[2024-01-24 12:29:25,312] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:25,317] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:25,317] [INFO] DQC Reference Directory: /var/lib/cwl/stg5984f792-bb78-4f6a-93d0-4fceda71066b/dqc_reference
[2024-01-24 12:29:26,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:26,541] [INFO] Task started: Prodigal
[2024-01-24 12:29:26,541] [INFO] Running command: gunzip -c /var/lib/cwl/stg67727287-f29a-4a58-9c1a-831109d19eec/GCF_003217355.1_ASM321735v1_genomic.fna.gz | prodigal -d GCF_003217355.1_ASM321735v1_genomic.fna/cds.fna -a GCF_003217355.1_ASM321735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:37,859] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:37,860] [INFO] Task started: HMMsearch
[2024-01-24 12:29:37,860] [INFO] Running command: hmmsearch --tblout GCF_003217355.1_ASM321735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5984f792-bb78-4f6a-93d0-4fceda71066b/dqc_reference/reference_markers.hmm GCF_003217355.1_ASM321735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:38,242] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:38,243] [INFO] Found 6/6 markers.
[2024-01-24 12:29:38,284] [INFO] Query marker FASTA was written to GCF_003217355.1_ASM321735v1_genomic.fna/markers.fasta
[2024-01-24 12:29:38,284] [INFO] Task started: Blastn
[2024-01-24 12:29:38,284] [INFO] Running command: blastn -query GCF_003217355.1_ASM321735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5984f792-bb78-4f6a-93d0-4fceda71066b/dqc_reference/reference_markers.fasta -out GCF_003217355.1_ASM321735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:39,436] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:39,441] [INFO] Selected 15 target genomes.
[2024-01-24 12:29:39,441] [INFO] Target genome list was writen to GCF_003217355.1_ASM321735v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:39,473] [INFO] Task started: fastANI
[2024-01-24 12:29:39,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg67727287-f29a-4a58-9c1a-831109d19eec/GCF_003217355.1_ASM321735v1_genomic.fna.gz --refList GCF_003217355.1_ASM321735v1_genomic.fna/target_genomes.txt --output GCF_003217355.1_ASM321735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:53,874] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:53,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5984f792-bb78-4f6a-93d0-4fceda71066b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:53,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5984f792-bb78-4f6a-93d0-4fceda71066b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:53,888] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:53,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:53,889] [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 viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	100.0	1258	1259	95	conclusive
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	89.2659	972	1259	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	81.8422	686	1259	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	81.7877	675	1259	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	81.7084	693	1259	95	below_threshold
Rhodobacter aestuarii	strain=DSM 19945	GCA_900156655.1	453582	453582	type	True	80.4203	660	1259	95	below_threshold
Rhodobacter aestuarii	strain=JA296	GCA_003053525.1	453582	453582	type	True	80.3282	672	1259	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.0106	457	1259	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.9826	509	1259	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.9818	475	1259	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.6703	550	1259	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	78.6383	469	1259	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	78.6042	472	1259	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.4299	433	1259	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.9539	390	1259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:53,890] [INFO] DFAST Taxonomy check result was written to GCF_003217355.1_ASM321735v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:53,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:53,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:53,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5984f792-bb78-4f6a-93d0-4fceda71066b/dqc_reference/checkm_data
[2024-01-24 12:29:53,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:53,932] [INFO] Task started: CheckM
[2024-01-24 12:29:53,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217355.1_ASM321735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217355.1_ASM321735v1_genomic.fna/checkm_input GCF_003217355.1_ASM321735v1_genomic.fna/checkm_result
[2024-01-24 12:30:54,628] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:54,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:54,652] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:54,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:54,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217355.1_ASM321735v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:54,653] [INFO] Task started: Blastn
[2024-01-24 12:30:54,653] [INFO] Running command: blastn -query GCF_003217355.1_ASM321735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5984f792-bb78-4f6a-93d0-4fceda71066b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217355.1_ASM321735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:56,584] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:56,589] [INFO] Selected 10 target genomes.
[2024-01-24 12:30:56,589] [INFO] Target genome list was writen to GCF_003217355.1_ASM321735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:56,600] [INFO] Task started: fastANI
[2024-01-24 12:30:56,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg67727287-f29a-4a58-9c1a-831109d19eec/GCF_003217355.1_ASM321735v1_genomic.fna.gz --refList GCF_003217355.1_ASM321735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217355.1_ASM321735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:05,796] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:05,805] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:05,806] [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_003217355.1	s__Rhodobacter viridis	100.0	1258	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005144475.1	s__Rhodobacter capsulatus_C	89.7579	950	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021865.1	s__Rhodobacter capsulatus_B	89.4754	998	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.13	98.02	0.96	0.92	8	-
GCF_003254295.1	s__Rhodobacter capsulatus	89.2483	974	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.61	98.47	0.97	0.92	5	-
GCF_900217815.1	s__Rhodobacter maris	82.2526	800	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	81.8418	686	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763785.1	s__SZUA-611 sp014763785	81.8387	553	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249215.1	s__SZUA-611 sp003249215	81.1368	573	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	80.942	621	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_004022215.1	s__Paenirhodobacter populi	80.2286	556	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:05,808] [INFO] GTDB search result was written to GCF_003217355.1_ASM321735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:05,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:05,815] [INFO] DFAST_QC result json was written to GCF_003217355.1_ASM321735v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:05,815] [INFO] DFAST_QC completed!
[2024-01-24 12:31:05,815] [INFO] Total running time: 0h1m41s