[2024-01-24 12:31:58,189] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,192] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dd6d251-48c8-4561-8f39-3b2d86603088/dqc_reference
[2024-01-24 12:31:59,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,712] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,712] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6ebdfd7-2a94-4497-a880-afe898bd7e2b/GCF_003050705.1_ASM305070v1_genomic.fna.gz | prodigal -d GCF_003050705.1_ASM305070v1_genomic.fna/cds.fna -a GCF_003050705.1_ASM305070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:12,748] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:12,748] [INFO] Task started: HMMsearch
[2024-01-24 12:32:12,748] [INFO] Running command: hmmsearch --tblout GCF_003050705.1_ASM305070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dd6d251-48c8-4561-8f39-3b2d86603088/dqc_reference/reference_markers.hmm GCF_003050705.1_ASM305070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:13,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:13,079] [INFO] Found 6/6 markers.
[2024-01-24 12:32:13,118] [INFO] Query marker FASTA was written to GCF_003050705.1_ASM305070v1_genomic.fna/markers.fasta
[2024-01-24 12:32:13,119] [INFO] Task started: Blastn
[2024-01-24 12:32:13,119] [INFO] Running command: blastn -query GCF_003050705.1_ASM305070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dd6d251-48c8-4561-8f39-3b2d86603088/dqc_reference/reference_markers.fasta -out GCF_003050705.1_ASM305070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:14,048] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:14,055] [INFO] Selected 15 target genomes.
[2024-01-24 12:32:14,055] [INFO] Target genome list was writen to GCF_003050705.1_ASM305070v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:14,060] [INFO] Task started: fastANI
[2024-01-24 12:32:14,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6ebdfd7-2a94-4497-a880-afe898bd7e2b/GCF_003050705.1_ASM305070v1_genomic.fna.gz --refList GCF_003050705.1_ASM305070v1_genomic.fna/target_genomes.txt --output GCF_003050705.1_ASM305070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:29,116] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:29,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dd6d251-48c8-4561-8f39-3b2d86603088/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:29,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dd6d251-48c8-4561-8f39-3b2d86603088/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:29,130] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:29,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:29,130] [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 aurantiaca	strain=MA101b	GCA_003050705.1	185949	185949	type	True	100.0	1463	1463	95	conclusive
Sphingomonas albertensis	strain=DOAB 1063	GCA_014358075.1	2762591	2762591	type	True	87.9695	946	1463	95	below_threshold
Sphingomonas faeni	strain=MA-olki	GCA_003053745.1	185950	185950	type	True	87.5289	985	1463	95	below_threshold
Sphingomonas aerolata	strain=NW12	GCA_003046295.1	185951	185951	type	True	85.7661	870	1463	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	84.1538	820	1463	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	80.5207	644	1463	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.8687	669	1463	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.7811	641	1463	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.7717	673	1463	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.49	584	1463	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.322	607	1463	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.9946	381	1463	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	77.5262	238	1463	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	76.0969	127	1463	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	75.9233	146	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:29,132] [INFO] DFAST Taxonomy check result was written to GCF_003050705.1_ASM305070v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:29,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:29,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:29,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dd6d251-48c8-4561-8f39-3b2d86603088/dqc_reference/checkm_data
[2024-01-24 12:32:29,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:29,179] [INFO] Task started: CheckM
[2024-01-24 12:32:29,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003050705.1_ASM305070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003050705.1_ASM305070v1_genomic.fna/checkm_input GCF_003050705.1_ASM305070v1_genomic.fna/checkm_result
[2024-01-24 12:33:08,351] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:08,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:08,377] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:08,378] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:08,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003050705.1_ASM305070v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:08,379] [INFO] Task started: Blastn
[2024-01-24 12:33:08,379] [INFO] Running command: blastn -query GCF_003050705.1_ASM305070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dd6d251-48c8-4561-8f39-3b2d86603088/dqc_reference/reference_markers_gtdb.fasta -out GCF_003050705.1_ASM305070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:09,947] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:09,951] [INFO] Selected 15 target genomes.
[2024-01-24 12:33:09,951] [INFO] Target genome list was writen to GCF_003050705.1_ASM305070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:09,960] [INFO] Task started: fastANI
[2024-01-24 12:33:09,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6ebdfd7-2a94-4497-a880-afe898bd7e2b/GCF_003050705.1_ASM305070v1_genomic.fna.gz --refList GCF_003050705.1_ASM305070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003050705.1_ASM305070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:26,826] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:26,843] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:26,844] [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_003050705.1	s__Sphingomonas aurantiaca	100.0	1463	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.29	95.02	0.87	0.86	4	conclusive
GCF_001421805.1	s__Sphingomonas sp001421805	90.8332	1009	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.24	98.24	0.93	0.93	2	-
GCF_013374115.1	s__Sphingomonas sp013374115	88.6422	940	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340945.1	s__Sphingomonas sp004340945	88.1926	1053	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.25	95.25	0.84	0.84	2	-
GCF_004101245.1	s__Sphingomonas sp004101245	88.0054	974	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014358075.1	s__Sphingomonas albertensis	87.9225	950	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115295.1	s__Sphingomonas sp900115295	87.649	988	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050745.1	s__Sphingomonas sp003050745	87.6436	958	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.19	95.12	0.89	0.88	3	-
GCF_004795835.1	s__Sphingomonas sp004795835	87.4357	949	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421415.1	s__Sphingomonas sp001421415	87.4138	965	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422045.1	s__Sphingomonas sp001422045	87.4023	949	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421535.1	s__Sphingomonas sp001421535	85.8267	890	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046295.1	s__Sphingomonas aerolata	85.7663	870	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.52	96.36	0.90	0.73	15	-
GCF_016743815.1	s__Sphingomonas sp016743815	79.4904	578	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314325.1	s__Sphingopyxis macrogoltabida	77.8305	406	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:26,846] [INFO] GTDB search result was written to GCF_003050705.1_ASM305070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:26,847] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:26,853] [INFO] DFAST_QC result json was written to GCF_003050705.1_ASM305070v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:26,853] [INFO] DFAST_QC completed!
[2024-01-24 12:33:26,853] [INFO] Total running time: 0h1m29s