[2024-01-24 13:23:10,848] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:10,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:10,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg4af37f28-7f2c-423a-a44a-24f55db4a6c9/dqc_reference
[2024-01-24 13:23:12,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:12,130] [INFO] Task started: Prodigal
[2024-01-24 13:23:12,130] [INFO] Running command: gunzip -c /var/lib/cwl/stg54dcf2ef-33c7-4e5a-ac03-e649da34afbc/GCF_005402645.1_ASM540264v1_genomic.fna.gz | prodigal -d GCF_005402645.1_ASM540264v1_genomic.fna/cds.fna -a GCF_005402645.1_ASM540264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:33,900] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:33,901] [INFO] Task started: HMMsearch
[2024-01-24 13:23:33,901] [INFO] Running command: hmmsearch --tblout GCF_005402645.1_ASM540264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4af37f28-7f2c-423a-a44a-24f55db4a6c9/dqc_reference/reference_markers.hmm GCF_005402645.1_ASM540264v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:34,195] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:34,196] [INFO] Found 6/6 markers.
[2024-01-24 13:23:34,246] [INFO] Query marker FASTA was written to GCF_005402645.1_ASM540264v1_genomic.fna/markers.fasta
[2024-01-24 13:23:34,246] [INFO] Task started: Blastn
[2024-01-24 13:23:34,246] [INFO] Running command: blastn -query GCF_005402645.1_ASM540264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4af37f28-7f2c-423a-a44a-24f55db4a6c9/dqc_reference/reference_markers.fasta -out GCF_005402645.1_ASM540264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:34,795] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:34,798] [INFO] Selected 16 target genomes.
[2024-01-24 13:23:34,798] [INFO] Target genome list was writen to GCF_005402645.1_ASM540264v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:34,821] [INFO] Task started: fastANI
[2024-01-24 13:23:34,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg54dcf2ef-33c7-4e5a-ac03-e649da34afbc/GCF_005402645.1_ASM540264v1_genomic.fna.gz --refList GCF_005402645.1_ASM540264v1_genomic.fna/target_genomes.txt --output GCF_005402645.1_ASM540264v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:50,669] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:50,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4af37f28-7f2c-423a-a44a-24f55db4a6c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:50,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4af37f28-7f2c-423a-a44a-24f55db4a6c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:50,676] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:23:50,676] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:50,677] [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
Thermosporothrix hazakensis	strain=SK20-1	GCA_005402645.1	644383	644383	type	True	100.0	2461	2463	95	conclusive
Thermosporothrix hazakensis	strain=ATCC BAA-1881	GCA_003253565.1	644383	644383	type	True	99.9706	2374	2463	95	conclusive
Ktedonospora formicarum	strain=SOSP1-1	GCA_016587355.1	2778364	2778364	type	True	77.5019	146	2463	95	below_threshold
Ktedonobacter racemifer	strain=SOSP1-21	GCA_000178855.1	363277	363277	type	True	77.1426	180	2463	95	below_threshold
Dictyobacter alpinus	strain=Uno16	GCA_003967575.1	2014873	2014873	type	True	77.0297	108	2463	95	below_threshold
Ktedonobacter robiniae	strain=SOSP1-30	GCA_016587375.1	2778365	2778365	type	True	76.9724	194	2463	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	76.7435	113	2463	95	below_threshold
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	76.6354	119	2463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:50,678] [INFO] DFAST Taxonomy check result was written to GCF_005402645.1_ASM540264v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:50,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:50,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:50,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4af37f28-7f2c-423a-a44a-24f55db4a6c9/dqc_reference/checkm_data
[2024-01-24 13:23:50,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:50,743] [INFO] Task started: CheckM
[2024-01-24 13:23:50,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005402645.1_ASM540264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005402645.1_ASM540264v1_genomic.fna/checkm_input GCF_005402645.1_ASM540264v1_genomic.fna/checkm_result
[2024-01-24 13:24:54,656] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:54,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:54,682] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:54,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:54,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005402645.1_ASM540264v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:54,683] [INFO] Task started: Blastn
[2024-01-24 13:24:54,683] [INFO] Running command: blastn -query GCF_005402645.1_ASM540264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4af37f28-7f2c-423a-a44a-24f55db4a6c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_005402645.1_ASM540264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:55,413] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:55,417] [INFO] Selected 26 target genomes.
[2024-01-24 13:24:55,417] [INFO] Target genome list was writen to GCF_005402645.1_ASM540264v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:55,545] [INFO] Task started: fastANI
[2024-01-24 13:24:55,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg54dcf2ef-33c7-4e5a-ac03-e649da34afbc/GCF_005402645.1_ASM540264v1_genomic.fna.gz --refList GCF_005402645.1_ASM540264v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005402645.1_ASM540264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:20,945] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:20,957] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:20,957] [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_003253565.1	s__Thermosporothrix hazakensis	99.9706	2374	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermosporothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015099395.1	s__Dictyobacter sp015099395	77.4044	99	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016587355.1	s__Ktedonobacter sp016587355	77.3578	145	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178855.1	s__Ktedonobacter racemifer	77.183	180	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587375.1	s__Ktedonobacter sp016587375	77.0297	196	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587415.1	s__Ktedonobacter sp016587415	76.9999	173	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587435.1	s__Dictyobacter sp016587435	76.9406	104	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967515.1	s__Dictyobacter aurantiacus	76.7908	114	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879655.1	s__CF-154 sp005879655	76.4003	86	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CF-154	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014896635.1	s__Bu33 sp014896635	76.2731	79	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Bu33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810755.1	s__CADDYT01 sp902810755	75.6279	87	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDYT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812455.1	s__CADDZH01 sp902812455	75.5586	68	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001748285.1	s__Thermogemmatispora onikobensis	75.4594	60	2463	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:20,959] [INFO] GTDB search result was written to GCF_005402645.1_ASM540264v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:20,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:20,962] [INFO] DFAST_QC result json was written to GCF_005402645.1_ASM540264v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:20,962] [INFO] DFAST_QC completed!
[2024-01-24 13:25:20,962] [INFO] Total running time: 0h2m10s