[2023-03-15 23:42:29,664] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,664] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c58ab39-6bd2-432c-b7e2-e130750cc78f/dqc_reference
[2023-03-15 23:42:31,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,277] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,277] [INFO] Running command: cat /var/lib/cwl/stga1c23f8d-7879-4bcf-8e7c-9a86ca91a575/OceanDNA-b26901.fa | prodigal -d OceanDNA-b26901/cds.fna -a OceanDNA-b26901/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:54,514] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:54,514] [INFO] Task started: HMMsearch
[2023-03-15 23:42:54,514] [INFO] Running command: hmmsearch --tblout OceanDNA-b26901/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c58ab39-6bd2-432c-b7e2-e130750cc78f/dqc_reference/reference_markers.hmm OceanDNA-b26901/protein.faa > /dev/null
[2023-03-15 23:42:54,739] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:54,739] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga1c23f8d-7879-4bcf-8e7c-9a86ca91a575/OceanDNA-b26901.fa]
[2023-03-15 23:42:54,767] [INFO] Query marker FASTA was written to OceanDNA-b26901/markers.fasta
[2023-03-15 23:42:54,768] [INFO] Task started: Blastn
[2023-03-15 23:42:54,768] [INFO] Running command: blastn -query OceanDNA-b26901/markers.fasta -db /var/lib/cwl/stg9c58ab39-6bd2-432c-b7e2-e130750cc78f/dqc_reference/reference_markers.fasta -out OceanDNA-b26901/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:55,574] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:55,575] [INFO] Selected 21 target genomes.
[2023-03-15 23:42:55,575] [INFO] Target genome list was writen to OceanDNA-b26901/target_genomes.txt
[2023-03-15 23:42:55,591] [INFO] Task started: fastANI
[2023-03-15 23:42:55,591] [INFO] Running command: fastANI --query /var/lib/cwl/stga1c23f8d-7879-4bcf-8e7c-9a86ca91a575/OceanDNA-b26901.fa --refList OceanDNA-b26901/target_genomes.txt --output OceanDNA-b26901/fastani_result.tsv --threads 1
[2023-03-15 23:43:21,317] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:21,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c58ab39-6bd2-432c-b7e2-e130750cc78f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:43:21,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c58ab39-6bd2-432c-b7e2-e130750cc78f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:43:21,330] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:43:21,330] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:43:21,330] [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
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	80.9545	742	1255	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	80.9164	727	1255	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	80.8857	723	1255	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	80.876	632	1255	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	80.8759	695	1255	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	80.8386	698	1255	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	80.8336	738	1255	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	80.7441	728	1255	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	80.7134	732	1255	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	80.6918	725	1255	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	80.6183	732	1255	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	80.6177	695	1255	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	80.574	706	1255	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	80.5739	673	1255	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	80.5722	656	1255	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	80.5715	658	1255	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	80.526	656	1255	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	80.2707	655	1255	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.2693	557	1255	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.2519	559	1255	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	78.4302	444	1255	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:43:21,331] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26901/tc_result.tsv
[2023-03-15 23:43:21,331] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:43:21,331] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:43:21,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c58ab39-6bd2-432c-b7e2-e130750cc78f/dqc_reference/checkm_data
[2023-03-15 23:43:21,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:43:21,468] [INFO] Task started: CheckM
[2023-03-15 23:43:21,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26901/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26901/checkm_input OceanDNA-b26901/checkm_result
[2023-03-15 23:44:18,743] [INFO] Task succeeded: CheckM
[2023-03-15 23:44:18,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:44:18,748] [INFO] ===== Completeness check finished =====
[2023-03-15 23:44:18,749] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:44:18,749] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26901/markers.fasta)
[2023-03-15 23:44:18,749] [INFO] Task started: Blastn
[2023-03-15 23:44:18,750] [INFO] Running command: blastn -query OceanDNA-b26901/markers.fasta -db /var/lib/cwl/stg9c58ab39-6bd2-432c-b7e2-e130750cc78f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26901/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:44:20,221] [INFO] Task succeeded: Blastn
[2023-03-15 23:44:20,223] [INFO] Selected 22 target genomes.
[2023-03-15 23:44:20,223] [INFO] Target genome list was writen to OceanDNA-b26901/target_genomes_gtdb.txt
[2023-03-15 23:44:20,258] [INFO] Task started: fastANI
[2023-03-15 23:44:20,259] [INFO] Running command: fastANI --query /var/lib/cwl/stga1c23f8d-7879-4bcf-8e7c-9a86ca91a575/OceanDNA-b26901.fa --refList OceanDNA-b26901/target_genomes_gtdb.txt --output OceanDNA-b26901/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:44:43,599] [INFO] Task succeeded: fastANI
[2023-03-15 23:44:43,611] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:44:43,611] [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_018823835.1	s__RCIZ01 sp018823835	91.5822	1080	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_003666685.1	s__RCIZ01 sp003666685	81.7934	766	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	81.1613	740	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCF_003601975.1	s__Mesorhizobium waimense	80.9896	737	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359125.1	s__Mesorhizobium sp000359125	80.8775	716	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	80.6979	615	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442315.1	s__Mesorhizobium sp006442315	80.6727	720	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010325.2	s__Mesorhizobium sp004010325	80.6636	686	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.05	98.94	0.91	0.90	4	-
GCF_900156895.1	s__Mesorhizobium prunaredense	80.6624	708	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020365.1	s__Mesorhizobium sp004020365	80.6279	699	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.10	96.06	0.82	0.80	8	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	80.6101	650	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	80.583	672	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138625.1	s__Aminobacter ciceronei	80.578	655	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.84	97.89	0.89	0.85	7	-
GCF_004801285.1	s__Mesorhizobium composti	80.5713	658	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCA_004020645.1	s__Mesorhizobium sp004020645	80.5427	706	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	80.4063	484	1255	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_905339215.1	s__DUSC01 sp008933895	80.3918	625	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	80.2755	654	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177325.1	s__Mesorhizobium_A australicum_A	80.2385	634	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793485.1	s__RCIZ01 sp016793485	80.0804	639	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148805.1	s__Aminobacter sp003148805	79.9935	604	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012842935.1	s__DUSC01 sp012842935	79.8025	540	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:44:43,612] [INFO] GTDB search result was written to OceanDNA-b26901/result_gtdb.tsv
[2023-03-15 23:44:43,613] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:44:43,615] [INFO] DFAST_QC result json was written to OceanDNA-b26901/dqc_result.json
[2023-03-15 23:44:43,615] [INFO] DFAST_QC completed!
[2023-03-15 23:44:43,616] [INFO] Total running time: 0h2m14s