[2024-01-25 20:03:05,470] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8de2042-7c7e-47fd-ba9a-4499a3291f27/dqc_reference
[2024-01-25 20:03:06,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:06,628] [INFO] Task started: Prodigal
[2024-01-25 20:03:06,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg1953d62c-204f-46a4-ab72-3ece83eadbfe/GCF_003967535.1_ASM396753v1_genomic.fna.gz | prodigal -d GCF_003967535.1_ASM396753v1_genomic.fna/cds.fna -a GCF_003967535.1_ASM396753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:25,243] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:25,244] [INFO] Task started: HMMsearch
[2024-01-25 20:03:25,244] [INFO] Running command: hmmsearch --tblout GCF_003967535.1_ASM396753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8de2042-7c7e-47fd-ba9a-4499a3291f27/dqc_reference/reference_markers.hmm GCF_003967535.1_ASM396753v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:25,592] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:25,593] [INFO] Found 6/6 markers.
[2024-01-25 20:03:25,646] [INFO] Query marker FASTA was written to GCF_003967535.1_ASM396753v1_genomic.fna/markers.fasta
[2024-01-25 20:03:25,647] [INFO] Task started: Blastn
[2024-01-25 20:03:25,647] [INFO] Running command: blastn -query GCF_003967535.1_ASM396753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8de2042-7c7e-47fd-ba9a-4499a3291f27/dqc_reference/reference_markers.fasta -out GCF_003967535.1_ASM396753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:26,175] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:26,178] [INFO] Selected 15 target genomes.
[2024-01-25 20:03:26,178] [INFO] Target genome list was writen to GCF_003967535.1_ASM396753v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:26,191] [INFO] Task started: fastANI
[2024-01-25 20:03:26,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg1953d62c-204f-46a4-ab72-3ece83eadbfe/GCF_003967535.1_ASM396753v1_genomic.fna.gz --refList GCF_003967535.1_ASM396753v1_genomic.fna/target_genomes.txt --output GCF_003967535.1_ASM396753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:46,006] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:46,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8de2042-7c7e-47fd-ba9a-4499a3291f27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:46,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8de2042-7c7e-47fd-ba9a-4499a3291f27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:46,014] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:46,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:46,015] [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
Tengunoibacter tsumagoiensis	strain=Uno3	GCA_003967535.1	2014871	2014871	type	True	100.0	2561	2565	95	conclusive
Ktedonobacter robiniae	strain=SOSP1-30	GCA_016587375.1	2778365	2778365	type	True	78.1206	191	2565	95	below_threshold
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	78.0977	207	2565	95	below_threshold
Ktedonobacter racemifer	strain=SOSP1-21	GCA_000178855.1	363277	363277	type	True	77.8736	194	2565	95	below_threshold
Dictyobacter formicarum	strain=SOSP1-9	GCA_016587435.1	2778368	2778368	type	True	77.7955	209	2565	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	77.7938	211	2565	95	below_threshold
Dictyobacter alpinus	strain=Uno16	GCA_003967575.1	2014873	2014873	type	True	77.7825	236	2565	95	below_threshold
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	77.54	228	2565	95	below_threshold
Ktedonosporobacter rubrisoli	strain=SCAWS-G2	GCA_004208415.1	2509675	2509675	type	True	77.3047	159	2565	95	below_threshold
Dictyobacter arantiisoli	strain=Uno17	GCA_008326305.1	2014874	2014874	type	True	77.2241	198	2565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:46,016] [INFO] DFAST Taxonomy check result was written to GCF_003967535.1_ASM396753v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:46,017] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:46,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:46,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8de2042-7c7e-47fd-ba9a-4499a3291f27/dqc_reference/checkm_data
[2024-01-25 20:03:46,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:46,089] [INFO] Task started: CheckM
[2024-01-25 20:03:46,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003967535.1_ASM396753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003967535.1_ASM396753v1_genomic.fna/checkm_input GCF_003967535.1_ASM396753v1_genomic.fna/checkm_result
[2024-01-25 20:04:44,969] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:44,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:44,990] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:44,991] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:44,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003967535.1_ASM396753v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:44,992] [INFO] Task started: Blastn
[2024-01-25 20:04:44,992] [INFO] Running command: blastn -query GCF_003967535.1_ASM396753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8de2042-7c7e-47fd-ba9a-4499a3291f27/dqc_reference/reference_markers_gtdb.fasta -out GCF_003967535.1_ASM396753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:45,719] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:45,722] [INFO] Selected 21 target genomes.
[2024-01-25 20:04:45,722] [INFO] Target genome list was writen to GCF_003967535.1_ASM396753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:45,745] [INFO] Task started: fastANI
[2024-01-25 20:04:45,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg1953d62c-204f-46a4-ab72-3ece83eadbfe/GCF_003967535.1_ASM396753v1_genomic.fna.gz --refList GCF_003967535.1_ASM396753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003967535.1_ASM396753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:15,747] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:15,754] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:15,755] [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_003967535.1	s__Tengunoibacter tsumagoiensis	100.0	2554	2565	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Tengunoibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016587375.1	s__Ktedonobacter sp016587375	78.2415	192	2565	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	77.8732	210	2565	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	77.8183	204	2565	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178855.1	s__Ktedonobacter racemifer	77.7913	193	2565	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016587355.1	s__Ktedonobacter sp016587355	77.7535	159	2565	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967515.1	s__Dictyobacter aurantiacus	77.752	210	2565	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	77.6125	230	2565	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208415.1	s__Ktedonosporobacter rubrisoli	77.2469	158	2565	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008326305.1	s__Dictyobacter sp008326305	77.2255	198	2565	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881495.1	s__UBA11361 sp005881495	76.3351	69	2565	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:15,756] [INFO] GTDB search result was written to GCF_003967535.1_ASM396753v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:15,757] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:15,759] [INFO] DFAST_QC result json was written to GCF_003967535.1_ASM396753v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:15,759] [INFO] DFAST_QC completed!
[2024-01-25 20:05:15,760] [INFO] Total running time: 0h2m10s