[2024-01-24 14:22:32,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:32,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:32,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg14ecdd20-ef12-49f7-95d0-f9684b6a9883/dqc_reference
[2024-01-24 14:22:33,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:33,714] [INFO] Task started: Prodigal
[2024-01-24 14:22:33,714] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a761549-2c1e-4589-a7ee-77c354c20f5c/GCF_016587455.1_ASM1658745v1_genomic.fna.gz | prodigal -d GCF_016587455.1_ASM1658745v1_genomic.fna/cds.fna -a GCF_016587455.1_ASM1658745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:11,864] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:11,864] [INFO] Task started: HMMsearch
[2024-01-24 14:23:11,864] [INFO] Running command: hmmsearch --tblout GCF_016587455.1_ASM1658745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14ecdd20-ef12-49f7-95d0-f9684b6a9883/dqc_reference/reference_markers.hmm GCF_016587455.1_ASM1658745v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:12,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:12,352] [INFO] Found 6/6 markers.
[2024-01-24 14:23:12,446] [INFO] Query marker FASTA was written to GCF_016587455.1_ASM1658745v1_genomic.fna/markers.fasta
[2024-01-24 14:23:12,446] [INFO] Task started: Blastn
[2024-01-24 14:23:12,447] [INFO] Running command: blastn -query GCF_016587455.1_ASM1658745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14ecdd20-ef12-49f7-95d0-f9684b6a9883/dqc_reference/reference_markers.fasta -out GCF_016587455.1_ASM1658745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:13,057] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:13,060] [INFO] Selected 24 target genomes.
[2024-01-24 14:23:13,061] [INFO] Target genome list was writen to GCF_016587455.1_ASM1658745v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:13,075] [INFO] Task started: fastANI
[2024-01-24 14:23:13,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a761549-2c1e-4589-a7ee-77c354c20f5c/GCF_016587455.1_ASM1658745v1_genomic.fna.gz --refList GCF_016587455.1_ASM1658745v1_genomic.fna/target_genomes.txt --output GCF_016587455.1_ASM1658745v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:41,244] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:41,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14ecdd20-ef12-49f7-95d0-f9684b6a9883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:41,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14ecdd20-ef12-49f7-95d0-f9684b6a9883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:41,266] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:41,266] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:41,267] [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
Reticulibacter mediterranei	strain=150040	GCA_016587455.1	2778369	2778369	type	True	100.0	4215	4221	95	conclusive
Ktedonobacter robiniae	strain=SOSP1-30	GCA_016587375.1	2778365	2778365	type	True	78.6209	384	4221	95	below_threshold
Ktedonobacter racemifer	strain=SOSP1-21	GCA_000178855.1	363277	363277	type	True	78.3506	438	4221	95	below_threshold
Ktedonosporobacter rubrisoli	strain=SCAWS-G2	GCA_004208415.1	2509675	2509675	type	True	78.0741	335	4221	95	below_threshold
Dictyobacter formicarum	strain=SOSP1-9	GCA_016587435.1	2778368	2778368	type	True	77.976	281	4221	95	below_threshold
Dictyobacter arantiisoli	strain=Uno17	GCA_008326305.1	2014874	2014874	type	True	77.6147	182	4221	95	below_threshold
Dictyobacter alpinus	strain=Uno16	GCA_003967575.1	2014873	2014873	type	True	77.468	192	4221	95	below_threshold
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	77.4319	194	4221	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	77.423	246	4221	95	below_threshold
Thermogemmatispora tikiterensis	strain=T81	GCA_003268475.1	1825093	1825093	type	True	75.7026	79	4221	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:41,269] [INFO] DFAST Taxonomy check result was written to GCF_016587455.1_ASM1658745v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:41,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:41,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:41,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14ecdd20-ef12-49f7-95d0-f9684b6a9883/dqc_reference/checkm_data
[2024-01-24 14:23:41,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:41,385] [INFO] Task started: CheckM
[2024-01-24 14:23:41,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016587455.1_ASM1658745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016587455.1_ASM1658745v1_genomic.fna/checkm_input GCF_016587455.1_ASM1658745v1_genomic.fna/checkm_result
[2024-01-24 14:25:29,134] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:29,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 11.57%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:29,170] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:29,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:29,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016587455.1_ASM1658745v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:29,171] [INFO] Task started: Blastn
[2024-01-24 14:25:29,171] [INFO] Running command: blastn -query GCF_016587455.1_ASM1658745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14ecdd20-ef12-49f7-95d0-f9684b6a9883/dqc_reference/reference_markers_gtdb.fasta -out GCF_016587455.1_ASM1658745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:30,008] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:30,013] [INFO] Selected 42 target genomes.
[2024-01-24 14:25:30,013] [INFO] Target genome list was writen to GCF_016587455.1_ASM1658745v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:30,088] [INFO] Task started: fastANI
[2024-01-24 14:25:30,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a761549-2c1e-4589-a7ee-77c354c20f5c/GCF_016587455.1_ASM1658745v1_genomic.fna.gz --refList GCF_016587455.1_ASM1658745v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016587455.1_ASM1658745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:06,600] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:06,693] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:26:06,694] [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_016587375.1	s__Ktedonobacter sp016587375	78.6815	387	4221	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	78.3065	436	4221	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	78.2617	359	4221	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208415.1	s__Ktedonosporobacter rubrisoli	78.0795	335	4221	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587435.1	s__Dictyobacter sp016587435	77.8874	278	4221	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	77.7156	198	4221	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	77.6322	182	4221	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	77.5352	197	4221	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	77.4263	245	4221	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881295.1	s__UBA11361 sp005881295	76.5811	75	4221	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	97.35	96.80	0.70	0.62	6	-
GCA_013695595.1	s__JACDAE01 sp013695595	76.4848	154	4221	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__JACDAE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253565.1	s__Thermosporothrix hazakensis	76.316	171	4221	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermosporothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881495.1	s__UBA11361 sp005881495	76.2376	119	4221	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389075.1	s__DTNP01 sp011389075	76.0588	132	4221	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__DTNP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812455.1	s__CADDZH01 sp902812455	75.7917	118	4221	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268475.1	s__Thermogemmatispora tikiterensis	75.7026	79	4221	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 14:26:06,696] [INFO] GTDB search result was written to GCF_016587455.1_ASM1658745v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:06,697] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:06,701] [INFO] DFAST_QC result json was written to GCF_016587455.1_ASM1658745v1_genomic.fna/dqc_result.json
[2024-01-24 14:26:06,702] [INFO] DFAST_QC completed!
[2024-01-24 14:26:06,702] [INFO] Total running time: 0h3m34s