[2023-06-29 23:53:25,899] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:53:25,901] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:53:25,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg009fcb51-90c9-41fa-b019-496e391d0147/dqc_reference
[2023-06-29 23:53:27,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:53:27,084] [INFO] Task started: Prodigal
[2023-06-29 23:53:27,085] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf4da2e2-f6c6-4b7f-a85e-67bd55306a66/GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna.gz | prodigal -d GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/cds.fna -a GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:53:40,911] [INFO] Task succeeded: Prodigal
[2023-06-29 23:53:40,911] [INFO] Task started: HMMsearch
[2023-06-29 23:53:40,911] [INFO] Running command: hmmsearch --tblout GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg009fcb51-90c9-41fa-b019-496e391d0147/dqc_reference/reference_markers.hmm GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:53:41,205] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:53:41,207] [INFO] Found 6/6 markers.
[2023-06-29 23:53:41,250] [INFO] Query marker FASTA was written to GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/markers.fasta
[2023-06-29 23:53:41,251] [INFO] Task started: Blastn
[2023-06-29 23:53:41,251] [INFO] Running command: blastn -query GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/markers.fasta -db /var/lib/cwl/stg009fcb51-90c9-41fa-b019-496e391d0147/dqc_reference/reference_markers.fasta -out GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:53:42,133] [INFO] Task succeeded: Blastn
[2023-06-29 23:53:42,138] [INFO] Selected 23 target genomes.
[2023-06-29 23:53:42,139] [INFO] Target genome list was writen to GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/target_genomes.txt
[2023-06-29 23:53:42,141] [INFO] Task started: fastANI
[2023-06-29 23:53:42,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf4da2e2-f6c6-4b7f-a85e-67bd55306a66/GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna.gz --refList GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/target_genomes.txt --output GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:53:58,467] [INFO] Task succeeded: fastANI
[2023-06-29 23:53:58,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg009fcb51-90c9-41fa-b019-496e391d0147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:53:58,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg009fcb51-90c9-41fa-b019-496e391d0147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:53:58,494] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:53:58,494] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:53:58,495] [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
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	77.8764	504	1477	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	77.3511	179	1477	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.1995	309	1477	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	76.9136	174	1477	95	below_threshold
Acidisoma cellulosilyticum	strain=HW T5.17	GCA_020621385.1	2802395	2802395	type	True	76.8668	156	1477	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	76.8643	160	1477	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	76.8536	162	1477	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	76.8157	95	1477	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.8061	164	1477	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	76.7926	107	1477	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	76.7592	246	1477	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	76.7168	165	1477	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	76.6393	96	1477	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	76.6194	258	1477	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.6123	208	1477	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.5757	231	1477	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	76.5517	266	1477	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	76.5505	234	1477	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.5276	252	1477	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.5251	213	1477	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.453	248	1477	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.3965	224	1477	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.3158	242	1477	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:53:58,497] [INFO] DFAST Taxonomy check result was written to GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/tc_result.tsv
[2023-06-29 23:53:58,498] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:53:58,498] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:53:58,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg009fcb51-90c9-41fa-b019-496e391d0147/dqc_reference/checkm_data
[2023-06-29 23:53:58,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:53:58,547] [INFO] Task started: CheckM
[2023-06-29 23:53:58,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/checkm_input GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/checkm_result
[2023-06-29 23:54:41,417] [INFO] Task succeeded: CheckM
[2023-06-29 23:54:41,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 23:54:41,443] [INFO] ===== Completeness check finished =====
[2023-06-29 23:54:41,443] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:54:41,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/markers.fasta)
[2023-06-29 23:54:41,444] [INFO] Task started: Blastn
[2023-06-29 23:54:41,444] [INFO] Running command: blastn -query GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/markers.fasta -db /var/lib/cwl/stg009fcb51-90c9-41fa-b019-496e391d0147/dqc_reference/reference_markers_gtdb.fasta -out GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:54:43,125] [INFO] Task succeeded: Blastn
[2023-06-29 23:54:43,130] [INFO] Selected 11 target genomes.
[2023-06-29 23:54:43,131] [INFO] Target genome list was writen to GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:54:43,137] [INFO] Task started: fastANI
[2023-06-29 23:54:43,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf4da2e2-f6c6-4b7f-a85e-67bd55306a66/GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna.gz --refList GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/target_genomes_gtdb.txt --output GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:54:54,504] [INFO] Task succeeded: fastANI
[2023-06-29 23:54:54,517] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:54:54,518] [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_903918315.1	s__CAIXEA01 sp903918315	99.9446	1427	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	99.91	99.85	0.96	0.93	5	conclusive
GCA_903900905.1	s__CAIXEA01 sp903900905	85.9636	899	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	98.81	98.71	0.81	0.80	4	-
GCA_903924985.1	s__CAIXEA01 sp903924985	79.466	771	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	99.91	99.91	0.93	0.93	2	-
GCA_903895595.1	s__CAIXEA01 sp903895595	79.45	804	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	99.85	99.70	0.96	0.93	10	-
GCA_903877125.1	s__CAIXEA01 sp903877125	78.6185	691	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_009765975.1	s__Rhodopila sp009765975	77.6391	494	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907955.1	s__BOG-930 sp903907955	77.338	283	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCA_018240405.1	s__Rhodopila sp018240405	77.2686	444	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	77.0436	255	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCF_004302915.1	s__Komagataeibacter xylinus_C	76.7034	93	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873995.1	s__CAIQQQ01 sp903873995	76.5896	199	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIQQQ01	95.0	99.67	99.67	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-29 23:54:54,520] [INFO] GTDB search result was written to GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/result_gtdb.tsv
[2023-06-29 23:54:54,520] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:54:54,524] [INFO] DFAST_QC result json was written to GCA_903908735.1_freshwater_MAG_---_Umea2_bin-0968_genomic.fna/dqc_result.json
[2023-06-29 23:54:54,525] [INFO] DFAST_QC completed!
[2023-06-29 23:54:54,525] [INFO] Total running time: 0h1m29s