[2023-06-28 16:28:16,102] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:28:16,114] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:28:16,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg90a78faf-1aac-44e2-81fc-dbaca68ee944/dqc_reference
[2023-06-28 16:28:17,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:28:17,275] [INFO] Task started: Prodigal
[2023-06-28 16:28:17,275] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4dd087f-0434-41c9-aa59-ffbab41436b6/GCA_020249405.1_ASM2024940v1_genomic.fna.gz | prodigal -d GCA_020249405.1_ASM2024940v1_genomic.fna/cds.fna -a GCA_020249405.1_ASM2024940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:28:29,196] [INFO] Task succeeded: Prodigal
[2023-06-28 16:28:29,196] [INFO] Task started: HMMsearch
[2023-06-28 16:28:29,196] [INFO] Running command: hmmsearch --tblout GCA_020249405.1_ASM2024940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90a78faf-1aac-44e2-81fc-dbaca68ee944/dqc_reference/reference_markers.hmm GCA_020249405.1_ASM2024940v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:28:29,414] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:28:29,415] [INFO] Found 6/6 markers.
[2023-06-28 16:28:29,446] [INFO] Query marker FASTA was written to GCA_020249405.1_ASM2024940v1_genomic.fna/markers.fasta
[2023-06-28 16:28:29,446] [INFO] Task started: Blastn
[2023-06-28 16:28:29,446] [INFO] Running command: blastn -query GCA_020249405.1_ASM2024940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90a78faf-1aac-44e2-81fc-dbaca68ee944/dqc_reference/reference_markers.fasta -out GCA_020249405.1_ASM2024940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:28:30,152] [INFO] Task succeeded: Blastn
[2023-06-28 16:28:30,156] [INFO] Selected 28 target genomes.
[2023-06-28 16:28:30,157] [INFO] Target genome list was writen to GCA_020249405.1_ASM2024940v1_genomic.fna/target_genomes.txt
[2023-06-28 16:28:30,159] [INFO] Task started: fastANI
[2023-06-28 16:28:30,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4dd087f-0434-41c9-aa59-ffbab41436b6/GCA_020249405.1_ASM2024940v1_genomic.fna.gz --refList GCA_020249405.1_ASM2024940v1_genomic.fna/target_genomes.txt --output GCA_020249405.1_ASM2024940v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:28:50,089] [INFO] Task succeeded: fastANI
[2023-06-28 16:28:50,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90a78faf-1aac-44e2-81fc-dbaca68ee944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:28:50,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90a78faf-1aac-44e2-81fc-dbaca68ee944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:28:50,111] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:28:50,111] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:28:50,112] [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
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	76.9845	385	1194	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.8171	326	1194	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	76.7154	341	1194	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.6211	249	1194	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.5971	335	1194	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	76.5338	320	1194	95	below_threshold
Roseomonas arctica	strain=LMG 28251	GCA_018128965.1	1509237	1509237	type	True	76.4287	213	1194	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.419	189	1194	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	76.3791	192	1194	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	76.3084	143	1194	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	76.2925	143	1194	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	76.2723	196	1194	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	76.2233	141	1194	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.1951	170	1194	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.1871	211	1194	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	76.162	162	1194	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	76.1554	149	1194	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	76.1227	145	1194	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	76.1049	135	1194	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	76.0576	76	1194	95	below_threshold
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	76.0032	52	1194	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	76.0005	66	1194	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	75.7429	106	1194	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	75.1778	53	1194	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:28:50,114] [INFO] DFAST Taxonomy check result was written to GCA_020249405.1_ASM2024940v1_genomic.fna/tc_result.tsv
[2023-06-28 16:28:50,115] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:28:50,115] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:28:50,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90a78faf-1aac-44e2-81fc-dbaca68ee944/dqc_reference/checkm_data
[2023-06-28 16:28:50,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:28:50,157] [INFO] Task started: CheckM
[2023-06-28 16:28:50,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020249405.1_ASM2024940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020249405.1_ASM2024940v1_genomic.fna/checkm_input GCA_020249405.1_ASM2024940v1_genomic.fna/checkm_result
[2023-06-28 16:29:27,859] [INFO] Task succeeded: CheckM
[2023-06-28 16:29:27,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:29:27,882] [INFO] ===== Completeness check finished =====
[2023-06-28 16:29:27,883] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:29:27,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020249405.1_ASM2024940v1_genomic.fna/markers.fasta)
[2023-06-28 16:29:27,883] [INFO] Task started: Blastn
[2023-06-28 16:29:27,884] [INFO] Running command: blastn -query GCA_020249405.1_ASM2024940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90a78faf-1aac-44e2-81fc-dbaca68ee944/dqc_reference/reference_markers_gtdb.fasta -out GCA_020249405.1_ASM2024940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:29:29,087] [INFO] Task succeeded: Blastn
[2023-06-28 16:29:29,091] [INFO] Selected 12 target genomes.
[2023-06-28 16:29:29,091] [INFO] Target genome list was writen to GCA_020249405.1_ASM2024940v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:29:29,092] [INFO] Task started: fastANI
[2023-06-28 16:29:29,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4dd087f-0434-41c9-aa59-ffbab41436b6/GCA_020249405.1_ASM2024940v1_genomic.fna.gz --refList GCA_020249405.1_ASM2024940v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020249405.1_ASM2024940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:29:39,315] [INFO] Task succeeded: fastANI
[2023-06-28 16:29:39,325] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:29:39,326] [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
GCA_903927465.1	s__Roseomonas_B sp903927465	90.0787	919	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	95.83	95.83	0.91	0.91	2	-
GCA_016869735.1	s__Roseomonas_B sp016869735	86.8106	855	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844785.1	s__Roseomonas_B sp903844785	86.8073	704	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869715.1	s__Roseomonas_B sp016869715	85.6778	863	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	76.9967	338	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	76.8935	321	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106015.1	s__Roseomonas_B sp016106015	76.8027	328	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012163135.1	s__Roseomonas_B oryzicola	76.7098	342	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012927745.1	s__Roseomonas_B sp012927745	76.6906	323	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464375.1	s__Roseomonas_B sp001464375	76.6602	363	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	76.5728	339	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_019024325.1	s__Roseomonas_A tokyonensis	76.5269	321	1194	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:29:39,328] [INFO] GTDB search result was written to GCA_020249405.1_ASM2024940v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:29:39,328] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:29:39,333] [INFO] DFAST_QC result json was written to GCA_020249405.1_ASM2024940v1_genomic.fna/dqc_result.json
[2023-06-28 16:29:39,333] [INFO] DFAST_QC completed!
[2023-06-28 16:29:39,333] [INFO] Total running time: 0h1m23s