[2024-01-25 19:57:05,757] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:05,758] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:05,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d519768-b9f0-4718-b500-2dd63e29c0b5/dqc_reference
[2024-01-25 19:57:06,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:06,886] [INFO] Task started: Prodigal
[2024-01-25 19:57:06,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg53376cda-942f-4cc5-9cfa-bf91ff6390d8/GCF_003967515.1_ASM396751v1_genomic.fna.gz | prodigal -d GCF_003967515.1_ASM396751v1_genomic.fna/cds.fna -a GCF_003967515.1_ASM396751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:29,578] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:29,579] [INFO] Task started: HMMsearch
[2024-01-25 19:57:29,579] [INFO] Running command: hmmsearch --tblout GCF_003967515.1_ASM396751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d519768-b9f0-4718-b500-2dd63e29c0b5/dqc_reference/reference_markers.hmm GCF_003967515.1_ASM396751v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:29,911] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:29,912] [INFO] Found 6/6 markers.
[2024-01-25 19:57:29,983] [INFO] Query marker FASTA was written to GCF_003967515.1_ASM396751v1_genomic.fna/markers.fasta
[2024-01-25 19:57:29,983] [INFO] Task started: Blastn
[2024-01-25 19:57:29,983] [INFO] Running command: blastn -query GCF_003967515.1_ASM396751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d519768-b9f0-4718-b500-2dd63e29c0b5/dqc_reference/reference_markers.fasta -out GCF_003967515.1_ASM396751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:30,533] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:30,535] [INFO] Selected 10 target genomes.
[2024-01-25 19:57:30,535] [INFO] Target genome list was writen to GCF_003967515.1_ASM396751v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:30,560] [INFO] Task started: fastANI
[2024-01-25 19:57:30,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg53376cda-942f-4cc5-9cfa-bf91ff6390d8/GCF_003967515.1_ASM396751v1_genomic.fna.gz --refList GCF_003967515.1_ASM396751v1_genomic.fna/target_genomes.txt --output GCF_003967515.1_ASM396751v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:48,937] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:48,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d519768-b9f0-4718-b500-2dd63e29c0b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:48,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d519768-b9f0-4718-b500-2dd63e29c0b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:48,945] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:48,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:48,945] [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
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	100.0	2949	2960	95	conclusive
Dictyobacter formicarum	strain=SOSP1-9	GCA_016587435.1	2778368	2778368	type	True	82.3728	1714	2960	95	below_threshold
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	80.0672	1285	2960	95	below_threshold
Dictyobacter alpinus	strain=Uno16	GCA_003967575.1	2014873	2014873	type	True	78.7129	736	2960	95	below_threshold
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	78.7051	724	2960	95	below_threshold
Tengunoibacter tsumagoiensis	strain=Uno3	GCA_003967535.1	2014871	2014871	type	True	77.767	218	2960	95	below_threshold
Dictyobacter arantiisoli	strain=Uno17	GCA_008326305.1	2014874	2014874	type	True	77.7429	436	2960	95	below_threshold
Reticulibacter mediterranei	strain=150040	GCA_016587455.1	2778369	2778369	type	True	76.9652	251	2960	95	below_threshold
Thermosporothrix hazakensis	strain=ATCC BAA-1881	GCA_003253565.1	644383	644383	type	True	76.3824	112	2960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:48,947] [INFO] DFAST Taxonomy check result was written to GCF_003967515.1_ASM396751v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:48,947] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:48,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:48,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d519768-b9f0-4718-b500-2dd63e29c0b5/dqc_reference/checkm_data
[2024-01-25 19:57:48,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:49,029] [INFO] Task started: CheckM
[2024-01-25 19:57:49,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003967515.1_ASM396751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003967515.1_ASM396751v1_genomic.fna/checkm_input GCF_003967515.1_ASM396751v1_genomic.fna/checkm_result
[2024-01-25 19:58:51,385] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:51,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.87%
Strain heterogeneity: 55.56%
--------------------------------------------------------------------------------
[2024-01-25 19:58:51,430] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:51,431] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:51,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003967515.1_ASM396751v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:51,432] [INFO] Task started: Blastn
[2024-01-25 19:58:51,432] [INFO] Running command: blastn -query GCF_003967515.1_ASM396751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d519768-b9f0-4718-b500-2dd63e29c0b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003967515.1_ASM396751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:52,240] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:52,245] [INFO] Selected 11 target genomes.
[2024-01-25 19:58:52,245] [INFO] Target genome list was writen to GCF_003967515.1_ASM396751v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:52,266] [INFO] Task started: fastANI
[2024-01-25 19:58:52,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg53376cda-942f-4cc5-9cfa-bf91ff6390d8/GCF_003967515.1_ASM396751v1_genomic.fna.gz --refList GCF_003967515.1_ASM396751v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003967515.1_ASM396751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:11,374] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:11,381] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:11,382] [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_003967515.1	s__Dictyobacter aurantiacus	100.0	2949	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016587435.1	s__Dictyobacter sp016587435	82.3584	1712	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967555.1	s__Dictyobacter kobayashii	80.0485	1284	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974265.1	s__Dictyobacter vulcani	78.7172	726	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015099395.1	s__Dictyobacter sp015099395	78.0218	321	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008326305.1	s__Dictyobacter sp008326305	77.7405	437	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967535.1	s__Tengunoibacter tsumagoiensis	77.6048	215	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Tengunoibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208415.1	s__Ktedonosporobacter rubrisoli	76.9382	189	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389075.1	s__DTNP01 sp011389075	76.1238	108	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__DTNP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014896635.1	s__Bu33 sp014896635	76.0474	143	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Bu33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268475.1	s__Thermogemmatispora tikiterensis	75.7347	95	2960	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:11,383] [INFO] GTDB search result was written to GCF_003967515.1_ASM396751v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:11,383] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:11,386] [INFO] DFAST_QC result json was written to GCF_003967515.1_ASM396751v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:11,386] [INFO] DFAST_QC completed!
[2024-01-25 19:59:11,386] [INFO] Total running time: 0h2m6s