[2023-03-14 10:55:58,910] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,921] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg753abd6f-ff2a-4444-a762-19f60eba1c8c/dqc_reference
[2023-03-14 10:56:00,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,677] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,677] [INFO] Running command: cat /var/lib/cwl/stg1617e399-679c-4e0f-a42f-c7868d1386b4/OceanDNA-b33392.fa | prodigal -d OceanDNA-b33392/cds.fna -a OceanDNA-b33392/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:27,163] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:27,163] [INFO] Task started: HMMsearch
[2023-03-14 10:56:27,163] [INFO] Running command: hmmsearch --tblout OceanDNA-b33392/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg753abd6f-ff2a-4444-a762-19f60eba1c8c/dqc_reference/reference_markers.hmm OceanDNA-b33392/protein.faa > /dev/null
[2023-03-14 10:56:27,427] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:27,428] [INFO] Found 6/6 markers.
[2023-03-14 10:56:27,455] [INFO] Query marker FASTA was written to OceanDNA-b33392/markers.fasta
[2023-03-14 10:56:27,455] [INFO] Task started: Blastn
[2023-03-14 10:56:27,455] [INFO] Running command: blastn -query OceanDNA-b33392/markers.fasta -db /var/lib/cwl/stg753abd6f-ff2a-4444-a762-19f60eba1c8c/dqc_reference/reference_markers.fasta -out OceanDNA-b33392/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:28,452] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:28,453] [INFO] Selected 18 target genomes.
[2023-03-14 10:56:28,453] [INFO] Target genome list was writen to OceanDNA-b33392/target_genomes.txt
[2023-03-14 10:56:28,464] [INFO] Task started: fastANI
[2023-03-14 10:56:28,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg1617e399-679c-4e0f-a42f-c7868d1386b4/OceanDNA-b33392.fa --refList OceanDNA-b33392/target_genomes.txt --output OceanDNA-b33392/fastani_result.tsv --threads 1
[2023-03-14 10:56:47,716] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:47,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg753abd6f-ff2a-4444-a762-19f60eba1c8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:47,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg753abd6f-ff2a-4444-a762-19f60eba1c8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:47,727] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:47,727] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:47,727] [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
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	87.6453	1052	1407	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	85.7837	1065	1407	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	80.8763	730	1407	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	80.3901	706	1407	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.2735	580	1407	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	80.2663	632	1407	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	80.0548	597	1407	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.0209	631	1407	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	80.0125	659	1407	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	79.9854	625	1407	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	79.9677	585	1407	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.9368	579	1407	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.9357	564	1407	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	79.9309	646	1407	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	79.7431	604	1407	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	79.4961	621	1407	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.4527	484	1407	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.4368	629	1407	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:47,728] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33392/tc_result.tsv
[2023-03-14 10:56:47,728] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:47,728] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:47,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg753abd6f-ff2a-4444-a762-19f60eba1c8c/dqc_reference/checkm_data
[2023-03-14 10:56:47,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:47,740] [INFO] Task started: CheckM
[2023-03-14 10:56:47,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33392/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33392/checkm_input OceanDNA-b33392/checkm_result
[2023-03-14 10:58:23,929] [INFO] Task succeeded: CheckM
[2023-03-14 10:58:23,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:58:23,933] [INFO] ===== Completeness check finished =====
[2023-03-14 10:58:23,933] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:58:23,933] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33392/markers.fasta)
[2023-03-14 10:58:23,934] [INFO] Task started: Blastn
[2023-03-14 10:58:23,934] [INFO] Running command: blastn -query OceanDNA-b33392/markers.fasta -db /var/lib/cwl/stg753abd6f-ff2a-4444-a762-19f60eba1c8c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33392/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:58:26,011] [INFO] Task succeeded: Blastn
[2023-03-14 10:58:26,033] [INFO] Selected 11 target genomes.
[2023-03-14 10:58:26,033] [INFO] Target genome list was writen to OceanDNA-b33392/target_genomes_gtdb.txt
[2023-03-14 10:58:26,045] [INFO] Task started: fastANI
[2023-03-14 10:58:26,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg1617e399-679c-4e0f-a42f-c7868d1386b4/OceanDNA-b33392.fa --refList OceanDNA-b33392/target_genomes_gtdb.txt --output OceanDNA-b33392/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:58:40,928] [INFO] Task succeeded: fastANI
[2023-03-14 10:58:40,935] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:58:40,935] [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_016195825.1	s__Pelomonas sp016195825	92.4726	1089	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342485.1	s__Pelomonas saccharophila	87.6345	1053	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426885.1	s__Pelomonas sp001426885	87.5537	1039	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996515.1	s__Pelomonas sp009996515	87.2355	959	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425055.1	s__Pelomonas sp001425055	86.9001	1079	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550215.1	s__Pelomonas sp003550215	86.8861	1065	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237615.1	s__Pelomonas sp019237615	86.8421	943	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425705.1	s__Pelomonas sp001425705	86.6399	1075	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425165.1	s__Pelomonas sp001425165	86.3995	1056	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016790285.1	s__Pelomonas sp016790285	86.2187	983	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503085.1	s__Paucibacter_A sp005503085	81.2614	769	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:58:40,935] [INFO] GTDB search result was written to OceanDNA-b33392/result_gtdb.tsv
[2023-03-14 10:58:40,935] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:58:40,937] [INFO] DFAST_QC result json was written to OceanDNA-b33392/dqc_result.json
[2023-03-14 10:58:40,937] [INFO] DFAST_QC completed!
[2023-03-14 10:58:40,937] [INFO] Total running time: 0h2m42s