[2023-03-18 05:35:37,309] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,310] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg423fbc9d-642c-4e31-a37e-30d40da52159/dqc_reference
[2023-03-18 05:35:38,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,962] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,962] [INFO] Running command: cat /var/lib/cwl/stg6c66217d-f482-4837-bbcf-5a05e9fb13fa/OceanDNA-b26792.fa | prodigal -d OceanDNA-b26792/cds.fna -a OceanDNA-b26792/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:36:00,968] [INFO] Task succeeded: Prodigal
[2023-03-18 05:36:00,968] [INFO] Task started: HMMsearch
[2023-03-18 05:36:00,968] [INFO] Running command: hmmsearch --tblout OceanDNA-b26792/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg423fbc9d-642c-4e31-a37e-30d40da52159/dqc_reference/reference_markers.hmm OceanDNA-b26792/protein.faa > /dev/null
[2023-03-18 05:36:01,177] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:36:01,178] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6c66217d-f482-4837-bbcf-5a05e9fb13fa/OceanDNA-b26792.fa]
[2023-03-18 05:36:01,226] [INFO] Query marker FASTA was written to OceanDNA-b26792/markers.fasta
[2023-03-18 05:36:01,228] [INFO] Task started: Blastn
[2023-03-18 05:36:01,228] [INFO] Running command: blastn -query OceanDNA-b26792/markers.fasta -db /var/lib/cwl/stg423fbc9d-642c-4e31-a37e-30d40da52159/dqc_reference/reference_markers.fasta -out OceanDNA-b26792/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:02,054] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:02,056] [INFO] Selected 24 target genomes.
[2023-03-18 05:36:02,056] [INFO] Target genome list was writen to OceanDNA-b26792/target_genomes.txt
[2023-03-18 05:36:02,069] [INFO] Task started: fastANI
[2023-03-18 05:36:02,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c66217d-f482-4837-bbcf-5a05e9fb13fa/OceanDNA-b26792.fa --refList OceanDNA-b26792/target_genomes.txt --output OceanDNA-b26792/fastani_result.tsv --threads 1
[2023-03-18 05:36:26,296] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:26,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg423fbc9d-642c-4e31-a37e-30d40da52159/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:36:26,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg423fbc9d-642c-4e31-a37e-30d40da52159/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:36:26,311] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:36:26,311] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:36:26,311] [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
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	78.9436	495	1158	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.9017	514	1158	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	78.7225	464	1158	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	78.6731	494	1158	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	78.6597	483	1158	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	78.6406	486	1158	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.6258	451	1158	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	78.6195	488	1158	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	78.607	472	1158	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	78.5924	505	1158	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	78.5891	483	1158	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.5732	520	1158	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	78.5294	456	1158	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.5135	479	1158	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	78.4477	458	1158	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	78.3808	488	1158	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	78.3734	433	1158	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	78.3397	482	1158	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	78.2554	449	1158	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	78.2414	424	1158	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.7407	347	1158	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.7312	348	1158	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	77.0386	214	1158	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.1661	142	1158	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:36:26,312] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26792/tc_result.tsv
[2023-03-18 05:36:26,316] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:36:26,316] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:36:26,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg423fbc9d-642c-4e31-a37e-30d40da52159/dqc_reference/checkm_data
[2023-03-18 05:36:26,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:36:26,324] [INFO] Task started: CheckM
[2023-03-18 05:36:26,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26792/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26792/checkm_input OceanDNA-b26792/checkm_result
[2023-03-18 05:37:20,764] [INFO] Task succeeded: CheckM
[2023-03-18 05:37:20,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:37:20,806] [INFO] ===== Completeness check finished =====
[2023-03-18 05:37:20,807] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:37:20,807] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26792/markers.fasta)
[2023-03-18 05:37:20,808] [INFO] Task started: Blastn
[2023-03-18 05:37:20,808] [INFO] Running command: blastn -query OceanDNA-b26792/markers.fasta -db /var/lib/cwl/stg423fbc9d-642c-4e31-a37e-30d40da52159/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26792/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:37:22,440] [INFO] Task succeeded: Blastn
[2023-03-18 05:37:22,443] [INFO] Selected 14 target genomes.
[2023-03-18 05:37:22,443] [INFO] Target genome list was writen to OceanDNA-b26792/target_genomes_gtdb.txt
[2023-03-18 05:37:22,452] [INFO] Task started: fastANI
[2023-03-18 05:37:22,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c66217d-f482-4837-bbcf-5a05e9fb13fa/OceanDNA-b26792.fa --refList OceanDNA-b26792/target_genomes_gtdb.txt --output OceanDNA-b26792/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:37:36,306] [INFO] Task succeeded: fastANI
[2023-03-18 05:37:36,315] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:37:36,315] [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_017643025.1	s__RCIO01 sp017643025	81.2724	717	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000235.1	s__RCIO01 sp004000235	80.0509	629	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	79.6573	558	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644005.1	s__RCIO01 sp017644005	79.6392	627	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640615.1	s__RCIO01 sp017640615	79.6336	649	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	96.47	96.47	0.92	0.92	2	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	78.8891	525	1158	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_003952385.1	s__Mesorhizobium sp003952385	78.868	486	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCF_003015025.1	s__Nitratireductor_D sp003015025	78.8104	523	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	78.7692	499	1158	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_003952465.1	s__Mesorhizobium sp003952465	78.7287	499	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_003863365.1	s__Mesorhizobium tamadayense	78.6121	502	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427025.1	s__Mesorhizobium sp001427025	78.5048	398	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009812055.1	s__Chelativorans xinjiangense	78.3822	432	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829525.1	s__VLJP01 sp007829525	77.918	339	1158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VLJP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:37:36,317] [INFO] GTDB search result was written to OceanDNA-b26792/result_gtdb.tsv
[2023-03-18 05:37:36,317] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:37:36,320] [INFO] DFAST_QC result json was written to OceanDNA-b26792/dqc_result.json
[2023-03-18 05:37:36,320] [INFO] DFAST_QC completed!
[2023-03-18 05:37:36,320] [INFO] Total running time: 0h1m59s