[2024-01-24 13:12:38,755] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg7af6608f-5920-4b5f-a2c0-d353891029b3/dqc_reference
[2024-01-24 13:12:40,217] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,218] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,218] [INFO] Running command: gunzip -c /var/lib/cwl/stg61aacc24-939a-47fd-b60c-2a213cfe47ea/GCF_000739895.2_ASM73989v2_genomic.fna.gz | prodigal -d GCF_000739895.2_ASM73989v2_genomic.fna/cds.fna -a GCF_000739895.2_ASM73989v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:53,075] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:53,075] [INFO] Task started: HMMsearch
[2024-01-24 13:12:53,075] [INFO] Running command: hmmsearch --tblout GCF_000739895.2_ASM73989v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7af6608f-5920-4b5f-a2c0-d353891029b3/dqc_reference/reference_markers.hmm GCF_000739895.2_ASM73989v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:53,450] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:53,452] [INFO] Found 6/6 markers.
[2024-01-24 13:12:53,494] [INFO] Query marker FASTA was written to GCF_000739895.2_ASM73989v2_genomic.fna/markers.fasta
[2024-01-24 13:12:53,495] [INFO] Task started: Blastn
[2024-01-24 13:12:53,495] [INFO] Running command: blastn -query GCF_000739895.2_ASM73989v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7af6608f-5920-4b5f-a2c0-d353891029b3/dqc_reference/reference_markers.fasta -out GCF_000739895.2_ASM73989v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:54,755] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:54,758] [INFO] Selected 11 target genomes.
[2024-01-24 13:12:54,758] [INFO] Target genome list was writen to GCF_000739895.2_ASM73989v2_genomic.fna/target_genomes.txt
[2024-01-24 13:12:54,763] [INFO] Task started: fastANI
[2024-01-24 13:12:54,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg61aacc24-939a-47fd-b60c-2a213cfe47ea/GCF_000739895.2_ASM73989v2_genomic.fna.gz --refList GCF_000739895.2_ASM73989v2_genomic.fna/target_genomes.txt --output GCF_000739895.2_ASM73989v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:06,881] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:06,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7af6608f-5920-4b5f-a2c0-d353891029b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:06,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7af6608f-5920-4b5f-a2c0-d353891029b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:06,895] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:06,896] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:06,896] [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 paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	100.0	1390	1395	95	conclusive
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	99.9986	1393	1395	95	conclusive
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	89.2453	994	1395	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	89.2152	1005	1395	95	below_threshold
Sphingomonas sanguinis	strain=NBRC 13937	GCA_001591005.1	33051	33051	suspected-type	True	87.2229	910	1395	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	87.2218	965	1395	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.9563	588	1395	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.6651	593	1395	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.5804	594	1395	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.4981	577	1395	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.0831	506	1395	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:06,900] [INFO] DFAST Taxonomy check result was written to GCF_000739895.2_ASM73989v2_genomic.fna/tc_result.tsv
[2024-01-24 13:13:06,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:06,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:06,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7af6608f-5920-4b5f-a2c0-d353891029b3/dqc_reference/checkm_data
[2024-01-24 13:13:06,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:06,947] [INFO] Task started: CheckM
[2024-01-24 13:13:06,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000739895.2_ASM73989v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000739895.2_ASM73989v2_genomic.fna/checkm_input GCF_000739895.2_ASM73989v2_genomic.fna/checkm_result
[2024-01-24 13:13:47,354] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:47,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:47,376] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:47,376] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:47,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000739895.2_ASM73989v2_genomic.fna/markers.fasta)
[2024-01-24 13:13:47,377] [INFO] Task started: Blastn
[2024-01-24 13:13:47,377] [INFO] Running command: blastn -query GCF_000739895.2_ASM73989v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7af6608f-5920-4b5f-a2c0-d353891029b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000739895.2_ASM73989v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:49,235] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:49,240] [INFO] Selected 9 target genomes.
[2024-01-24 13:13:49,240] [INFO] Target genome list was writen to GCF_000739895.2_ASM73989v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:49,256] [INFO] Task started: fastANI
[2024-01-24 13:13:49,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg61aacc24-939a-47fd-b60c-2a213cfe47ea/GCF_000739895.2_ASM73989v2_genomic.fna.gz --refList GCF_000739895.2_ASM73989v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000739895.2_ASM73989v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:58,238] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:58,251] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:58,252] [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_000739895.2	s__Sphingomonas paucimobilis	100.0	1390	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	conclusive
GCF_014196255.1	s__Sphingomonas pseudosanguinis	89.2603	993	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000787715.1	s__Sphingomonas parapaucimobilis	87.367	876	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.90	97.90	0.87	0.87	2	-
GCF_014199595.1	s__Sphingomonas yabuuchiae	87.2606	950	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.94	96.78	0.92	0.88	4	-
GCF_001591005.1	s__Sphingomonas sanguinis	87.2511	908	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.09	96.84	0.89	0.83	8	-
GCF_014197135.1	s__Sphingomonas zeae	87.1522	933	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001477495.1	s__Sphingomonas yabuuchiae_A	87.094	853	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	86.9582	862	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCA_019112965.1	s__Sphingomonas excrementigallinarum	86.95	827	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:58,253] [INFO] GTDB search result was written to GCF_000739895.2_ASM73989v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:58,254] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:58,257] [INFO] DFAST_QC result json was written to GCF_000739895.2_ASM73989v2_genomic.fna/dqc_result.json
[2024-01-24 13:13:58,257] [INFO] DFAST_QC completed!
[2024-01-24 13:13:58,257] [INFO] Total running time: 0h1m20s