[2024-01-24 13:55:19,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,519] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9381fe6-10af-4072-8dab-805c826e673d/dqc_reference
[2024-01-24 13:55:20,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:20,879] [INFO] Task started: Prodigal
[2024-01-24 13:55:20,879] [INFO] Running command: gunzip -c /var/lib/cwl/stgb503c3e7-c19f-4d5f-81b3-24e76453e59e/GCF_006334985.2_ASM633498v2_genomic.fna.gz | prodigal -d GCF_006334985.2_ASM633498v2_genomic.fna/cds.fna -a GCF_006334985.2_ASM633498v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:52,455] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:52,455] [INFO] Task started: HMMsearch
[2024-01-24 13:55:52,456] [INFO] Running command: hmmsearch --tblout GCF_006334985.2_ASM633498v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9381fe6-10af-4072-8dab-805c826e673d/dqc_reference/reference_markers.hmm GCF_006334985.2_ASM633498v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:52,950] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:52,951] [INFO] Found 6/6 markers.
[2024-01-24 13:55:53,040] [INFO] Query marker FASTA was written to GCF_006334985.2_ASM633498v2_genomic.fna/markers.fasta
[2024-01-24 13:55:53,041] [INFO] Task started: Blastn
[2024-01-24 13:55:53,041] [INFO] Running command: blastn -query GCF_006334985.2_ASM633498v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9381fe6-10af-4072-8dab-805c826e673d/dqc_reference/reference_markers.fasta -out GCF_006334985.2_ASM633498v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:54,440] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:54,443] [INFO] Selected 14 target genomes.
[2024-01-24 13:55:54,444] [INFO] Target genome list was writen to GCF_006334985.2_ASM633498v2_genomic.fna/target_genomes.txt
[2024-01-24 13:55:54,454] [INFO] Task started: fastANI
[2024-01-24 13:55:54,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgb503c3e7-c19f-4d5f-81b3-24e76453e59e/GCF_006334985.2_ASM633498v2_genomic.fna.gz --refList GCF_006334985.2_ASM633498v2_genomic.fna/target_genomes.txt --output GCF_006334985.2_ASM633498v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:37,351] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:37,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9381fe6-10af-4072-8dab-805c826e673d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:37,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9381fe6-10af-4072-8dab-805c826e673d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:37,369] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:37,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:37,370] [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
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	100.0	3642	3645	95	conclusive
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	99.34	3527	3645	95	conclusive
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	87.6301	2529	3645	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	87.5345	2514	3645	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	85.9122	2180	3645	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.6342	2451	3645	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.631	2238	3645	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	85.607	2143	3645	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	85.5039	2356	3645	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	85.4728	2201	3645	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	85.4027	2217	3645	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.8836	1221	3645	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	83.5737	1918	3645	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.4084	2069	3645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:37,372] [INFO] DFAST Taxonomy check result was written to GCF_006334985.2_ASM633498v2_genomic.fna/tc_result.tsv
[2024-01-24 13:56:37,372] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:37,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:37,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9381fe6-10af-4072-8dab-805c826e673d/dqc_reference/checkm_data
[2024-01-24 13:56:37,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:37,470] [INFO] Task started: CheckM
[2024-01-24 13:56:37,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006334985.2_ASM633498v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006334985.2_ASM633498v2_genomic.fna/checkm_input GCF_006334985.2_ASM633498v2_genomic.fna/checkm_result
[2024-01-24 13:58:33,639] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:33,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.43%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:33,670] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:33,670] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:33,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006334985.2_ASM633498v2_genomic.fna/markers.fasta)
[2024-01-24 13:58:33,671] [INFO] Task started: Blastn
[2024-01-24 13:58:33,671] [INFO] Running command: blastn -query GCF_006334985.2_ASM633498v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9381fe6-10af-4072-8dab-805c826e673d/dqc_reference/reference_markers_gtdb.fasta -out GCF_006334985.2_ASM633498v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:35,849] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:35,854] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:35,854] [INFO] Target genome list was writen to GCF_006334985.2_ASM633498v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:35,876] [INFO] Task started: fastANI
[2024-01-24 13:58:35,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgb503c3e7-c19f-4d5f-81b3-24e76453e59e/GCF_006334985.2_ASM633498v2_genomic.fna.gz --refList GCF_006334985.2_ASM633498v2_genomic.fna/target_genomes_gtdb.txt --output GCF_006334985.2_ASM633498v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:20,871] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:20,893] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:20,894] [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_006334985.2	s__Nonomuraea phyllanthi	100.0	3642	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	conclusive
GCF_014873145.1	s__Nonomuraea angiospora	87.6421	2525	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	87.5186	2518	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348685.1	s__Nonomuraea deserti	85.9055	2181	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_014207985.1	s__Nonomuraea rubra	85.6634	2444	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	85.6504	2236	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	85.5149	2224	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108335.1	s__Nonomuraea solani	85.4946	2359	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725485.1	s__Nonomuraea candida	85.4759	2200	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011505.1	s__Nonomuraea polychroma	85.3952	2218	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	85.3352	2392	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323885.1	s__Nonomuraea parvosata	85.0529	2450	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_900109355.1	s__Nonomuraea pusilla	83.6122	1910	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_013283785.1	s__Nonomuraea sp013283785	83.6058	1948	3645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:20,895] [INFO] GTDB search result was written to GCF_006334985.2_ASM633498v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:20,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:20,902] [INFO] DFAST_QC result json was written to GCF_006334985.2_ASM633498v2_genomic.fna/dqc_result.json
[2024-01-24 13:59:20,902] [INFO] DFAST_QC completed!
[2024-01-24 13:59:20,902] [INFO] Total running time: 0h4m1s