[2024-01-24 14:22:33,483] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgc796334b-cf11-4d8c-acc0-291f1ca57bc9/dqc_reference
[2024-01-24 14:22:34,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,786] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg202d2289-207a-4889-bc8d-8c398d3456a1/GCF_003034965.1_ASM303496v1_genomic.fna.gz | prodigal -d GCF_003034965.1_ASM303496v1_genomic.fna/cds.fna -a GCF_003034965.1_ASM303496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:45,527] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:45,528] [INFO] Task started: HMMsearch
[2024-01-24 14:22:45,528] [INFO] Running command: hmmsearch --tblout GCF_003034965.1_ASM303496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc796334b-cf11-4d8c-acc0-291f1ca57bc9/dqc_reference/reference_markers.hmm GCF_003034965.1_ASM303496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:45,818] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:45,820] [INFO] Found 6/6 markers.
[2024-01-24 14:22:45,853] [INFO] Query marker FASTA was written to GCF_003034965.1_ASM303496v1_genomic.fna/markers.fasta
[2024-01-24 14:22:45,854] [INFO] Task started: Blastn
[2024-01-24 14:22:45,854] [INFO] Running command: blastn -query GCF_003034965.1_ASM303496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc796334b-cf11-4d8c-acc0-291f1ca57bc9/dqc_reference/reference_markers.fasta -out GCF_003034965.1_ASM303496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:46,964] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:46,967] [INFO] Selected 20 target genomes.
[2024-01-24 14:22:46,968] [INFO] Target genome list was writen to GCF_003034965.1_ASM303496v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:47,002] [INFO] Task started: fastANI
[2024-01-24 14:22:47,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg202d2289-207a-4889-bc8d-8c398d3456a1/GCF_003034965.1_ASM303496v1_genomic.fna.gz --refList GCF_003034965.1_ASM303496v1_genomic.fna/target_genomes.txt --output GCF_003034965.1_ASM303496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:04,176] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:04,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc796334b-cf11-4d8c-acc0-291f1ca57bc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:04,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc796334b-cf11-4d8c-acc0-291f1ca57bc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:04,193] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:04,193] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:04,193] [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 calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	80.6873	668	1161	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	80.4729	651	1161	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	80.4059	634	1161	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	80.3203	669	1161	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	80.1678	630	1161	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	80.0815	618	1161	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.07	620	1161	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.8706	651	1161	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.8486	626	1161	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	79.6634	623	1161	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	79.6468	559	1161	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.6229	620	1161	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	79.6216	632	1161	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	79.6043	596	1161	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.5052	573	1161	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	79.2869	594	1161	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.0853	467	1161	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	79.0196	487	1161	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	78.9748	490	1161	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	78.5242	500	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:04,197] [INFO] DFAST Taxonomy check result was written to GCF_003034965.1_ASM303496v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:04,198] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:04,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:04,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc796334b-cf11-4d8c-acc0-291f1ca57bc9/dqc_reference/checkm_data
[2024-01-24 14:23:04,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:04,242] [INFO] Task started: CheckM
[2024-01-24 14:23:04,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003034965.1_ASM303496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003034965.1_ASM303496v1_genomic.fna/checkm_input GCF_003034965.1_ASM303496v1_genomic.fna/checkm_result
[2024-01-24 14:23:47,620] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:47,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:47,644] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:47,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:47,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003034965.1_ASM303496v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:47,645] [INFO] Task started: Blastn
[2024-01-24 14:23:47,645] [INFO] Running command: blastn -query GCF_003034965.1_ASM303496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc796334b-cf11-4d8c-acc0-291f1ca57bc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003034965.1_ASM303496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:49,727] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:49,732] [INFO] Selected 16 target genomes.
[2024-01-24 14:23:49,732] [INFO] Target genome list was writen to GCF_003034965.1_ASM303496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:49,746] [INFO] Task started: fastANI
[2024-01-24 14:23:49,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg202d2289-207a-4889-bc8d-8c398d3456a1/GCF_003034965.1_ASM303496v1_genomic.fna.gz --refList GCF_003034965.1_ASM303496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003034965.1_ASM303496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:05,028] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:05,046] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:05,046] [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_003034965.1	s__Fuscovulum blasticum	100.0	1159	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fuscovulum	95.0	97.58	97.58	0.96	0.96	2	conclusive
GCA_018058035.1	s__JAAKGP01 sp018058035	82.1157	655	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043545.1	s__JAAKGP01 sp011043545	81.9468	799	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	81.4834	564	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704435.1	s__JAAKGP01 sp016704435	81.3462	762	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	99.06	99.06	0.93	0.93	2	-
GCA_014879735.1	s__Pseudogemmobacter sp014879735	80.8462	635	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011174775.1	s__Tabrizicola sp011174775	80.6688	670	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004762095.1	s__Tabrizicola sp004762095	80.2988	629	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	99.01	99.01	0.96	0.96	2	-
GCF_900609055.1	s__Pseudogemmobacter humi	80.1984	622	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011059185.1	s__Gemmobacter_B sp011059185	80.1767	645	1161	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	80.1765	629	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	80.0788	619	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003570715.1	s__Gemmobacter lutimaris	79.8485	626	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824055.1	s__Tabrizicola sp013824055	79.8408	463	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	98.98	98.98	0.93	0.93	2	-
GCF_005222785.1	s__Tabrizicola sp005222785	79.8351	638	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	79.5872	598	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:05,051] [INFO] GTDB search result was written to GCF_003034965.1_ASM303496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:05,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:05,059] [INFO] DFAST_QC result json was written to GCF_003034965.1_ASM303496v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:05,060] [INFO] DFAST_QC completed!
[2024-01-24 14:24:05,060] [INFO] Total running time: 0h1m32s