[2024-01-24 14:46:57,167] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,169] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,169] [INFO] DQC Reference Directory: /var/lib/cwl/stga12b7713-c361-4934-8271-d1a3915bd723/dqc_reference
[2024-01-24 14:46:58,534] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,535] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,536] [INFO] Running command: gunzip -c /var/lib/cwl/stgd956aca0-4340-42cb-a626-a1d6b2293d06/GCF_004366635.1_ASM436663v1_genomic.fna.gz | prodigal -d GCF_004366635.1_ASM436663v1_genomic.fna/cds.fna -a GCF_004366635.1_ASM436663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:11,867] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:11,867] [INFO] Task started: HMMsearch
[2024-01-24 14:47:11,867] [INFO] Running command: hmmsearch --tblout GCF_004366635.1_ASM436663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga12b7713-c361-4934-8271-d1a3915bd723/dqc_reference/reference_markers.hmm GCF_004366635.1_ASM436663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:12,174] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:12,180] [INFO] Found 6/6 markers.
[2024-01-24 14:47:12,228] [INFO] Query marker FASTA was written to GCF_004366635.1_ASM436663v1_genomic.fna/markers.fasta
[2024-01-24 14:47:12,229] [INFO] Task started: Blastn
[2024-01-24 14:47:12,229] [INFO] Running command: blastn -query GCF_004366635.1_ASM436663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga12b7713-c361-4934-8271-d1a3915bd723/dqc_reference/reference_markers.fasta -out GCF_004366635.1_ASM436663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:13,217] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:13,220] [INFO] Selected 11 target genomes.
[2024-01-24 14:47:13,220] [INFO] Target genome list was writen to GCF_004366635.1_ASM436663v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:13,225] [INFO] Task started: fastANI
[2024-01-24 14:47:13,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgd956aca0-4340-42cb-a626-a1d6b2293d06/GCF_004366635.1_ASM436663v1_genomic.fna.gz --refList GCF_004366635.1_ASM436663v1_genomic.fna/target_genomes.txt --output GCF_004366635.1_ASM436663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:22,308] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:22,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga12b7713-c361-4934-8271-d1a3915bd723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:22,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga12b7713-c361-4934-8271-d1a3915bd723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:22,319] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:47:22,319] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:47:22,319] [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 bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	100.0	1287	1289	95	inconclusive
Rhodobaca bogoriensis	strain=LBB1	GCA_014197665.1	119542	119542	suspected-type	True	99.9973	1289	1289	95	inconclusive
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	99.9971	1277	1289	95	inconclusive
Rhodobaca barguzinensis	strain=DSM 19920	GCA_004365885.1	441209	441209	suspected-type	True	99.9927	1269	1289	95	inconclusive
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	82.4095	777	1289	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.256	380	1289	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.0822	204	1289	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.0701	205	1289	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.9199	195	1289	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.792	247	1289	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	76.6888	218	1289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:22,321] [INFO] DFAST Taxonomy check result was written to GCF_004366635.1_ASM436663v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:22,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:22,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:22,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga12b7713-c361-4934-8271-d1a3915bd723/dqc_reference/checkm_data
[2024-01-24 14:47:22,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:22,388] [INFO] Task started: CheckM
[2024-01-24 14:47:22,388] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004366635.1_ASM436663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004366635.1_ASM436663v1_genomic.fna/checkm_input GCF_004366635.1_ASM436663v1_genomic.fna/checkm_result
[2024-01-24 14:48:06,112] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:06,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:06,129] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:06,130] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:06,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004366635.1_ASM436663v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:06,131] [INFO] Task started: Blastn
[2024-01-24 14:48:06,131] [INFO] Running command: blastn -query GCF_004366635.1_ASM436663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga12b7713-c361-4934-8271-d1a3915bd723/dqc_reference/reference_markers_gtdb.fasta -out GCF_004366635.1_ASM436663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:07,746] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:07,750] [INFO] Selected 11 target genomes.
[2024-01-24 14:48:07,750] [INFO] Target genome list was writen to GCF_004366635.1_ASM436663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:07,761] [INFO] Task started: fastANI
[2024-01-24 14:48:07,761] [INFO] Running command: fastANI --query /var/lib/cwl/stgd956aca0-4340-42cb-a626-a1d6b2293d06/GCF_004366635.1_ASM436663v1_genomic.fna.gz --refList GCF_004366635.1_ASM436663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004366635.1_ASM436663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:16,853] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:16,864] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:16,865] [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	100.0	1287	1289	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	86.8095	789	1289	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	82.4122	777	1289	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	81.8169	808	1289	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	79.5985	584	1289	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	79.5875	493	1289	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	79.1024	445	1289	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	78.8458	291	1289	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	78.6611	437	1289	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	76.6191	202	1289	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	76.583	157	1289	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 14:48:16,866] [INFO] GTDB search result was written to GCF_004366635.1_ASM436663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:16,867] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:16,871] [INFO] DFAST_QC result json was written to GCF_004366635.1_ASM436663v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:16,871] [INFO] DFAST_QC completed!
[2024-01-24 14:48:16,871] [INFO] Total running time: 0h1m20s