[2024-01-24 13:48:40,141] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:40,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:40,144] [INFO] DQC Reference Directory: /var/lib/cwl/stgc84b1db7-d432-4f9b-84bf-226dbe5478e2/dqc_reference
[2024-01-24 13:48:41,365] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:41,366] [INFO] Task started: Prodigal
[2024-01-24 13:48:41,366] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4275da7-d621-42c5-ae3f-afa22332fafb/GCF_000178855.1_ASM17885v1_genomic.fna.gz | prodigal -d GCF_000178855.1_ASM17885v1_genomic.fna/cds.fna -a GCF_000178855.1_ASM17885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:21,338] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:21,338] [INFO] Task started: HMMsearch
[2024-01-24 13:49:21,338] [INFO] Running command: hmmsearch --tblout GCF_000178855.1_ASM17885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc84b1db7-d432-4f9b-84bf-226dbe5478e2/dqc_reference/reference_markers.hmm GCF_000178855.1_ASM17885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:21,802] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:21,803] [INFO] Found 6/6 markers.
[2024-01-24 13:49:21,894] [INFO] Query marker FASTA was written to GCF_000178855.1_ASM17885v1_genomic.fna/markers.fasta
[2024-01-24 13:49:21,895] [INFO] Task started: Blastn
[2024-01-24 13:49:21,895] [INFO] Running command: blastn -query GCF_000178855.1_ASM17885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc84b1db7-d432-4f9b-84bf-226dbe5478e2/dqc_reference/reference_markers.fasta -out GCF_000178855.1_ASM17885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:22,530] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:22,534] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:22,535] [INFO] Target genome list was writen to GCF_000178855.1_ASM17885v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:22,543] [INFO] Task started: fastANI
[2024-01-24 13:49:22,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4275da7-d621-42c5-ae3f-afa22332fafb/GCF_000178855.1_ASM17885v1_genomic.fna.gz --refList GCF_000178855.1_ASM17885v1_genomic.fna/target_genomes.txt --output GCF_000178855.1_ASM17885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:59,952] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:59,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc84b1db7-d432-4f9b-84bf-226dbe5478e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:59,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc84b1db7-d432-4f9b-84bf-226dbe5478e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:59,972] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:59,973] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:59,973] [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
Ktedonobacter racemifer	strain=SOSP1-21	GCA_000178855.1	363277	363277	type	True	100.0	4549	4551	95	conclusive
Ktedonobacter robiniae	strain=SOSP1-30	GCA_016587375.1	2778365	2778365	type	True	92.2054	2627	4551	95	below_threshold
Dictyobacter formicarum	strain=SOSP1-9	GCA_016587435.1	2778368	2778368	type	True	80.6837	386	4551	95	below_threshold
Ktedonospora formicarum	strain=SOSP1-1	GCA_016587355.1	2778364	2778364	type	True	79.8074	968	4551	95	below_threshold
Reticulibacter mediterranei	strain=150040	GCA_016587455.1	2778369	2778369	type	True	78.4231	432	4551	95	below_threshold
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	78.118	242	4551	95	below_threshold
Tengunoibacter tsumagoiensis	strain=Uno3	GCA_003967535.1	2014871	2014871	type	True	78.0085	195	4551	95	below_threshold
Ktedonosporobacter rubrisoli	strain=SCAWS-G2	GCA_004208415.1	2509675	2509675	type	True	77.7648	272	4551	95	below_threshold
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	77.6931	232	4551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:59,975] [INFO] DFAST Taxonomy check result was written to GCF_000178855.1_ASM17885v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:59,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:59,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:59,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc84b1db7-d432-4f9b-84bf-226dbe5478e2/dqc_reference/checkm_data
[2024-01-24 13:49:59,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:00,106] [INFO] Task started: CheckM
[2024-01-24 13:50:00,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000178855.1_ASM17885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000178855.1_ASM17885v1_genomic.fna/checkm_input GCF_000178855.1_ASM17885v1_genomic.fna/checkm_result
[2024-01-24 13:51:49,002] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:49,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.48%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2024-01-24 13:51:49,039] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:49,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:49,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000178855.1_ASM17885v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:49,040] [INFO] Task started: Blastn
[2024-01-24 13:51:49,040] [INFO] Running command: blastn -query GCF_000178855.1_ASM17885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc84b1db7-d432-4f9b-84bf-226dbe5478e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000178855.1_ASM17885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:49,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:49,911] [INFO] Selected 14 target genomes.
[2024-01-24 13:51:49,911] [INFO] Target genome list was writen to GCF_000178855.1_ASM17885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:50,014] [INFO] Task started: fastANI
[2024-01-24 13:51:50,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4275da7-d621-42c5-ae3f-afa22332fafb/GCF_000178855.1_ASM17885v1_genomic.fna.gz --refList GCF_000178855.1_ASM17885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000178855.1_ASM17885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:22,093] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:22,109] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:22,109] [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_000178855.1	s__Ktedonobacter racemifer	100.0	4549	4551	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016587375.1	s__Ktedonobacter sp016587375	92.1766	2633	4551	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	92.1699	2707	4551	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	79.8321	967	4551	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967555.1	s__Dictyobacter kobayashii	78.1559	243	4551	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	77.8169	270	4551	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967535.1	s__Tengunoibacter tsumagoiensis	77.7842	194	4551	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Tengunoibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974265.1	s__Dictyobacter vulcani	77.7124	230	4551	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	76.937	71	4551	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	97.35	96.80	0.70	0.62	6	-
GCA_902810755.1	s__CADDYT01 sp902810755	76.1513	156	4551	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDYT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:22,111] [INFO] GTDB search result was written to GCF_000178855.1_ASM17885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:22,111] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:22,115] [INFO] DFAST_QC result json was written to GCF_000178855.1_ASM17885v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:22,116] [INFO] DFAST_QC completed!
[2024-01-24 13:52:22,116] [INFO] Total running time: 0h3m42s