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.7594	1519	2691	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	84.1614	1795	2691	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.5898	1548	2691	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.4694	1389	2691	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	80.7644	1377	2691	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	78.4824	995	2691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:02,193] [INFO] DFAST Taxonomy check result was written to GCF_014648675.1_ASM1464867v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:02,193] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:02,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:02,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf09574a3-c7c1-45aa-b849-284cf40ba67e/dqc_reference/checkm_data
[2024-01-25 17:36:02,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:02,265] [INFO] Task started: CheckM
[2024-01-25 17:36:02,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648675.1_ASM1464867v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648675.1_ASM1464867v1_genomic.fna/checkm_input GCF_014648675.1_ASM1464867v1_genomic.fna/checkm_result
[2024-01-25 17:37:23,982] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:23,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:24,015] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:24,015] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:24,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648675.1_ASM1464867v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:24,016] [INFO] Task started: Blastn
[2024-01-25 17:37:24,016] [INFO] Running command: blastn -query GCF_014648675.1_ASM1464867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf09574a3-c7c1-45aa-b849-284cf40ba67e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648675.1_ASM1464867v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:26,061] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:26,064] [INFO] Selected 12 target genomes.
[2024-01-25 17:37:26,064] [INFO] Target genome list was writen to GCF_014648675.1_ASM1464867v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:26,070] [INFO] Task started: fastANI
[2024-01-25 17:37:26,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d9f5ca-24ed-4638-b241-bfd075e860e0/GCF_014648675.1_ASM1464867v1_genomic.fna.gz --refList GCF_014648675.1_ASM1464867v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648675.1_ASM1464867v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:54,743] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:54,751] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:54,751] [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_014648675.1	s__Spirillospora livida	100.0	2689	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	conclusive
GCF_004349245.1	s__Spirillospora sp004349245	94.0763	2075	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348665.1	s__Spirillospora sp004348665	92.5232	1786	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716765.1	s__Spirillospora hallensis	89.046	1872	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348515.1	s__Spirillospora sp004348515	88.2771	1713	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348425.1	s__Spirillospora sp004348425	88.2638	1939	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	86.1599	1890	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_004348735.1	s__Spirillospora sp004348735	85.8827	1667	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	85.712	1862	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547145.1	s__Spirillospora sp006547145	85.4854	1853	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008085905.1	s__Spirillospora syzygii	84.8076	1729	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.88	95.88	0.90	0.90	2	-
GCF_003432485.1	s__Spirillospora sp003432485	84.761	1518	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:54,753] [INFO] GTDB search result was written to GCF_014648675.1_ASM1464867v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:54,754] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:54,757] [INFO] DFAST_QC result json was written to GCF_014648675.1_ASM1464867v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:54,757] [INFO] DFAST_QC completed!
[2024-01-25 17:37:54,757] [INFO] Total running time: 0h3m4s