[2024-01-24 14:28:02,238] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f39733b-1ba1-41a7-9271-9cdbcd0a014c/dqc_reference
[2024-01-24 14:28:03,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:03,519] [INFO] Task started: Prodigal
[2024-01-24 14:28:03,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg71ded079-392a-46bc-b02c-45e55acfec07/GCF_008326305.1_ASM832630v1_genomic.fna.gz | prodigal -d GCF_008326305.1_ASM832630v1_genomic.fna/cds.fna -a GCF_008326305.1_ASM832630v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:23,298] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:23,299] [INFO] Task started: HMMsearch
[2024-01-24 14:28:23,299] [INFO] Running command: hmmsearch --tblout GCF_008326305.1_ASM832630v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f39733b-1ba1-41a7-9271-9cdbcd0a014c/dqc_reference/reference_markers.hmm GCF_008326305.1_ASM832630v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:23,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:23,772] [INFO] Found 6/6 markers.
[2024-01-24 14:28:23,829] [INFO] Query marker FASTA was written to GCF_008326305.1_ASM832630v1_genomic.fna/markers.fasta
[2024-01-24 14:28:23,830] [INFO] Task started: Blastn
[2024-01-24 14:28:23,830] [INFO] Running command: blastn -query GCF_008326305.1_ASM832630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f39733b-1ba1-41a7-9271-9cdbcd0a014c/dqc_reference/reference_markers.fasta -out GCF_008326305.1_ASM832630v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:24,458] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:24,464] [INFO] Selected 13 target genomes.
[2024-01-24 14:28:24,464] [INFO] Target genome list was writen to GCF_008326305.1_ASM832630v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:24,479] [INFO] Task started: fastANI
[2024-01-24 14:28:24,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg71ded079-392a-46bc-b02c-45e55acfec07/GCF_008326305.1_ASM832630v1_genomic.fna.gz --refList GCF_008326305.1_ASM832630v1_genomic.fna/target_genomes.txt --output GCF_008326305.1_ASM832630v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:41,627] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:41,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f39733b-1ba1-41a7-9271-9cdbcd0a014c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:41,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f39733b-1ba1-41a7-9271-9cdbcd0a014c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:41,635] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:41,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:41,636] [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 arantiisoli	strain=Uno17	GCA_008326305.1	2014874	2014874	type	True	100.0	2252	2265	95	conclusive
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	78.4102	501	2265	95	below_threshold
Dictyobacter formicarum	strain=SOSP1-9	GCA_016587435.1	2778368	2778368	type	True	78.2749	458	2265	95	below_threshold
Ktedonobacter robiniae	strain=SOSP1-30	GCA_016587375.1	2778365	2778365	type	True	78.2117	213	2265	95	below_threshold
Dictyobacter alpinus	strain=Uno16	GCA_003967575.1	2014873	2014873	type	True	77.9639	467	2265	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	77.7663	425	2265	95	below_threshold
Tengunoibacter tsumagoiensis	strain=Uno3	GCA_003967535.1	2014871	2014871	type	True	77.3212	194	2265	95	below_threshold
Thermogemmatispora carboxidivorans	strain=PM5	GCA_000702505.1	1382306	1382306	type	True	75.5251	50	2265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:41,637] [INFO] DFAST Taxonomy check result was written to GCF_008326305.1_ASM832630v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:41,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:41,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:41,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f39733b-1ba1-41a7-9271-9cdbcd0a014c/dqc_reference/checkm_data
[2024-01-24 14:28:41,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:41,710] [INFO] Task started: CheckM
[2024-01-24 14:28:41,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008326305.1_ASM832630v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008326305.1_ASM832630v1_genomic.fna/checkm_input GCF_008326305.1_ASM832630v1_genomic.fna/checkm_result
[2024-01-24 14:29:41,627] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:41,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:41,652] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:41,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:41,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008326305.1_ASM832630v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:41,653] [INFO] Task started: Blastn
[2024-01-24 14:29:41,653] [INFO] Running command: blastn -query GCF_008326305.1_ASM832630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f39733b-1ba1-41a7-9271-9cdbcd0a014c/dqc_reference/reference_markers_gtdb.fasta -out GCF_008326305.1_ASM832630v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:42,401] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:42,404] [INFO] Selected 15 target genomes.
[2024-01-24 14:29:42,404] [INFO] Target genome list was writen to GCF_008326305.1_ASM832630v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:42,465] [INFO] Task started: fastANI
[2024-01-24 14:29:42,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg71ded079-392a-46bc-b02c-45e55acfec07/GCF_008326305.1_ASM832630v1_genomic.fna.gz --refList GCF_008326305.1_ASM832630v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008326305.1_ASM832630v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:01,103] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:01,116] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:01,116] [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_008326305.1	s__Dictyobacter sp008326305	100.0	2252	2265	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_003967555.1	s__Dictyobacter kobayashii	78.4467	498	2265	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	78.3398	471	2265	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587375.1	s__Ktedonobacter sp016587375	78.28	214	2265	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	78.2654	459	2265	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	78.1857	310	2265	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	77.7509	425	2265	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	77.3212	194	2265	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Tengunoibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702505.1	s__Thermogemmatispora carboxidivorans	75.509	51	2265	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 14:30:01,118] [INFO] GTDB search result was written to GCF_008326305.1_ASM832630v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:01,119] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:01,124] [INFO] DFAST_QC result json was written to GCF_008326305.1_ASM832630v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:01,124] [INFO] DFAST_QC completed!
[2024-01-24 14:30:01,124] [INFO] Total running time: 0h1m59s