[2023-06-30 16:08:22,070] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:08:22,072] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:08:22,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg49ff578a-98ec-4f78-942d-53efecf36aca/dqc_reference
[2023-06-30 16:08:23,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:08:23,228] [INFO] Task started: Prodigal
[2023-06-30 16:08:23,228] [INFO] Running command: gunzip -c /var/lib/cwl/stg96b7edce-8eaf-46bf-9baa-e4cc0a34d142/GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna.gz | prodigal -d GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/cds.fna -a GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:08:33,547] [INFO] Task succeeded: Prodigal
[2023-06-30 16:08:33,547] [INFO] Task started: HMMsearch
[2023-06-30 16:08:33,547] [INFO] Running command: hmmsearch --tblout GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49ff578a-98ec-4f78-942d-53efecf36aca/dqc_reference/reference_markers.hmm GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:08:33,761] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:08:33,762] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg96b7edce-8eaf-46bf-9baa-e4cc0a34d142/GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna.gz]
[2023-06-30 16:08:33,800] [INFO] Query marker FASTA was written to GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/markers.fasta
[2023-06-30 16:08:33,800] [INFO] Task started: Blastn
[2023-06-30 16:08:33,800] [INFO] Running command: blastn -query GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/markers.fasta -db /var/lib/cwl/stg49ff578a-98ec-4f78-942d-53efecf36aca/dqc_reference/reference_markers.fasta -out GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:08:34,490] [INFO] Task succeeded: Blastn
[2023-06-30 16:08:34,493] [INFO] Selected 18 target genomes.
[2023-06-30 16:08:34,494] [INFO] Target genome list was writen to GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/target_genomes.txt
[2023-06-30 16:08:34,495] [INFO] Task started: fastANI
[2023-06-30 16:08:34,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b7edce-8eaf-46bf-9baa-e4cc0a34d142/GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna.gz --refList GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/target_genomes.txt --output GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:08:49,560] [INFO] Task succeeded: fastANI
[2023-06-30 16:08:49,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49ff578a-98ec-4f78-942d-53efecf36aca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:08:49,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49ff578a-98ec-4f78-942d-53efecf36aca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:08:49,572] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:08:49,572] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:08:49,572] [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	78.4025	393	972	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	77.6853	168	972	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.4376	258	972	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	77.1432	141	972	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.9755	246	972	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	76.9645	158	972	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	76.9339	262	972	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.9036	207	972	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	76.8949	230	972	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	76.8923	257	972	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.7068	235	972	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.7029	174	972	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	76.6466	273	972	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.6112	110	972	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	76.6033	278	972	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.5608	208	972	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.9066	152	972	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.6472	101	972	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:08:49,574] [INFO] DFAST Taxonomy check result was written to GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/tc_result.tsv
[2023-06-30 16:08:49,575] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:08:49,575] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:08:49,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49ff578a-98ec-4f78-942d-53efecf36aca/dqc_reference/checkm_data
[2023-06-30 16:08:49,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:08:49,623] [INFO] Task started: CheckM
[2023-06-30 16:08:49,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/checkm_input GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/checkm_result
[2023-06-30 16:09:25,181] [INFO] Task succeeded: CheckM
[2023-06-30 16:09:25,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.64%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 16:09:25,210] [INFO] ===== Completeness check finished =====
[2023-06-30 16:09:25,210] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:09:25,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/markers.fasta)
[2023-06-30 16:09:25,212] [INFO] Task started: Blastn
[2023-06-30 16:09:25,212] [INFO] Running command: blastn -query GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/markers.fasta -db /var/lib/cwl/stg49ff578a-98ec-4f78-942d-53efecf36aca/dqc_reference/reference_markers_gtdb.fasta -out GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:09:26,455] [INFO] Task succeeded: Blastn
[2023-06-30 16:09:26,458] [INFO] Selected 14 target genomes.
[2023-06-30 16:09:26,458] [INFO] Target genome list was writen to GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:09:26,461] [INFO] Task started: fastANI
[2023-06-30 16:09:26,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b7edce-8eaf-46bf-9baa-e4cc0a34d142/GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna.gz --refList GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/target_genomes_gtdb.txt --output GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:09:41,700] [INFO] Task succeeded: fastANI
[2023-06-30 16:09:41,710] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 16:09:41,711] [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_002422345.1	s__UBA6159 sp002422345	80.7149	526	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__UBA6159	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	78.8244	426	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898425.1	s__69-11 sp001898425	78.5008	447	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	99.84	99.84	0.96	0.96	2	-
GCF_002937115.1	s__Rhodopila globiformis	78.4122	392	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	78.0686	280	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240405.1	s__Rhodopila sp018240405	77.9429	361	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	77.8689	335	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCA_903895595.1	s__CAIXEA01 sp903895595	77.8169	342	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	99.85	99.70	0.96	0.93	10	-
GCA_903918315.1	s__CAIXEA01 sp903918315	77.7282	349	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	99.91	99.85	0.96	0.93	5	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	77.6598	170	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903851415.1	s__Rhodopila sp903851415	77.5844	278	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.89	99.89	0.92	0.92	2	-
GCA_903944925.1	s__Rhodopila sp903944925	77.5179	276	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.96	99.95	0.97	0.97	3	-
GCA_903915725.1	s__Rhodopila sp903915725	77.4559	281	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	100.00	100.00	0.99	0.99	3	-
GCF_009765975.1	s__Rhodopila sp009765975	77.422	333	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:09:41,713] [INFO] GTDB search result was written to GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/result_gtdb.tsv
[2023-06-30 16:09:41,713] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:09:41,717] [INFO] DFAST_QC result json was written to GCA_903894945.1_freshwater_MAG_---_LaPlata_bin-2068_genomic.fna/dqc_result.json
[2023-06-30 16:09:41,717] [INFO] DFAST_QC completed!
[2023-06-30 16:09:41,717] [INFO] Total running time: 0h1m20s