[2024-01-24 10:47:11,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f76f951-271e-4a1d-92c4-95e1b455c21f/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a4b8d74-a2d9-4275-8c5c-6231d4a97efe/GCF_014243445.1_ASM1424344v1_genomic.fna.gz | prodigal -d GCF_014243445.1_ASM1424344v1_genomic.fna/cds.fna -a GCF_014243445.1_ASM1424344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:32,048] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:32,048] [INFO] Task started: HMMsearch
[2024-01-24 10:47:32,048] [INFO] Running command: hmmsearch --tblout GCF_014243445.1_ASM1424344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f76f951-271e-4a1d-92c4-95e1b455c21f/dqc_reference/reference_markers.hmm GCF_014243445.1_ASM1424344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:32,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:32,313] [INFO] Found 6/6 markers.
[2024-01-24 10:47:32,353] [INFO] Query marker FASTA was written to GCF_014243445.1_ASM1424344v1_genomic.fna/markers.fasta
[2024-01-24 10:47:32,354] [INFO] Task started: Blastn
[2024-01-24 10:47:32,354] [INFO] Running command: blastn -query GCF_014243445.1_ASM1424344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f76f951-271e-4a1d-92c4-95e1b455c21f/dqc_reference/reference_markers.fasta -out GCF_014243445.1_ASM1424344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:33,427] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:33,432] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:33,433] [INFO] Target genome list was writen to GCF_014243445.1_ASM1424344v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:41,933] [INFO] Task started: fastANI
[2024-01-24 10:47:41,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a4b8d74-a2d9-4275-8c5c-6231d4a97efe/GCF_014243445.1_ASM1424344v1_genomic.fna.gz --refList GCF_014243445.1_ASM1424344v1_genomic.fna/target_genomes.txt --output GCF_014243445.1_ASM1424344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:56,987] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:56,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f76f951-271e-4a1d-92c4-95e1b455c21f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:56,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f76f951-271e-4a1d-92c4-95e1b455c21f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:57,011] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:57,011] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:57,011] [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
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	100.0	1367	1367	95	conclusive
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	84.3094	972	1367	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	82.4043	833	1367	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	82.3947	835	1367	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	81.0057	787	1367	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.7866	610	1367	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	79.5953	608	1367	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	79.5574	609	1367	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.4758	593	1367	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	79.4313	593	1367	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.3763	608	1367	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	79.2997	586	1367	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	79.2788	594	1367	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.2194	597	1367	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	79.1652	564	1367	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	79.1545	585	1367	95	below_threshold
Gemmobacter megaterium	strain=CGMCC 1.11024	GCA_014636395.1	1086013	1086013	type	True	78.1925	390	1367	95	below_threshold
Gemmobacter megaterium	strain=DSM 26375	GCA_900156815.1	1086013	1086013	type	True	78.1255	397	1367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:57,013] [INFO] DFAST Taxonomy check result was written to GCF_014243445.1_ASM1424344v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:57,013] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:57,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:57,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f76f951-271e-4a1d-92c4-95e1b455c21f/dqc_reference/checkm_data
[2024-01-24 10:47:57,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:57,068] [INFO] Task started: CheckM
[2024-01-24 10:47:57,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014243445.1_ASM1424344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014243445.1_ASM1424344v1_genomic.fna/checkm_input GCF_014243445.1_ASM1424344v1_genomic.fna/checkm_result
[2024-01-24 10:48:41,180] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:41,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:41,206] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:41,206] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:41,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014243445.1_ASM1424344v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:41,207] [INFO] Task started: Blastn
[2024-01-24 10:48:41,207] [INFO] Running command: blastn -query GCF_014243445.1_ASM1424344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f76f951-271e-4a1d-92c4-95e1b455c21f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014243445.1_ASM1424344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:43,113] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:43,117] [INFO] Selected 19 target genomes.
[2024-01-24 10:48:43,117] [INFO] Target genome list was writen to GCF_014243445.1_ASM1424344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:43,341] [INFO] Task started: fastANI
[2024-01-24 10:48:43,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a4b8d74-a2d9-4275-8c5c-6231d4a97efe/GCF_014243445.1_ASM1424344v1_genomic.fna.gz --refList GCF_014243445.1_ASM1424344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014243445.1_ASM1424344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:00,104] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:00,122] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:00,122] [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_014243445.1	s__Gemmobacter_B straminiformis	100.0	1367	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003060865.1	s__Gemmobacter_B sp003060865	84.3062	973	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	82.4124	832	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000500915.1	s__Gemmobacter_B sp000500915	81.9446	706	1367	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_011059185.1	s__Gemmobacter_B sp011059185	81.4968	814	1367	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_002855575.1	s__Gemmobacter_B sp002855575	81.1113	813	1367	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_009908315.1	s__Gemmobacter_B sp009908315	81.0304	784	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824045.1	s__Gemmobacter_B sp013824045	80.6154	502	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256185.1	s__Gemmobacter_B sp002256185	80.2585	654	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	80.12	523	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058035.1	s__JAAKGP01 sp018058035	79.718	584	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	79.6495	641	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574395.1	s__Tabrizicola thermarum	79.5963	609	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	97.33	97.31	0.93	0.92	4	-
GCF_008271655.1	s__Gemmobacter caeruleus	79.5486	611	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303485.1	s__Tabrizicola sp017303485	79.4395	539	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054195.1	s__Gemmobacter caeni	79.2834	588	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCF_003570715.1	s__Gemmobacter lutimaris	79.2384	597	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	79.0896	470	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156815.1	s__Wagnerdoeblera megaterium	78.1424	396	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:00,124] [INFO] GTDB search result was written to GCF_014243445.1_ASM1424344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:00,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:00,129] [INFO] DFAST_QC result json was written to GCF_014243445.1_ASM1424344v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:00,130] [INFO] DFAST_QC completed!
[2024-01-24 10:49:00,130] [INFO] Total running time: 0h1m48s