[2024-01-25 20:05:35,651] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:35,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:35,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c239e82-39e2-4578-8e37-c29f055022d4/dqc_reference
[2024-01-25 20:05:36,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:36,824] [INFO] Task started: Prodigal
[2024-01-25 20:05:36,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bcd0795-519d-4b37-9406-7e80f1f56fed/GCF_020866845.1_ASM2086684v1_genomic.fna.gz | prodigal -d GCF_020866845.1_ASM2086684v1_genomic.fna/cds.fna -a GCF_020866845.1_ASM2086684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:46,583] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:46,583] [INFO] Task started: HMMsearch
[2024-01-25 20:05:46,583] [INFO] Running command: hmmsearch --tblout GCF_020866845.1_ASM2086684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c239e82-39e2-4578-8e37-c29f055022d4/dqc_reference/reference_markers.hmm GCF_020866845.1_ASM2086684v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:46,805] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:46,806] [INFO] Found 6/6 markers.
[2024-01-25 20:05:46,836] [INFO] Query marker FASTA was written to GCF_020866845.1_ASM2086684v1_genomic.fna/markers.fasta
[2024-01-25 20:05:46,837] [INFO] Task started: Blastn
[2024-01-25 20:05:46,837] [INFO] Running command: blastn -query GCF_020866845.1_ASM2086684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c239e82-39e2-4578-8e37-c29f055022d4/dqc_reference/reference_markers.fasta -out GCF_020866845.1_ASM2086684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:47,806] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:47,809] [INFO] Selected 14 target genomes.
[2024-01-25 20:05:47,809] [INFO] Target genome list was writen to GCF_020866845.1_ASM2086684v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:47,824] [INFO] Task started: fastANI
[2024-01-25 20:05:47,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bcd0795-519d-4b37-9406-7e80f1f56fed/GCF_020866845.1_ASM2086684v1_genomic.fna.gz --refList GCF_020866845.1_ASM2086684v1_genomic.fna/target_genomes.txt --output GCF_020866845.1_ASM2086684v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:00,311] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:00,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c239e82-39e2-4578-8e37-c29f055022d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:00,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c239e82-39e2-4578-8e37-c29f055022d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:00,324] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:06:00,324] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:00,324] [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
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	100.0	1226	1226	95	conclusive
Sphingomonas jeddahensis	strain=G39	GCA_001981525.1	1915074	1915074	type	True	81.9346	661	1226	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	81.7334	671	1226	95	below_threshold
Sphingomonas mucosissima	strain=DSM 17494	GCA_002197665.1	370959	370959	type	True	81.1487	621	1226	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	80.0745	575	1226	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	80.0062	546	1226	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.8983	553	1226	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.8418	585	1226	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.6754	587	1226	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.6338	600	1226	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.5253	585	1226	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	79.3978	540	1226	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.3107	486	1226	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	77.8726	361	1226	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:00,325] [INFO] DFAST Taxonomy check result was written to GCF_020866845.1_ASM2086684v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:00,326] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:00,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:00,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c239e82-39e2-4578-8e37-c29f055022d4/dqc_reference/checkm_data
[2024-01-25 20:06:00,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:00,369] [INFO] Task started: CheckM
[2024-01-25 20:06:00,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020866845.1_ASM2086684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020866845.1_ASM2086684v1_genomic.fna/checkm_input GCF_020866845.1_ASM2086684v1_genomic.fna/checkm_result
[2024-01-25 20:06:31,005] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:31,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:31,025] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:31,026] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:31,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020866845.1_ASM2086684v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:31,027] [INFO] Task started: Blastn
[2024-01-25 20:06:31,027] [INFO] Running command: blastn -query GCF_020866845.1_ASM2086684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c239e82-39e2-4578-8e37-c29f055022d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_020866845.1_ASM2086684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:33,020] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:33,024] [INFO] Selected 14 target genomes.
[2024-01-25 20:06:33,024] [INFO] Target genome list was writen to GCF_020866845.1_ASM2086684v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:33,041] [INFO] Task started: fastANI
[2024-01-25 20:06:33,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bcd0795-519d-4b37-9406-7e80f1f56fed/GCF_020866845.1_ASM2086684v1_genomic.fna.gz --refList GCF_020866845.1_ASM2086684v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020866845.1_ASM2086684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:44,516] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:44,525] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:06:44,525] [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_014217605.1	s__Sphingomonas sp014217605	83.2384	746	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117915.1	s__Sphingomonas sp002117915	83.0777	751	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001981525.1	s__Sphingomonas jeddahensis	81.94	660	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980895.1	s__Sphingomonas olei	81.7335	651	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.98	97.88	0.87	0.83	3	-
GCF_002197685.1	s__Sphingomonas dokdonensis	81.7267	671	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109205.1	s__Sphingomonas sp900109205	81.1678	600	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.87	0.87	2	-
GCF_002197665.1	s__Sphingomonas mucosissima	81.138	622	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	80.5085	582	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_014204695.1	s__Sphingomonas sp001897045	80.483	618	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_013344685.1	s__Sphingomonas sp013344685	80.3734	592	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002374835.1	s__Sphingomonas ginsenosidimutans	80.0728	574	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.62	98.43	0.85	0.81	6	-
GCF_902506455.1	s__Sphingomonas sp902506455	79.8384	520	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	79.4686	586	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_014641735.1	s__Sphingomonas metalli	79.3375	484	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:44,527] [INFO] GTDB search result was written to GCF_020866845.1_ASM2086684v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:44,527] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:44,530] [INFO] DFAST_QC result json was written to GCF_020866845.1_ASM2086684v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:44,531] [INFO] DFAST_QC completed!
[2024-01-25 20:06:44,531] [INFO] Total running time: 0h1m9s