[2023-03-18 01:14:00,924] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:14:00,924] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:14:00,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bf8e6b6-abd5-43ad-9cc5-651681d9b072/dqc_reference
[2023-03-18 01:14:02,038] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:14:02,038] [INFO] Task started: Prodigal
[2023-03-18 01:14:02,038] [INFO] Running command: cat /var/lib/cwl/stgfe729962-7dda-416a-9b9e-8fc1624aa644/OceanDNA-b33525.fa | prodigal -d OceanDNA-b33525/cds.fna -a OceanDNA-b33525/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:14:29,919] [INFO] Task succeeded: Prodigal
[2023-03-18 01:14:29,919] [INFO] Task started: HMMsearch
[2023-03-18 01:14:29,919] [INFO] Running command: hmmsearch --tblout OceanDNA-b33525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bf8e6b6-abd5-43ad-9cc5-651681d9b072/dqc_reference/reference_markers.hmm OceanDNA-b33525/protein.faa > /dev/null
[2023-03-18 01:14:30,146] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:14:30,146] [INFO] Found 6/6 markers.
[2023-03-18 01:14:30,172] [INFO] Query marker FASTA was written to OceanDNA-b33525/markers.fasta
[2023-03-18 01:14:30,173] [INFO] Task started: Blastn
[2023-03-18 01:14:30,174] [INFO] Running command: blastn -query OceanDNA-b33525/markers.fasta -db /var/lib/cwl/stg4bf8e6b6-abd5-43ad-9cc5-651681d9b072/dqc_reference/reference_markers.fasta -out OceanDNA-b33525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:14:31,158] [INFO] Task succeeded: Blastn
[2023-03-18 01:14:31,159] [INFO] Selected 20 target genomes.
[2023-03-18 01:14:31,159] [INFO] Target genome list was writen to OceanDNA-b33525/target_genomes.txt
[2023-03-18 01:14:31,172] [INFO] Task started: fastANI
[2023-03-18 01:14:31,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe729962-7dda-416a-9b9e-8fc1624aa644/OceanDNA-b33525.fa --refList OceanDNA-b33525/target_genomes.txt --output OceanDNA-b33525/fastani_result.tsv --threads 1
[2023-03-18 01:14:51,450] [INFO] Task succeeded: fastANI
[2023-03-18 01:14:51,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bf8e6b6-abd5-43ad-9cc5-651681d9b072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:14:51,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bf8e6b6-abd5-43ad-9cc5-651681d9b072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:14:51,462] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:14:51,462] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:14:51,463] [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
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	81.4912	662	1425	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	81.4116	699	1425	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	80.9994	718	1425	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	80.8592	732	1425	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.0505	688	1425	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.0233	733	1425	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.9866	634	1425	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.9334	742	1425	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	79.9119	583	1425	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.8863	600	1425	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.8364	578	1425	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	79.7985	618	1425	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.7285	610	1425	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.698	668	1425	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.5809	598	1425	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.3362	603	1425	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.1333	505	1425	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	78.941	478	1425	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	78.6338	368	1425	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.5501	433	1425	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:14:51,463] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33525/tc_result.tsv
[2023-03-18 01:14:51,463] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:14:51,463] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:14:51,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bf8e6b6-abd5-43ad-9cc5-651681d9b072/dqc_reference/checkm_data
[2023-03-18 01:14:51,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:14:51,472] [INFO] Task started: CheckM
[2023-03-18 01:14:51,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33525/checkm_input OceanDNA-b33525/checkm_result
[2023-03-18 01:17:01,935] [INFO] Task succeeded: CheckM
[2023-03-18 01:17:01,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:17:01,938] [INFO] ===== Completeness check finished =====
[2023-03-18 01:17:01,938] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:17:01,938] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33525/markers.fasta)
[2023-03-18 01:17:01,940] [INFO] Task started: Blastn
[2023-03-18 01:17:01,940] [INFO] Running command: blastn -query OceanDNA-b33525/markers.fasta -db /var/lib/cwl/stg4bf8e6b6-abd5-43ad-9cc5-651681d9b072/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:17:04,183] [INFO] Task succeeded: Blastn
[2023-03-18 01:17:04,184] [INFO] Selected 17 target genomes.
[2023-03-18 01:17:04,184] [INFO] Target genome list was writen to OceanDNA-b33525/target_genomes_gtdb.txt
[2023-03-18 01:17:04,199] [INFO] Task started: fastANI
[2023-03-18 01:17:04,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe729962-7dda-416a-9b9e-8fc1624aa644/OceanDNA-b33525.fa --refList OceanDNA-b33525/target_genomes_gtdb.txt --output OceanDNA-b33525/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:17:21,995] [INFO] Task succeeded: fastANI
[2023-03-18 01:17:22,005] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:17:22,005] [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
GCF_004016515.1	s__Rubrivivax albus	84.2022	994	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780805.1	s__Rubrivivax sp018780805	84.1093	874	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938815.1	s__Rubrivivax sp903938815	83.7771	906	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.66	99.41	0.96	0.94	10	-
GCA_013822265.1	s__Rubrivivax sp013822265	81.5736	716	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	81.4831	629	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001295905.1	s__Rubrivivax sp001295905	81.3176	774	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725505.1	s__Rubrivivax sp001725505	81.2557	626	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904426505.1	s__Rubrivivax sp904426505	81.2549	752	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191995.1	s__Rubrivivax sp016191995	81.2114	692	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707445.1	s__Rubrivivax sp016707445	81.0786	736	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.23	99.17	0.94	0.91	3	-
GCA_018240325.1	s__Rubrivivax sp018240325	80.8762	634	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000244995.1	s__Aquabacterium_A sp000244995	80.6594	754	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	80.6533	732	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790515.1	s__Aquabacterium_A sp016790515	80.5538	651	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999135.1	s__Aquabacterium_A sp017999135	80.4357	513	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789955.1	s__Rubrivivax sp016789955	80.0963	647	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215705.1	s__Ramlibacter tataouinensis	79.9152	583	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:17:22,005] [INFO] GTDB search result was written to OceanDNA-b33525/result_gtdb.tsv
[2023-03-18 01:17:22,005] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:17:22,007] [INFO] DFAST_QC result json was written to OceanDNA-b33525/dqc_result.json
[2023-03-18 01:17:22,007] [INFO] DFAST_QC completed!
[2023-03-18 01:17:22,007] [INFO] Total running time: 0h3m21s