[2024-01-24 15:26:37,211] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:37,214] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:37,214] [INFO] DQC Reference Directory: /var/lib/cwl/stgf322b163-4326-4442-81fa-9dba0c75118f/dqc_reference
[2024-01-24 15:26:39,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,066] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg87180d92-b38a-4019-b050-d34943bd6c6a/GCF_004365885.1_ASM436588v1_genomic.fna.gz | prodigal -d GCF_004365885.1_ASM436588v1_genomic.fna/cds.fna -a GCF_004365885.1_ASM436588v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:52,247] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:52,247] [INFO] Task started: HMMsearch
[2024-01-24 15:26:52,247] [INFO] Running command: hmmsearch --tblout GCF_004365885.1_ASM436588v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf322b163-4326-4442-81fa-9dba0c75118f/dqc_reference/reference_markers.hmm GCF_004365885.1_ASM436588v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:52,569] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:52,571] [INFO] Found 6/6 markers.
[2024-01-24 15:26:52,615] [INFO] Query marker FASTA was written to GCF_004365885.1_ASM436588v1_genomic.fna/markers.fasta
[2024-01-24 15:26:52,615] [INFO] Task started: Blastn
[2024-01-24 15:26:52,616] [INFO] Running command: blastn -query GCF_004365885.1_ASM436588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf322b163-4326-4442-81fa-9dba0c75118f/dqc_reference/reference_markers.fasta -out GCF_004365885.1_ASM436588v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:53,514] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:53,519] [INFO] Selected 11 target genomes.
[2024-01-24 15:26:53,520] [INFO] Target genome list was writen to GCF_004365885.1_ASM436588v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:53,525] [INFO] Task started: fastANI
[2024-01-24 15:26:53,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg87180d92-b38a-4019-b050-d34943bd6c6a/GCF_004365885.1_ASM436588v1_genomic.fna.gz --refList GCF_004365885.1_ASM436588v1_genomic.fna/target_genomes.txt --output GCF_004365885.1_ASM436588v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:02,291] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:02,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf322b163-4326-4442-81fa-9dba0c75118f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:02,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf322b163-4326-4442-81fa-9dba0c75118f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:02,301] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:27:02,301] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:27:02,302] [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
Rhodobaca barguzinensis	strain=DSM 19920	GCA_004365885.1	441209	441209	suspected-type	True	100.0	1275	1276	95	inconclusive
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	99.9966	1276	1276	95	inconclusive
Rhodobaca bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	99.9912	1268	1276	95	inconclusive
Rhodobaca bogoriensis	strain=LBB1	GCA_014197665.1	119542	119542	suspected-type	True	99.9908	1268	1276	95	inconclusive
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	82.4686	792	1276	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.3087	387	1276	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.0551	209	1276	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.0421	210	1276	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.9492	232	1276	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	76.8227	216	1276	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.6485	203	1276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:02,303] [INFO] DFAST Taxonomy check result was written to GCF_004365885.1_ASM436588v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:02,304] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:02,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:02,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf322b163-4326-4442-81fa-9dba0c75118f/dqc_reference/checkm_data
[2024-01-24 15:27:02,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:02,349] [INFO] Task started: CheckM
[2024-01-24 15:27:02,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365885.1_ASM436588v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365885.1_ASM436588v1_genomic.fna/checkm_input GCF_004365885.1_ASM436588v1_genomic.fna/checkm_result
[2024-01-24 15:27:44,031] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:44,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:44,054] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:44,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:44,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365885.1_ASM436588v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:44,055] [INFO] Task started: Blastn
[2024-01-24 15:27:44,055] [INFO] Running command: blastn -query GCF_004365885.1_ASM436588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf322b163-4326-4442-81fa-9dba0c75118f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365885.1_ASM436588v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:45,563] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:45,566] [INFO] Selected 11 target genomes.
[2024-01-24 15:27:45,566] [INFO] Target genome list was writen to GCF_004365885.1_ASM436588v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:45,575] [INFO] Task started: fastANI
[2024-01-24 15:27:45,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg87180d92-b38a-4019-b050-d34943bd6c6a/GCF_004365885.1_ASM436588v1_genomic.fna.gz --refList GCF_004365885.1_ASM436588v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365885.1_ASM436588v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:54,015] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:54,035] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:54,036] [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_004366635.1	s__Roseinatronobacter bogoriensis	99.9912	1268	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	100.00	99.99	0.99	0.99	4	conclusive
GCA_007126715.1	s__Roseinatronobacter sp007126715	86.7709	794	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.26	99.26	0.87	0.87	2	-
GCF_001870675.1	s__Roseinatronobacter thiooxidans	82.4586	793	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	97.65	95.32	0.95	0.92	3	-
GCF_006716865.1	s__Roseinatronobacter monicus	81.9634	795	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	95.80	95.17	0.91	0.77	10	-
GCF_001884735.1	s__Roseinatronobacter thiooxidans_A	79.6967	585	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118295.1	s__Roseinatronobacter sp007118295	79.6866	487	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.27	99.27	0.83	0.83	2	-
GCA_003561595.1	s__Roseinatronobacter sp003561595	79.2991	441	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	98.99	98.90	0.87	0.78	5	-
GCA_007116445.1	s__Roseinatronobacter sp007116445	78.704	299	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517585.1	s__Roseinatronobacter calidilacus	78.6703	449	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000176015.1	s__Pseudorhodobacter_B sp000176015	76.5809	193	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	76.461	159	1276	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:54,038] [INFO] GTDB search result was written to GCF_004365885.1_ASM436588v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:54,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:54,042] [INFO] DFAST_QC result json was written to GCF_004365885.1_ASM436588v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:54,042] [INFO] DFAST_QC completed!
[2024-01-24 15:27:54,042] [INFO] Total running time: 0h1m17s