[2023-06-27 14:44:02,690] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:44:02,697] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:44:02,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a111c00-40f7-4535-a854-b2abe2a8b34c/dqc_reference
[2023-06-27 14:44:04,544] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:44:04,545] [INFO] Task started: Prodigal
[2023-06-27 14:44:04,545] [INFO] Running command: gunzip -c /var/lib/cwl/stg92830a60-ce9b-4cd8-b912-ac86ec9a93f4/GCA_026400325.1_ASM2640032v1_genomic.fna.gz | prodigal -d GCA_026400325.1_ASM2640032v1_genomic.fna/cds.fna -a GCA_026400325.1_ASM2640032v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:44:14,906] [INFO] Task succeeded: Prodigal
[2023-06-27 14:44:14,907] [INFO] Task started: HMMsearch
[2023-06-27 14:44:14,907] [INFO] Running command: hmmsearch --tblout GCA_026400325.1_ASM2640032v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a111c00-40f7-4535-a854-b2abe2a8b34c/dqc_reference/reference_markers.hmm GCA_026400325.1_ASM2640032v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:44:15,209] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:44:15,210] [INFO] Found 6/6 markers.
[2023-06-27 14:44:15,245] [INFO] Query marker FASTA was written to GCA_026400325.1_ASM2640032v1_genomic.fna/markers.fasta
[2023-06-27 14:44:15,245] [INFO] Task started: Blastn
[2023-06-27 14:44:15,246] [INFO] Running command: blastn -query GCA_026400325.1_ASM2640032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a111c00-40f7-4535-a854-b2abe2a8b34c/dqc_reference/reference_markers.fasta -out GCA_026400325.1_ASM2640032v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:44:16,256] [INFO] Task succeeded: Blastn
[2023-06-27 14:44:16,260] [INFO] Selected 14 target genomes.
[2023-06-27 14:44:16,260] [INFO] Target genome list was writen to GCA_026400325.1_ASM2640032v1_genomic.fna/target_genomes.txt
[2023-06-27 14:44:16,263] [INFO] Task started: fastANI
[2023-06-27 14:44:16,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg92830a60-ce9b-4cd8-b912-ac86ec9a93f4/GCA_026400325.1_ASM2640032v1_genomic.fna.gz --refList GCA_026400325.1_ASM2640032v1_genomic.fna/target_genomes.txt --output GCA_026400325.1_ASM2640032v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:44:30,336] [INFO] Task succeeded: fastANI
[2023-06-27 14:44:30,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a111c00-40f7-4535-a854-b2abe2a8b34c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:44:30,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a111c00-40f7-4535-a854-b2abe2a8b34c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:44:30,353] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 14:44:30,354] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 14:44:30,354] [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
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	81.1279	675	1062	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	81.0296	683	1062	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	80.782	674	1062	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	78.7903	527	1062	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.7854	527	1062	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	78.7727	489	1062	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.6113	417	1062	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	78.5906	513	1062	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	78.4233	427	1062	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.4089	435	1062	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	78.3758	453	1062	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	78.2756	437	1062	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.1502	417	1062	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	78.0976	406	1062	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 14:44:30,358] [INFO] DFAST Taxonomy check result was written to GCA_026400325.1_ASM2640032v1_genomic.fna/tc_result.tsv
[2023-06-27 14:44:30,358] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:44:30,358] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:44:30,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a111c00-40f7-4535-a854-b2abe2a8b34c/dqc_reference/checkm_data
[2023-06-27 14:44:30,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:44:30,406] [INFO] Task started: CheckM
[2023-06-27 14:44:30,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400325.1_ASM2640032v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400325.1_ASM2640032v1_genomic.fna/checkm_input GCA_026400325.1_ASM2640032v1_genomic.fna/checkm_result
[2023-06-27 14:45:09,025] [INFO] Task succeeded: CheckM
[2023-06-27 14:45:09,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:45:09,056] [INFO] ===== Completeness check finished =====
[2023-06-27 14:45:09,056] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:45:09,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400325.1_ASM2640032v1_genomic.fna/markers.fasta)
[2023-06-27 14:45:09,057] [INFO] Task started: Blastn
[2023-06-27 14:45:09,057] [INFO] Running command: blastn -query GCA_026400325.1_ASM2640032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a111c00-40f7-4535-a854-b2abe2a8b34c/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400325.1_ASM2640032v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:45:10,868] [INFO] Task succeeded: Blastn
[2023-06-27 14:45:10,873] [INFO] Selected 19 target genomes.
[2023-06-27 14:45:10,874] [INFO] Target genome list was writen to GCA_026400325.1_ASM2640032v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:45:10,886] [INFO] Task started: fastANI
[2023-06-27 14:45:10,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg92830a60-ce9b-4cd8-b912-ac86ec9a93f4/GCA_026400325.1_ASM2640032v1_genomic.fna.gz --refList GCA_026400325.1_ASM2640032v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400325.1_ASM2640032v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:45:25,893] [INFO] Task succeeded: fastANI
[2023-06-27 14:45:25,912] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 14:45:25,913] [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_003940805.1	s__Tabrizicola piscis	81.7094	755	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	81.5794	727	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012036325.1	s__Tabrizicola sp012036325	81.4335	586	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057165.1	s__Tabrizicola sp018057165	81.0928	470	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821825.1	s__Tabrizicola sp013821825	80.9798	653	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999335.1	s__Tabrizicola soli	80.9471	676	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222785.1	s__Tabrizicola sp005222785	80.9014	710	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792905.1	s__Tabrizicola sp016792905	80.8275	617	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824055.1	s__Tabrizicola sp013824055	80.8274	510	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	98.98	98.98	0.93	0.93	2	-
GCF_008271465.1	s__Tabrizicola flagellata	80.7847	674	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303485.1	s__Tabrizicola sp017303485	80.7659	633	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917595.1	s__Tabrizicola sp903917595	80.7365	583	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280405.1	s__Tabrizicola sp002280405	80.6962	540	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793705.1	s__Tabrizicola sp016793705	80.6457	654	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792685.1	s__Tabrizicola sp016792685	80.363	605	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704435.1	s__JAAKGP01 sp016704435	79.5061	578	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	99.06	99.06	0.93	0.93	2	-
GCA_012032275.1	s__JAAURK01 sp012032275	79.1176	463	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAURK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011059185.1	s__Gemmobacter_B sp011059185	78.8493	513	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	78.2933	435	1062	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 14:45:25,915] [INFO] GTDB search result was written to GCA_026400325.1_ASM2640032v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:45:25,915] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:45:25,921] [INFO] DFAST_QC result json was written to GCA_026400325.1_ASM2640032v1_genomic.fna/dqc_result.json
[2023-06-27 14:45:25,921] [INFO] DFAST_QC completed!
[2023-06-27 14:45:25,921] [INFO] Total running time: 0h1m23s