[2023-06-30 07:45:12,847] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:45:12,849] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:45:12,849] [INFO] DQC Reference Directory: /var/lib/cwl/stg083f0326-9fed-4a51-aa0d-bce45ce86979/dqc_reference
[2023-06-30 07:45:14,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:45:14,758] [INFO] Task started: Prodigal
[2023-06-30 07:45:14,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg168830b6-ed43-4e5e-acf0-410f6306d8c3/GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna.gz | prodigal -d GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/cds.fna -a GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:45:27,285] [INFO] Task succeeded: Prodigal
[2023-06-30 07:45:27,285] [INFO] Task started: HMMsearch
[2023-06-30 07:45:27,286] [INFO] Running command: hmmsearch --tblout GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg083f0326-9fed-4a51-aa0d-bce45ce86979/dqc_reference/reference_markers.hmm GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:45:27,555] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:45:27,557] [INFO] Found 6/6 markers.
[2023-06-30 07:45:27,597] [INFO] Query marker FASTA was written to GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/markers.fasta
[2023-06-30 07:45:27,598] [INFO] Task started: Blastn
[2023-06-30 07:45:27,598] [INFO] Running command: blastn -query GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/markers.fasta -db /var/lib/cwl/stg083f0326-9fed-4a51-aa0d-bce45ce86979/dqc_reference/reference_markers.fasta -out GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:45:28,531] [INFO] Task succeeded: Blastn
[2023-06-30 07:45:28,535] [INFO] Selected 23 target genomes.
[2023-06-30 07:45:28,535] [INFO] Target genome list was writen to GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/target_genomes.txt
[2023-06-30 07:45:28,538] [INFO] Task started: fastANI
[2023-06-30 07:45:28,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg168830b6-ed43-4e5e-acf0-410f6306d8c3/GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna.gz --refList GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/target_genomes.txt --output GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:45:48,235] [INFO] Task succeeded: fastANI
[2023-06-30 07:45:48,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg083f0326-9fed-4a51-aa0d-bce45ce86979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:45:48,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg083f0326-9fed-4a51-aa0d-bce45ce86979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:45:48,262] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:45:48,262] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:45:48,263] [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
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	80.5531	716	1302	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	78.3903	484	1302	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.387	266	1302	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	77.8951	181	1302	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.8718	387	1302	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	77.6493	281	1302	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.6352	409	1302	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	77.6197	409	1302	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	77.3064	342	1302	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	77.283	409	1302	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	77.2664	403	1302	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	77.2359	329	1302	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.2217	292	1302	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	77.2141	410	1302	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	77.17	285	1302	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	77.1425	312	1302	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	77.0881	380	1302	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	77.0493	316	1302	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.0166	373	1302	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.9843	274	1302	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	76.9671	408	1302	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.9528	320	1302	95	below_threshold
Novacetimonas pomaceti	strain=T5K1	GCA_003207955.1	2021998	2021998	type	True	76.5146	119	1302	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:45:48,265] [INFO] DFAST Taxonomy check result was written to GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/tc_result.tsv
[2023-06-30 07:45:48,265] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:45:48,266] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:45:48,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg083f0326-9fed-4a51-aa0d-bce45ce86979/dqc_reference/checkm_data
[2023-06-30 07:45:48,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:45:49,401] [INFO] Task started: CheckM
[2023-06-30 07:45:49,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/checkm_input GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/checkm_result
[2023-06-30 07:46:29,207] [INFO] Task succeeded: CheckM
[2023-06-30 07:46:29,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-30 07:46:29,237] [INFO] ===== Completeness check finished =====
[2023-06-30 07:46:29,237] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:46:29,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/markers.fasta)
[2023-06-30 07:46:29,238] [INFO] Task started: Blastn
[2023-06-30 07:46:29,238] [INFO] Running command: blastn -query GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/markers.fasta -db /var/lib/cwl/stg083f0326-9fed-4a51-aa0d-bce45ce86979/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:46:31,021] [INFO] Task succeeded: Blastn
[2023-06-30 07:46:31,026] [INFO] Selected 11 target genomes.
[2023-06-30 07:46:31,026] [INFO] Target genome list was writen to GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:46:31,030] [INFO] Task started: fastANI
[2023-06-30 07:46:31,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg168830b6-ed43-4e5e-acf0-410f6306d8c3/GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna.gz --refList GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/target_genomes_gtdb.txt --output GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:46:42,141] [INFO] Task succeeded: fastANI
[2023-06-30 07:46:42,157] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:46:42,158] [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_903918195.1	s__BOG-930 sp903918195	99.8266	1221	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	conclusive
GCA_903907955.1	s__BOG-930 sp903907955	85.1124	857	1302	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_003164455.1	s__BOG-930 sp003164455	81.5322	487	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839965.1	s__BOG-930 sp903839965	81.0866	525	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630155.1	s__Rhodovastum atsumiense	80.5913	685	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	79.8771	603	1302	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_018971455.1	s__REEB85 sp018971455	79.1369	286	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133265.1	s__PALSA-911 sp003133265	78.6838	365	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307285.1	s__JAFKFI01 sp017307285	78.4922	392	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	78.3792	400	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918315.1	s__CAIXEA01 sp903918315	77.3213	263	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	99.91	99.85	0.96	0.93	5	-
--------------------------------------------------------------------------------
[2023-06-30 07:46:42,160] [INFO] GTDB search result was written to GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/result_gtdb.tsv
[2023-06-30 07:46:42,160] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:46:42,165] [INFO] DFAST_QC result json was written to GCA_903830085.1_freshwater_MAG_---_B2_bin-0466_genomic.fna/dqc_result.json
[2023-06-30 07:46:42,166] [INFO] DFAST_QC completed!
[2023-06-30 07:46:42,166] [INFO] Total running time: 0h1m29s