[2024-01-24 13:57:42,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,937] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa5a6d3a-98dc-4fe5-938e-bde51eb5c127/dqc_reference
[2024-01-24 13:57:44,217] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,218] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,218] [INFO] Running command: gunzip -c /var/lib/cwl/stg11d02851-d0fa-488d-939f-abf04205032f/GCF_009687845.1_ASM968784v1_genomic.fna.gz | prodigal -d GCF_009687845.1_ASM968784v1_genomic.fna/cds.fna -a GCF_009687845.1_ASM968784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:09,337] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:09,338] [INFO] Task started: HMMsearch
[2024-01-24 13:58:09,338] [INFO] Running command: hmmsearch --tblout GCF_009687845.1_ASM968784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa5a6d3a-98dc-4fe5-938e-bde51eb5c127/dqc_reference/reference_markers.hmm GCF_009687845.1_ASM968784v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:09,765] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:09,767] [INFO] Found 6/6 markers.
[2024-01-24 13:58:09,841] [INFO] Query marker FASTA was written to GCF_009687845.1_ASM968784v1_genomic.fna/markers.fasta
[2024-01-24 13:58:09,842] [INFO] Task started: Blastn
[2024-01-24 13:58:09,842] [INFO] Running command: blastn -query GCF_009687845.1_ASM968784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa5a6d3a-98dc-4fe5-938e-bde51eb5c127/dqc_reference/reference_markers.fasta -out GCF_009687845.1_ASM968784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:11,146] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:11,150] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:11,151] [INFO] Target genome list was writen to GCF_009687845.1_ASM968784v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:11,157] [INFO] Task started: fastANI
[2024-01-24 13:58:11,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d02851-d0fa-488d-939f-abf04205032f/GCF_009687845.1_ASM968784v1_genomic.fna.gz --refList GCF_009687845.1_ASM968784v1_genomic.fna/target_genomes.txt --output GCF_009687845.1_ASM968784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:37,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:37,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa5a6d3a-98dc-4fe5-938e-bde51eb5c127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:37,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa5a6d3a-98dc-4fe5-938e-bde51eb5c127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:37,873] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:37,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:37,873] [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
Acrocarpospora corrugata	strain=NBRC 13972	GCA_009687845.1	35763	35763	type	True	100.0	2993	3007	95	conclusive
Acrocarpospora macrocephala	strain=NBRC 16266	GCA_009687865.1	150177	150177	type	True	88.3859	2195	3007	95	below_threshold
Acrocarpospora pleiomorpha	strain=NBRC 16267	GCA_009687885.1	90975	90975	type	True	88.2461	2135	3007	95	below_threshold
Acrocarpospora phusangensis	strain=NBRC 108782	GCA_016862995.1	1070424	1070424	type	True	87.6283	2053	3007	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	84.3174	1790	3007	95	below_threshold
Herbidospora galbida	strain=NEAU-GS14	GCA_005233835.1	2575442	2575442	type	True	81.503	1498	3007	95	below_threshold
Herbidospora sakaeratensis	strain=NBRC 102641	GCA_001570525.1	564415	564415	type	True	81.3962	1557	3007	95	below_threshold
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	81.3494	1533	3007	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	79.8747	862	3007	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.7302	835	3007	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.2941	1262	3007	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.0649	1303	3007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:37,887] [INFO] DFAST Taxonomy check result was written to GCF_009687845.1_ASM968784v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:37,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:37,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:37,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa5a6d3a-98dc-4fe5-938e-bde51eb5c127/dqc_reference/checkm_data
[2024-01-24 13:58:37,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:37,981] [INFO] Task started: CheckM
[2024-01-24 13:58:37,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009687845.1_ASM968784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009687845.1_ASM968784v1_genomic.fna/checkm_input GCF_009687845.1_ASM968784v1_genomic.fna/checkm_result
[2024-01-24 13:59:52,756] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:52,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:52,784] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:52,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:52,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009687845.1_ASM968784v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:52,785] [INFO] Task started: Blastn
[2024-01-24 13:59:52,785] [INFO] Running command: blastn -query GCF_009687845.1_ASM968784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa5a6d3a-98dc-4fe5-938e-bde51eb5c127/dqc_reference/reference_markers_gtdb.fasta -out GCF_009687845.1_ASM968784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:54,753] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:54,757] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:54,757] [INFO] Target genome list was writen to GCF_009687845.1_ASM968784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:54,765] [INFO] Task started: fastANI
[2024-01-24 13:59:54,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d02851-d0fa-488d-939f-abf04205032f/GCF_009687845.1_ASM968784v1_genomic.fna.gz --refList GCF_009687845.1_ASM968784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009687845.1_ASM968784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:16,732] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:16,747] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:16,747] [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_009687845.1	s__Acrocarpospora corrugata	100.0	2993	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009687865.1	s__Acrocarpospora macrocephala	88.4167	2191	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009687885.1	s__Acrocarpospora pleiomorpha	88.2513	2134	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862995.1	s__Acrocarpospora phusangensis	87.6196	2055	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018476525.1	s__Acrocarpospora sp018476525	84.3332	1786	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233835.1	s__Herbidospora galbida	81.5287	1494	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570525.1	s__Herbidospora sakaeratensis	81.3874	1559	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570585.1	s__Herbidospora daliensis	81.3686	1559	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901565.1	s__Herbidospora solisilvae	81.3617	1530	3007	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	95.93	95.93	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:16,749] [INFO] GTDB search result was written to GCF_009687845.1_ASM968784v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:16,750] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:16,753] [INFO] DFAST_QC result json was written to GCF_009687845.1_ASM968784v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:16,753] [INFO] DFAST_QC completed!
[2024-01-24 14:00:16,753] [INFO] Total running time: 0h2m34s