[2024-01-24 13:40:25,155] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:25,157] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:25,157] [INFO] DQC Reference Directory: /var/lib/cwl/stg50134edf-601a-4cad-ba2c-c9dc70f6e152/dqc_reference
[2024-01-24 13:40:26,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:26,322] [INFO] Task started: Prodigal
[2024-01-24 13:40:26,323] [INFO] Running command: gunzip -c /var/lib/cwl/stge8fa71d4-7d9c-4191-86ef-a986eceee1a8/GCF_022664465.1_ASM2266446v1_genomic.fna.gz | prodigal -d GCF_022664465.1_ASM2266446v1_genomic.fna/cds.fna -a GCF_022664465.1_ASM2266446v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:37,807] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:37,808] [INFO] Task started: HMMsearch
[2024-01-24 13:40:37,808] [INFO] Running command: hmmsearch --tblout GCF_022664465.1_ASM2266446v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50134edf-601a-4cad-ba2c-c9dc70f6e152/dqc_reference/reference_markers.hmm GCF_022664465.1_ASM2266446v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:38,146] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:38,147] [INFO] Found 6/6 markers.
[2024-01-24 13:40:38,185] [INFO] Query marker FASTA was written to GCF_022664465.1_ASM2266446v1_genomic.fna/markers.fasta
[2024-01-24 13:40:38,186] [INFO] Task started: Blastn
[2024-01-24 13:40:38,186] [INFO] Running command: blastn -query GCF_022664465.1_ASM2266446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50134edf-601a-4cad-ba2c-c9dc70f6e152/dqc_reference/reference_markers.fasta -out GCF_022664465.1_ASM2266446v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:39,024] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:39,028] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:39,028] [INFO] Target genome list was writen to GCF_022664465.1_ASM2266446v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:39,049] [INFO] Task started: fastANI
[2024-01-24 13:40:39,049] [INFO] Running command: fastANI --query /var/lib/cwl/stge8fa71d4-7d9c-4191-86ef-a986eceee1a8/GCF_022664465.1_ASM2266446v1_genomic.fna.gz --refList GCF_022664465.1_ASM2266446v1_genomic.fna/target_genomes.txt --output GCF_022664465.1_ASM2266446v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:56,718] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:56,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50134edf-601a-4cad-ba2c-c9dc70f6e152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:56,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50134edf-601a-4cad-ba2c-c9dc70f6e152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:56,733] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:56,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:56,733] [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 hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	100.0	1302	1304	95	conclusive
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	87.7161	951	1304	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.9035	542	1304	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.8899	540	1304	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	79.8432	590	1304	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.6895	632	1304	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.6365	568	1304	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	79.5128	538	1304	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	79.494	603	1304	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	79.4355	606	1304	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	79.4127	589	1304	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	79.0109	575	1304	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.8306	555	1304	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.7852	579	1304	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	78.6009	560	1304	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	78.5478	412	1304	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.3103	482	1304	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	78.0275	308	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:56,735] [INFO] DFAST Taxonomy check result was written to GCF_022664465.1_ASM2266446v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:56,735] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:56,735] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:56,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50134edf-601a-4cad-ba2c-c9dc70f6e152/dqc_reference/checkm_data
[2024-01-24 13:40:56,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:56,780] [INFO] Task started: CheckM
[2024-01-24 13:40:56,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022664465.1_ASM2266446v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022664465.1_ASM2266446v1_genomic.fna/checkm_input GCF_022664465.1_ASM2266446v1_genomic.fna/checkm_result
[2024-01-24 13:41:35,192] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:35,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:35,212] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:35,213] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:35,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022664465.1_ASM2266446v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:35,214] [INFO] Task started: Blastn
[2024-01-24 13:41:35,214] [INFO] Running command: blastn -query GCF_022664465.1_ASM2266446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50134edf-601a-4cad-ba2c-c9dc70f6e152/dqc_reference/reference_markers_gtdb.fasta -out GCF_022664465.1_ASM2266446v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:36,582] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:36,586] [INFO] Selected 8 target genomes.
[2024-01-24 13:41:36,586] [INFO] Target genome list was writen to GCF_022664465.1_ASM2266446v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:36,596] [INFO] Task started: fastANI
[2024-01-24 13:41:36,597] [INFO] Running command: fastANI --query /var/lib/cwl/stge8fa71d4-7d9c-4191-86ef-a986eceee1a8/GCF_022664465.1_ASM2266446v1_genomic.fna.gz --refList GCF_022664465.1_ASM2266446v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022664465.1_ASM2266446v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:46,655] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:46,669] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:41:46,669] [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_003946805.1	s__Sphingomonas sp003946805	90.1726	970	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	89.6411	849	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001619955.1	s__Sphingomonas hankookensis	88.1408	963	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.49	99.35	0.90	0.87	3	-
GCF_001421355.1	s__Sphingomonas sp001421355	88.0305	967	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
GCF_001421765.1	s__Sphingomonas sp001421765	88.0243	986	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001421715.1	s__Sphingomonas sp001421715	86.9711	966	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.52	97.51	0.91	0.91	3	-
GCF_001421245.1	s__Sphingomonas sp001421245	86.9218	959	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421965.1	s__Sphingomonas sp001421965	86.6404	927	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.43	97.43	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:46,671] [INFO] GTDB search result was written to GCF_022664465.1_ASM2266446v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:46,672] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:46,682] [INFO] DFAST_QC result json was written to GCF_022664465.1_ASM2266446v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:46,682] [INFO] DFAST_QC completed!
[2024-01-24 13:41:46,683] [INFO] Total running time: 0h1m22s