[2023-03-18 23:22:48,490] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:22:48,490] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:22:48,490] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd57d87a-b294-48bd-8c30-c418d707e5bb/dqc_reference
[2023-03-18 23:22:49,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:22:49,618] [INFO] Task started: Prodigal
[2023-03-18 23:22:49,619] [INFO] Running command: cat /var/lib/cwl/stg19841b6f-7a0b-40c7-bb17-ee5a6926da18/OceanDNA-b26823.fa | prodigal -d OceanDNA-b26823/cds.fna -a OceanDNA-b26823/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:23:14,448] [INFO] Task succeeded: Prodigal
[2023-03-18 23:23:14,448] [INFO] Task started: HMMsearch
[2023-03-18 23:23:14,448] [INFO] Running command: hmmsearch --tblout OceanDNA-b26823/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd57d87a-b294-48bd-8c30-c418d707e5bb/dqc_reference/reference_markers.hmm OceanDNA-b26823/protein.faa > /dev/null
[2023-03-18 23:23:14,656] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:23:14,656] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg19841b6f-7a0b-40c7-bb17-ee5a6926da18/OceanDNA-b26823.fa]
[2023-03-18 23:23:14,685] [INFO] Query marker FASTA was written to OceanDNA-b26823/markers.fasta
[2023-03-18 23:23:14,686] [INFO] Task started: Blastn
[2023-03-18 23:23:14,686] [INFO] Running command: blastn -query OceanDNA-b26823/markers.fasta -db /var/lib/cwl/stgfd57d87a-b294-48bd-8c30-c418d707e5bb/dqc_reference/reference_markers.fasta -out OceanDNA-b26823/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:23:15,341] [INFO] Task succeeded: Blastn
[2023-03-18 23:23:15,342] [INFO] Selected 21 target genomes.
[2023-03-18 23:23:15,342] [INFO] Target genome list was writen to OceanDNA-b26823/target_genomes.txt
[2023-03-18 23:23:15,387] [INFO] Task started: fastANI
[2023-03-18 23:23:15,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg19841b6f-7a0b-40c7-bb17-ee5a6926da18/OceanDNA-b26823.fa --refList OceanDNA-b26823/target_genomes.txt --output OceanDNA-b26823/fastani_result.tsv --threads 1
[2023-03-18 23:23:36,671] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:36,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd57d87a-b294-48bd-8c30-c418d707e5bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:23:36,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd57d87a-b294-48bd-8c30-c418d707e5bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:23:36,683] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:23:36,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:23:36,684] [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
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	96.5135	1230	1370	95	conclusive
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	81.5615	830	1370	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	80.8326	720	1370	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.2522	574	1370	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	79.002	532	1370	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	78.8795	532	1370	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.8378	563	1370	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.8232	482	1370	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	78.7948	509	1370	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.7893	538	1370	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	78.7769	545	1370	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	78.7584	443	1370	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	78.6302	518	1370	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	78.6133	519	1370	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	78.5439	450	1370	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	78.4446	500	1370	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	78.3702	439	1370	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	78.0044	401	1370	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.1984	280	1370	95	below_threshold
Aquamicrobium zhengzhouense	strain=cd-1	GCA_016124105.1	2781738	2781738	type	True	76.8982	188	1370	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	76.6877	260	1370	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:23:36,684] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26823/tc_result.tsv
[2023-03-18 23:23:36,684] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:23:36,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:23:36,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd57d87a-b294-48bd-8c30-c418d707e5bb/dqc_reference/checkm_data
[2023-03-18 23:23:36,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:23:36,692] [INFO] Task started: CheckM
[2023-03-18 23:23:36,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26823/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26823/checkm_input OceanDNA-b26823/checkm_result
[2023-03-18 23:24:36,748] [INFO] Task succeeded: CheckM
[2023-03-18 23:24:36,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:24:36,751] [INFO] ===== Completeness check finished =====
[2023-03-18 23:24:36,752] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:24:36,752] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26823/markers.fasta)
[2023-03-18 23:24:36,753] [INFO] Task started: Blastn
[2023-03-18 23:24:36,753] [INFO] Running command: blastn -query OceanDNA-b26823/markers.fasta -db /var/lib/cwl/stgfd57d87a-b294-48bd-8c30-c418d707e5bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26823/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:24:37,916] [INFO] Task succeeded: Blastn
[2023-03-18 23:24:37,917] [INFO] Selected 20 target genomes.
[2023-03-18 23:24:37,917] [INFO] Target genome list was writen to OceanDNA-b26823/target_genomes_gtdb.txt
[2023-03-18 23:24:37,936] [INFO] Task started: fastANI
[2023-03-18 23:24:37,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg19841b6f-7a0b-40c7-bb17-ee5a6926da18/OceanDNA-b26823.fa --refList OceanDNA-b26823/target_genomes_gtdb.txt --output OceanDNA-b26823/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:24:58,301] [INFO] Task succeeded: fastANI
[2023-03-18 23:24:58,312] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:24:58,312] [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_001889605.1	s__Mesorhizobium_E oceanicum	96.5135	1230	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014495845.1	s__Mesorhizobium_E sp014495845	81.5616	831	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970795.1	s__Mesorhizobium_E carbonis	80.8465	718	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	79.8382	565	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	79.5111	664	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339215.1	s__DUSC01 sp008933895	79.4417	612	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	79.4064	309	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	79.3488	475	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	79.2952	594	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	79.1249	579	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442815.1	s__Mesorhizobium sp006442815	78.9587	531	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCA_001510895.1	s__Mesorhizobium loti_A	78.9492	542	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289965.1	s__Mesorhizobium atlanticum	78.8453	537	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009742725.1	s__Nitratireductor_D arenosus	78.8423	562	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289945.1	s__Mesorhizobium hawassense	78.7818	545	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	78.7785	512	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016445.2	s__Mesorhizobium sp004016445	78.7401	547	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCF_014873545.1	s__OAS926 sp014873545	78.6734	507	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__OAS926	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520985.1	s__Mesorhizobium sp013520985	78.6104	522	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185715.1	s__Bosea sp900185715	76.5243	273	1370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:24:58,312] [INFO] GTDB search result was written to OceanDNA-b26823/result_gtdb.tsv
[2023-03-18 23:24:58,313] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:24:58,315] [INFO] DFAST_QC result json was written to OceanDNA-b26823/dqc_result.json
[2023-03-18 23:24:58,315] [INFO] DFAST_QC completed!
[2023-03-18 23:24:58,315] [INFO] Total running time: 0h2m10s