[2024-01-25 19:00:20,395] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:20,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:20,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg607aa3de-0b96-468a-b51e-62701209d534/dqc_reference
[2024-01-25 19:00:21,535] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:21,536] [INFO] Task started: Prodigal
[2024-01-25 19:00:21,536] [INFO] Running command: gunzip -c /var/lib/cwl/stg9652ac25-4b82-42f3-8afa-1fef5f691353/GCF_000166055.1_ASM16605v1_genomic.fna.gz | prodigal -d GCF_000166055.1_ASM16605v1_genomic.fna/cds.fna -a GCF_000166055.1_ASM16605v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:32,099] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:32,100] [INFO] Task started: HMMsearch
[2024-01-25 19:00:32,100] [INFO] Running command: hmmsearch --tblout GCF_000166055.1_ASM16605v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg607aa3de-0b96-468a-b51e-62701209d534/dqc_reference/reference_markers.hmm GCF_000166055.1_ASM16605v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:32,332] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:32,333] [INFO] Found 6/6 markers.
[2024-01-25 19:00:32,363] [INFO] Query marker FASTA was written to GCF_000166055.1_ASM16605v1_genomic.fna/markers.fasta
[2024-01-25 19:00:32,363] [INFO] Task started: Blastn
[2024-01-25 19:00:32,363] [INFO] Running command: blastn -query GCF_000166055.1_ASM16605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg607aa3de-0b96-468a-b51e-62701209d534/dqc_reference/reference_markers.fasta -out GCF_000166055.1_ASM16605v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:33,192] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:33,195] [INFO] Selected 18 target genomes.
[2024-01-25 19:00:33,195] [INFO] Target genome list was writen to GCF_000166055.1_ASM16605v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:33,213] [INFO] Task started: fastANI
[2024-01-25 19:00:33,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg9652ac25-4b82-42f3-8afa-1fef5f691353/GCF_000166055.1_ASM16605v1_genomic.fna.gz --refList GCF_000166055.1_ASM16605v1_genomic.fna/target_genomes.txt --output GCF_000166055.1_ASM16605v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:47,927] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:47,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg607aa3de-0b96-468a-b51e-62701209d534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:47,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg607aa3de-0b96-468a-b51e-62701209d534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:47,938] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:00:47,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:00:47,938] [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
Rhodomicrobium udaipurense	strain=JA643	GCA_016461795.1	1202716	1202716	type	True	94.8943	1048	1338	95	below_threshold
Rhodomicrobium udaipurense	strain=JA643	GCA_000636015.1	1202716	1202716	type	True	94.7551	954	1338	95	below_threshold
Rhodomicrobium lacus	strain=JA980	GCA_003992725.1	2498452	2498452	type	True	87.6471	1007	1338	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	77.0678	126	1338	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	76.7795	138	1338	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.7513	124	1338	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	76.7184	94	1338	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.686	165	1338	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	76.6599	133	1338	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	76.6163	91	1338	95	below_threshold
Dichotomicrobium thermohalophilum	strain=DSM 5002	GCA_003550175.1	933063	933063	type	True	76.5736	131	1338	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	76.5279	131	1338	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	76.466	105	1338	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.4433	162	1338	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	76.4381	128	1338	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.3696	164	1338	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.0754	166	1338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:47,955] [INFO] DFAST Taxonomy check result was written to GCF_000166055.1_ASM16605v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:47,956] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:47,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:47,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg607aa3de-0b96-468a-b51e-62701209d534/dqc_reference/checkm_data
[2024-01-25 19:00:47,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:47,997] [INFO] Task started: CheckM
[2024-01-25 19:00:47,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000166055.1_ASM16605v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000166055.1_ASM16605v1_genomic.fna/checkm_input GCF_000166055.1_ASM16605v1_genomic.fna/checkm_result
[2024-01-25 19:01:20,221] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:20,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:20,250] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:20,250] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:20,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000166055.1_ASM16605v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:20,251] [INFO] Task started: Blastn
[2024-01-25 19:01:20,251] [INFO] Running command: blastn -query GCF_000166055.1_ASM16605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg607aa3de-0b96-468a-b51e-62701209d534/dqc_reference/reference_markers_gtdb.fasta -out GCF_000166055.1_ASM16605v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:21,898] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:21,901] [INFO] Selected 9 target genomes.
[2024-01-25 19:01:21,902] [INFO] Target genome list was writen to GCF_000166055.1_ASM16605v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:21,911] [INFO] Task started: fastANI
[2024-01-25 19:01:21,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg9652ac25-4b82-42f3-8afa-1fef5f691353/GCF_000166055.1_ASM16605v1_genomic.fna.gz --refList GCF_000166055.1_ASM16605v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000166055.1_ASM16605v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:29,898] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:29,905] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:01:29,905] [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_000166055.1	s__Rhodomicrobium vannielii	100.0	1338	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000636015.1	s__Rhodomicrobium udaipurense	94.7551	954	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	98.25	96.51	0.94	0.88	3	-
GCF_018619475.1	s__Rhodomicrobium sp018619475	88.5088	921	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992725.1	s__Rhodomicrobium lacus	87.6528	1006	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153975.1	s__Rhodomicrobium sp003153975	77.5407	320	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198715.1	s__R-RK-3 sp002198715	77.0825	250	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__R-RK-3	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	76.6435	172	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550175.1	s__Dichotomicrobium thermohalophilum	76.5736	131	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Dichotomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640615.1	s__RCIO01 sp017640615	76.038	78	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	96.47	96.47	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:29,906] [INFO] GTDB search result was written to GCF_000166055.1_ASM16605v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:29,907] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:29,909] [INFO] DFAST_QC result json was written to GCF_000166055.1_ASM16605v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:29,910] [INFO] DFAST_QC completed!
[2024-01-25 19:01:29,910] [INFO] Total running time: 0h1m10s