[2023-06-29 09:02:33,835] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:33,838] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:33,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg70a44c70-b821-43b1-9ef7-fc9e98cd4ce2/dqc_reference
[2023-06-29 09:02:35,396] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:35,396] [INFO] Task started: Prodigal
[2023-06-29 09:02:35,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg721ad979-251f-48b9-88b3-bf756fe7014a/GCA_020249525.1_ASM2024952v1_genomic.fna.gz | prodigal -d GCA_020249525.1_ASM2024952v1_genomic.fna/cds.fna -a GCA_020249525.1_ASM2024952v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:48,056] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:48,056] [INFO] Task started: HMMsearch
[2023-06-29 09:02:48,056] [INFO] Running command: hmmsearch --tblout GCA_020249525.1_ASM2024952v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70a44c70-b821-43b1-9ef7-fc9e98cd4ce2/dqc_reference/reference_markers.hmm GCA_020249525.1_ASM2024952v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:48,310] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:48,311] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg721ad979-251f-48b9-88b3-bf756fe7014a/GCA_020249525.1_ASM2024952v1_genomic.fna.gz]
[2023-06-29 09:02:48,350] [INFO] Query marker FASTA was written to GCA_020249525.1_ASM2024952v1_genomic.fna/markers.fasta
[2023-06-29 09:02:48,351] [INFO] Task started: Blastn
[2023-06-29 09:02:48,351] [INFO] Running command: blastn -query GCA_020249525.1_ASM2024952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70a44c70-b821-43b1-9ef7-fc9e98cd4ce2/dqc_reference/reference_markers.fasta -out GCA_020249525.1_ASM2024952v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:49,009] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:49,019] [INFO] Selected 21 target genomes.
[2023-06-29 09:02:49,020] [INFO] Target genome list was writen to GCA_020249525.1_ASM2024952v1_genomic.fna/target_genomes.txt
[2023-06-29 09:02:49,021] [INFO] Task started: fastANI
[2023-06-29 09:02:49,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg721ad979-251f-48b9-88b3-bf756fe7014a/GCA_020249525.1_ASM2024952v1_genomic.fna.gz --refList GCA_020249525.1_ASM2024952v1_genomic.fna/target_genomes.txt --output GCA_020249525.1_ASM2024952v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:03:05,881] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:05,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70a44c70-b821-43b1-9ef7-fc9e98cd4ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:03:05,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70a44c70-b821-43b1-9ef7-fc9e98cd4ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:03:05,899] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:03:05,900] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:03:05,900] [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 alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.0049	301	1156	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.9556	291	1156	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	76.8004	323	1156	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	76.7011	251	1156	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	76.6947	295	1156	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.5798	222	1156	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.5268	251	1156	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	76.4322	269	1156	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	76.4125	199	1156	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.3845	199	1156	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	76.3617	170	1156	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	76.2847	237	1156	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	76.2071	153	1156	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.1713	178	1156	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1627	152	1156	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.0684	159	1156	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	76.027	60	1156	95	below_threshold
Acidocella aromatica	strain=DSM 27026	GCA_014201825.1	1303579	1303579	type	True	75.804	67	1156	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	74.946	51	1156	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:03:05,925] [INFO] DFAST Taxonomy check result was written to GCA_020249525.1_ASM2024952v1_genomic.fna/tc_result.tsv
[2023-06-29 09:03:05,925] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:03:05,926] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:03:05,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70a44c70-b821-43b1-9ef7-fc9e98cd4ce2/dqc_reference/checkm_data
[2023-06-29 09:03:05,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:03:05,976] [INFO] Task started: CheckM
[2023-06-29 09:03:05,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020249525.1_ASM2024952v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020249525.1_ASM2024952v1_genomic.fna/checkm_input GCA_020249525.1_ASM2024952v1_genomic.fna/checkm_result
[2023-06-29 09:03:47,192] [INFO] Task succeeded: CheckM
[2023-06-29 09:03:47,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.26%
Contamintation: 5.73%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 09:03:47,218] [INFO] ===== Completeness check finished =====
[2023-06-29 09:03:47,219] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:03:47,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020249525.1_ASM2024952v1_genomic.fna/markers.fasta)
[2023-06-29 09:03:47,219] [INFO] Task started: Blastn
[2023-06-29 09:03:47,220] [INFO] Running command: blastn -query GCA_020249525.1_ASM2024952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70a44c70-b821-43b1-9ef7-fc9e98cd4ce2/dqc_reference/reference_markers_gtdb.fasta -out GCA_020249525.1_ASM2024952v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:48,266] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:48,271] [INFO] Selected 8 target genomes.
[2023-06-29 09:03:48,271] [INFO] Target genome list was writen to GCA_020249525.1_ASM2024952v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:03:48,273] [INFO] Task started: fastANI
[2023-06-29 09:03:48,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg721ad979-251f-48b9-88b3-bf756fe7014a/GCA_020249525.1_ASM2024952v1_genomic.fna.gz --refList GCA_020249525.1_ASM2024952v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020249525.1_ASM2024952v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:03:55,560] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:55,575] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:03:55,575] [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_016869735.1	s__Roseomonas_B sp016869735	87.2702	782	1156	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_903927465.1	s__Roseomonas_B sp903927465	86.9991	818	1156	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_016869715.1	s__Roseomonas_B sp016869715	86.5651	807	1156	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	85.2108	641	1156	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	77.0039	301	1156	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_018129065.1	s__Roseomonas_B soli	76.8632	290	1156	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	76.795	326	1156	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_014644535.1	s__Roseomonas_B lacus	76.787	325	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:03:55,577] [INFO] GTDB search result was written to GCA_020249525.1_ASM2024952v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:03:55,578] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:03:55,582] [INFO] DFAST_QC result json was written to GCA_020249525.1_ASM2024952v1_genomic.fna/dqc_result.json
[2023-06-29 09:03:55,582] [INFO] DFAST_QC completed!
[2023-06-29 09:03:55,582] [INFO] Total running time: 0h1m22s