[2024-01-25 19:36:35,656] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:35,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:35,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d12a623-75e5-4772-9552-f4b39f69cbee/dqc_reference
[2024-01-25 19:36:36,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:36,782] [INFO] Task started: Prodigal
[2024-01-25 19:36:36,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dd52e82-77af-431f-9d9c-f382b7fb0818/GCF_014204715.1_ASM1420471v1_genomic.fna.gz | prodigal -d GCF_014204715.1_ASM1420471v1_genomic.fna/cds.fna -a GCF_014204715.1_ASM1420471v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:52,894] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:52,894] [INFO] Task started: HMMsearch
[2024-01-25 19:36:52,894] [INFO] Running command: hmmsearch --tblout GCF_014204715.1_ASM1420471v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d12a623-75e5-4772-9552-f4b39f69cbee/dqc_reference/reference_markers.hmm GCF_014204715.1_ASM1420471v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:53,149] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:53,150] [INFO] Found 6/6 markers.
[2024-01-25 19:36:53,193] [INFO] Query marker FASTA was written to GCF_014204715.1_ASM1420471v1_genomic.fna/markers.fasta
[2024-01-25 19:36:53,194] [INFO] Task started: Blastn
[2024-01-25 19:36:53,194] [INFO] Running command: blastn -query GCF_014204715.1_ASM1420471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d12a623-75e5-4772-9552-f4b39f69cbee/dqc_reference/reference_markers.fasta -out GCF_014204715.1_ASM1420471v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:54,278] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:54,280] [INFO] Selected 21 target genomes.
[2024-01-25 19:36:54,280] [INFO] Target genome list was writen to GCF_014204715.1_ASM1420471v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:54,286] [INFO] Task started: fastANI
[2024-01-25 19:36:54,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dd52e82-77af-431f-9d9c-f382b7fb0818/GCF_014204715.1_ASM1420471v1_genomic.fna.gz --refList GCF_014204715.1_ASM1420471v1_genomic.fna/target_genomes.txt --output GCF_014204715.1_ASM1420471v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:21,337] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:21,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d12a623-75e5-4772-9552-f4b39f69cbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:21,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d12a623-75e5-4772-9552-f4b39f69cbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:21,349] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:37:21,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:21,350] [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
Streptomonospora salina	strain=DSM 44593	GCA_014204715.1	104205	104205	type	True	100.0	1866	1868	95	conclusive
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	89.2064	1423	1868	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	84.7856	1340	1868	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	80.5802	822	1868	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	80.5557	754	1868	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	80.5122	873	1868	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	80.058	995	1868	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	79.888	966	1868	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	79.8502	686	1868	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	79.765	727	1868	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	79.7339	815	1868	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	79.6528	746	1868	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.5095	722	1868	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	79.1613	762	1868	95	below_threshold
Nocardiopsis valliformis	strain=DSM 45023	GCA_000340985.1	239974	239974	type	True	79.0088	709	1868	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	78.9294	777	1868	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	77.4955	549	1868	95	below_threshold
Actinomadura hallensis	strain=DSM 45043	GCA_006716765.1	337895	337895	type	True	77.1917	585	1868	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	76.8064	666	1868	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	76.7202	608	1868	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	76.5984	655	1868	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:21,351] [INFO] DFAST Taxonomy check result was written to GCF_014204715.1_ASM1420471v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:21,352] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:21,352] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:21,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d12a623-75e5-4772-9552-f4b39f69cbee/dqc_reference/checkm_data
[2024-01-25 19:37:21,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:21,406] [INFO] Task started: CheckM
[2024-01-25 19:37:21,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014204715.1_ASM1420471v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014204715.1_ASM1420471v1_genomic.fna/checkm_input GCF_014204715.1_ASM1420471v1_genomic.fna/checkm_result
[2024-01-25 19:38:13,632] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:13,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:13,652] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:13,652] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:13,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014204715.1_ASM1420471v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:13,653] [INFO] Task started: Blastn
[2024-01-25 19:38:13,653] [INFO] Running command: blastn -query GCF_014204715.1_ASM1420471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d12a623-75e5-4772-9552-f4b39f69cbee/dqc_reference/reference_markers_gtdb.fasta -out GCF_014204715.1_ASM1420471v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:15,369] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:15,372] [INFO] Selected 14 target genomes.
[2024-01-25 19:38:15,372] [INFO] Target genome list was writen to GCF_014204715.1_ASM1420471v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:15,381] [INFO] Task started: fastANI
[2024-01-25 19:38:15,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dd52e82-77af-431f-9d9c-f382b7fb0818/GCF_014204715.1_ASM1420471v1_genomic.fna.gz --refList GCF_014204715.1_ASM1420471v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014204715.1_ASM1420471v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:35,544] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:35,554] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:35,554] [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_014204715.1	s__Streptomonospora salina	100.0	1866	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000826685.1	s__Streptomonospora alba	89.1806	1426	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728995.1	s__Streptomonospora sp009728995	85.9337	1347	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004323735.1	s__Streptomonospora sp004323735	84.7849	1335	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	82.6213	1195	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_013408795.1	s__Spinactinospora alkalitolerans	80.6721	996	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	80.1136	988	1868	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_001517975.1	s__Thermobifida cellulosilytica	79.8571	685	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981225.1	s__Allosalinactinospora lopnorensis	79.7424	792	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allosalinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201115.1	s__Nocardiopsis metallicus	79.2088	763	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716765.1	s__Spirillospora hallensis	77.1482	589	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698395.1	s__JACCUZ01 sp013698395	76.785	163	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__JACCUZ01;f__JACCUZ01;g__JACCUZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409045.1	s__Spirillospora citrea	76.755	680	1868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188105.1	s__Spirillospora mexicana	76.6956	616	1868	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 19:38:35,556] [INFO] GTDB search result was written to GCF_014204715.1_ASM1420471v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:35,556] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:35,560] [INFO] DFAST_QC result json was written to GCF_014204715.1_ASM1420471v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:35,560] [INFO] DFAST_QC completed!
[2024-01-25 19:38:35,560] [INFO] Total running time: 0h1m60s