[2024-01-24 13:13:26,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:26,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:26,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f9174b8-a56c-4920-92c7-585f417637df/dqc_reference
[2024-01-24 13:13:27,775] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:27,776] [INFO] Task started: Prodigal
[2024-01-24 13:13:27,776] [INFO] Running command: gunzip -c /var/lib/cwl/stg1434a128-d200-43b8-a267-559c5a443a9c/GCF_009720775.1_ASM972077v1_genomic.fna.gz | prodigal -d GCF_009720775.1_ASM972077v1_genomic.fna/cds.fna -a GCF_009720775.1_ASM972077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:44,517] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:44,518] [INFO] Task started: HMMsearch
[2024-01-24 13:13:44,518] [INFO] Running command: hmmsearch --tblout GCF_009720775.1_ASM972077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f9174b8-a56c-4920-92c7-585f417637df/dqc_reference/reference_markers.hmm GCF_009720775.1_ASM972077v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:44,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:44,870] [INFO] Found 6/6 markers.
[2024-01-24 13:13:44,913] [INFO] Query marker FASTA was written to GCF_009720775.1_ASM972077v1_genomic.fna/markers.fasta
[2024-01-24 13:13:44,914] [INFO] Task started: Blastn
[2024-01-24 13:13:44,914] [INFO] Running command: blastn -query GCF_009720775.1_ASM972077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f9174b8-a56c-4920-92c7-585f417637df/dqc_reference/reference_markers.fasta -out GCF_009720775.1_ASM972077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:45,708] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:45,712] [INFO] Selected 20 target genomes.
[2024-01-24 13:13:45,712] [INFO] Target genome list was writen to GCF_009720775.1_ASM972077v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:45,735] [INFO] Task started: fastANI
[2024-01-24 13:13:45,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg1434a128-d200-43b8-a267-559c5a443a9c/GCF_009720775.1_ASM972077v1_genomic.fna.gz --refList GCF_009720775.1_ASM972077v1_genomic.fna/target_genomes.txt --output GCF_009720775.1_ASM972077v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:12,157] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:12,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f9174b8-a56c-4920-92c7-585f417637df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:12,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f9174b8-a56c-4920-92c7-585f417637df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:12,176] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:14:12,176] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:14:12,176] [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
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	82.9263	1151	1697	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	82.8118	1151	1697	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	81.9611	1066	1697	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	81.9197	1081	1697	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	81.8632	1032	1697	95	below_threshold
Duganella sacchari	strain=Sac-22	GCA_900143065.1	551987	551987	type	True	81.693	1057	1697	95	below_threshold
Duganella guangzhouensis	strain=FT80W	GCA_009674535.1	2666084	2666084	type	True	81.6677	1065	1697	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	81.6345	951	1697	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	81.5505	1035	1697	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	81.5444	996	1697	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	81.5322	995	1697	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.4807	967	1697	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	81.4799	987	1697	95	below_threshold
Duganella flavida	strain=FT135W	GCA_009857445.1	2692175	2692175	type	True	81.2478	1043	1697	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	80.8068	907	1697	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.1752	135	1697	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.7713	52	1697	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	74.7223	73	1697	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	74.7192	74	1697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:12,179] [INFO] DFAST Taxonomy check result was written to GCF_009720775.1_ASM972077v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:12,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:12,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:12,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f9174b8-a56c-4920-92c7-585f417637df/dqc_reference/checkm_data
[2024-01-24 13:14:12,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:12,234] [INFO] Task started: CheckM
[2024-01-24 13:14:12,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009720775.1_ASM972077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009720775.1_ASM972077v1_genomic.fna/checkm_input GCF_009720775.1_ASM972077v1_genomic.fna/checkm_result
[2024-01-24 13:15:02,966] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:02,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:02,988] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:02,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:02,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009720775.1_ASM972077v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:02,989] [INFO] Task started: Blastn
[2024-01-24 13:15:02,989] [INFO] Running command: blastn -query GCF_009720775.1_ASM972077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f9174b8-a56c-4920-92c7-585f417637df/dqc_reference/reference_markers_gtdb.fasta -out GCF_009720775.1_ASM972077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:04,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:04,340] [INFO] Selected 15 target genomes.
[2024-01-24 13:15:04,341] [INFO] Target genome list was writen to GCF_009720775.1_ASM972077v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:04,356] [INFO] Task started: fastANI
[2024-01-24 13:15:04,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg1434a128-d200-43b8-a267-559c5a443a9c/GCF_009720775.1_ASM972077v1_genomic.fna.gz --refList GCF_009720775.1_ASM972077v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009720775.1_ASM972077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:22,812] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:22,831] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:22,831] [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_009720775.1	s__Duganella danionis	100.0	1693	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009857835.1	s__Duganella fentianensis	94.3798	1490	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857915.1	s__Duganella sp009857915	89.1252	1444	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000335815.1	s__Duganella sp000335815	82.8628	1150	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.81	95.66	0.89	0.89	4	-
GCF_009380215.1	s__Duganella sp009380215	82.8135	1152	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416895.1	s__Duganella sp003416895	82.6147	1165	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	99.92	99.92	0.99	0.99	2	-
GCA_000381565.1	s__Duganella sp000381565	82.5172	1167	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_013375995.1	s__Duganella sp013375995	82.455	1123	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674495.1	s__Duganella alba	81.9455	1077	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
GCF_900143065.1	s__Duganella sacchari	81.688	1057	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.30	97.30	0.91	0.91	2	-
GCF_019219065.1	s__Duganella sp019219065	81.4178	1035	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911005.1	s__Aromatoleum toluolicum	76.1586	135	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464365.1	s__Sandaracinobacter sp016464365	74.7236	51	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	74.71	54	1697	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:22,833] [INFO] GTDB search result was written to GCF_009720775.1_ASM972077v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:22,834] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:22,837] [INFO] DFAST_QC result json was written to GCF_009720775.1_ASM972077v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:22,838] [INFO] DFAST_QC completed!
[2024-01-24 13:15:22,838] [INFO] Total running time: 0h1m56s