[2023-06-28 15:04:01,471] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:04:01,475] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:04:01,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg06ca2333-2e46-42bd-8f66-f6f2e46de736/dqc_reference
[2023-06-28 15:04:02,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:04:02,831] [INFO] Task started: Prodigal
[2023-06-28 15:04:02,831] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf17be4f-1c83-48d2-b317-27ae05379f20/GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna.gz | prodigal -d GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/cds.fna -a GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:04:11,799] [INFO] Task succeeded: Prodigal
[2023-06-28 15:04:11,799] [INFO] Task started: HMMsearch
[2023-06-28 15:04:11,800] [INFO] Running command: hmmsearch --tblout GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06ca2333-2e46-42bd-8f66-f6f2e46de736/dqc_reference/reference_markers.hmm GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:04:12,050] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:04:12,052] [INFO] Found 6/6 markers.
[2023-06-28 15:04:12,088] [INFO] Query marker FASTA was written to GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/markers.fasta
[2023-06-28 15:04:12,089] [INFO] Task started: Blastn
[2023-06-28 15:04:12,089] [INFO] Running command: blastn -query GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/markers.fasta -db /var/lib/cwl/stg06ca2333-2e46-42bd-8f66-f6f2e46de736/dqc_reference/reference_markers.fasta -out GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:04:13,092] [INFO] Task succeeded: Blastn
[2023-06-28 15:04:13,096] [INFO] Selected 14 target genomes.
[2023-06-28 15:04:13,097] [INFO] Target genome list was writen to GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/target_genomes.txt
[2023-06-28 15:04:13,098] [INFO] Task started: fastANI
[2023-06-28 15:04:13,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf17be4f-1c83-48d2-b317-27ae05379f20/GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna.gz --refList GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/target_genomes.txt --output GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:04:26,075] [INFO] Task succeeded: fastANI
[2023-06-28 15:04:26,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06ca2333-2e46-42bd-8f66-f6f2e46de736/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:04:26,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06ca2333-2e46-42bd-8f66-f6f2e46de736/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:04:26,098] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:04:26,098] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 15:04:26,099] [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 sanguinis	strain=NBRC 13937	GCA_001591005.1	33051	33051	suspected-type	True	94.583	906	1055	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_014199595.1	172044	172044	type	True	89.0562	818	1055	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	89.047	825	1055	95	below_threshold
Sphingomonas parapaucimobilis	strain=NBRC 15100	GCA_000787715.1	28213	28213	type	True	88.7624	791	1055	95	below_threshold
Sphingomonas zeae	strain=DSM 100049	GCA_014197135.1	1646122	1646122	type	True	87.5733	805	1055	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	87.5525	807	1055	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	87.4047	819	1055	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	86.8321	779	1055	95	below_threshold
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	86.7903	808	1055	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.7434	496	1055	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.4904	505	1055	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.3708	515	1055	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.2933	515	1055	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.1811	518	1055	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:04:26,101] [INFO] DFAST Taxonomy check result was written to GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/tc_result.tsv
[2023-06-28 15:04:26,102] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:04:26,102] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:04:26,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06ca2333-2e46-42bd-8f66-f6f2e46de736/dqc_reference/checkm_data
[2023-06-28 15:04:26,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:04:26,144] [INFO] Task started: CheckM
[2023-06-28 15:04:26,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/checkm_input GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/checkm_result
[2023-06-28 15:04:56,645] [INFO] Task succeeded: CheckM
[2023-06-28 15:04:56,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:04:56,666] [INFO] ===== Completeness check finished =====
[2023-06-28 15:04:56,666] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:04:56,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/markers.fasta)
[2023-06-28 15:04:56,667] [INFO] Task started: Blastn
[2023-06-28 15:04:56,667] [INFO] Running command: blastn -query GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/markers.fasta -db /var/lib/cwl/stg06ca2333-2e46-42bd-8f66-f6f2e46de736/dqc_reference/reference_markers_gtdb.fasta -out GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:04:58,587] [INFO] Task succeeded: Blastn
[2023-06-28 15:04:58,592] [INFO] Selected 9 target genomes.
[2023-06-28 15:04:58,592] [INFO] Target genome list was writen to GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:04:58,593] [INFO] Task started: fastANI
[2023-06-28 15:04:58,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf17be4f-1c83-48d2-b317-27ae05379f20/GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna.gz --refList GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/target_genomes_gtdb.txt --output GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:05:07,694] [INFO] Task succeeded: fastANI
[2023-06-28 15:05:07,710] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 15:05:07,710] [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_001476905.1	s__Sphingomonas sanguinis_B	96.0766	918	1055	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	conclusive
GCF_001591005.1	s__Sphingomonas sanguinis	94.5878	905	1055	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.09	96.84	0.89	0.83	8	-
GCF_014199595.1	s__Sphingomonas yabuuchiae	89.0562	818	1055	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.94	96.78	0.92	0.88	4	-
GCF_001477495.1	s__Sphingomonas yabuuchiae_A	88.9928	779	1055	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787715.1	s__Sphingomonas parapaucimobilis	88.7757	791	1055	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.90	97.90	0.87	0.87	2	-
GCA_019112965.1	s__Sphingomonas excrementigallinarum	88.5105	762	1055	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197135.1	s__Sphingomonas zeae	87.5732	805	1055	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	87.4303	817	1055	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000739895.2	s__Sphingomonas paucimobilis	86.8002	781	1055	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	-
--------------------------------------------------------------------------------
[2023-06-28 15:05:07,712] [INFO] GTDB search result was written to GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/result_gtdb.tsv
[2023-06-28 15:05:07,712] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:05:07,716] [INFO] DFAST_QC result json was written to GCA_913773755.1_SP237_1_metabat2_genome_mining.5_genomic.fna/dqc_result.json
[2023-06-28 15:05:07,716] [INFO] DFAST_QC completed!
[2023-06-28 15:05:07,716] [INFO] Total running time: 0h1m6s