[2023-03-14 11:17:27,797] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:17:27,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:17:27,797] [INFO] DQC Reference Directory: /var/lib/cwl/stgec0b3e4d-c614-44c2-b82c-28dc26bbb247/dqc_reference
[2023-03-14 11:17:28,911] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:17:28,911] [INFO] Task started: Prodigal
[2023-03-14 11:17:28,911] [INFO] Running command: cat /var/lib/cwl/stg66ca340c-dac5-47ad-a0df-cc9d71c4817b/OceanDNA-b26794.fa | prodigal -d OceanDNA-b26794/cds.fna -a OceanDNA-b26794/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:17:46,819] [INFO] Task succeeded: Prodigal
[2023-03-14 11:17:46,819] [INFO] Task started: HMMsearch
[2023-03-14 11:17:46,819] [INFO] Running command: hmmsearch --tblout OceanDNA-b26794/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec0b3e4d-c614-44c2-b82c-28dc26bbb247/dqc_reference/reference_markers.hmm OceanDNA-b26794/protein.faa > /dev/null
[2023-03-14 11:17:47,010] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:17:47,011] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg66ca340c-dac5-47ad-a0df-cc9d71c4817b/OceanDNA-b26794.fa]
[2023-03-14 11:17:47,037] [INFO] Query marker FASTA was written to OceanDNA-b26794/markers.fasta
[2023-03-14 11:17:47,037] [INFO] Task started: Blastn
[2023-03-14 11:17:47,037] [INFO] Running command: blastn -query OceanDNA-b26794/markers.fasta -db /var/lib/cwl/stgec0b3e4d-c614-44c2-b82c-28dc26bbb247/dqc_reference/reference_markers.fasta -out OceanDNA-b26794/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:17:47,688] [INFO] Task succeeded: Blastn
[2023-03-14 11:17:47,689] [INFO] Selected 20 target genomes.
[2023-03-14 11:17:47,690] [INFO] Target genome list was writen to OceanDNA-b26794/target_genomes.txt
[2023-03-14 11:17:47,704] [INFO] Task started: fastANI
[2023-03-14 11:17:47,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg66ca340c-dac5-47ad-a0df-cc9d71c4817b/OceanDNA-b26794.fa --refList OceanDNA-b26794/target_genomes.txt --output OceanDNA-b26794/fastani_result.tsv --threads 1
[2023-03-14 11:18:05,448] [INFO] Task succeeded: fastANI
[2023-03-14 11:18:05,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec0b3e4d-c614-44c2-b82c-28dc26bbb247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:18:05,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec0b3e4d-c614-44c2-b82c-28dc26bbb247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:18:05,460] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:18:05,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:18:05,460] [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
Rhizobium halophytocola	strain=DSM 21600	GCA_017873095.1	735519	735519	type	True	79.1015	418	942	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	78.8419	394	942	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	78.6997	351	942	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	78.5663	371	942	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	78.5543	369	942	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	78.5065	379	942	95	below_threshold
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	78.4535	356	942	95	below_threshold
Rhizobium daejeonense	strain=CCBAU10050	GCA_011045155.1	240521	240521	type	True	78.4165	359	942	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	78.0522	322	942	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	77.9913	309	942	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.9412	314	942	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	77.9123	324	942	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	77.8056	271	942	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	77.8024	315	942	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	77.7718	317	942	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	77.7169	308	942	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	77.688	314	942	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	77.6653	314	942	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	77.6539	276	942	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	77.3674	270	942	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:18:05,461] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26794/tc_result.tsv
[2023-03-14 11:18:05,461] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:18:05,461] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:18:05,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec0b3e4d-c614-44c2-b82c-28dc26bbb247/dqc_reference/checkm_data
[2023-03-14 11:18:05,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:18:05,468] [INFO] Task started: CheckM
[2023-03-14 11:18:05,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26794/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26794/checkm_input OceanDNA-b26794/checkm_result
[2023-03-14 11:18:52,780] [INFO] Task succeeded: CheckM
[2023-03-14 11:18:52,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:18:52,856] [INFO] ===== Completeness check finished =====
[2023-03-14 11:18:52,856] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:18:52,856] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26794/markers.fasta)
[2023-03-14 11:18:52,856] [INFO] Task started: Blastn
[2023-03-14 11:18:52,856] [INFO] Running command: blastn -query OceanDNA-b26794/markers.fasta -db /var/lib/cwl/stgec0b3e4d-c614-44c2-b82c-28dc26bbb247/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26794/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:18:53,869] [INFO] Task succeeded: Blastn
[2023-03-14 11:18:53,872] [INFO] Selected 24 target genomes.
[2023-03-14 11:18:53,872] [INFO] Target genome list was writen to OceanDNA-b26794/target_genomes_gtdb.txt
[2023-03-14 11:18:53,947] [INFO] Task started: fastANI
[2023-03-14 11:18:53,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg66ca340c-dac5-47ad-a0df-cc9d71c4817b/OceanDNA-b26794.fa --refList OceanDNA-b26794/target_genomes_gtdb.txt --output OceanDNA-b26794/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:19:14,940] [INFO] Task succeeded: fastANI
[2023-03-14 11:19:14,953] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:19:14,954] [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_017873095.1	s__Allorhizobium halophytocola	79.1015	418	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900492205.1	s__Allorhizobium naphthalenivorans_A	78.8032	395	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.27	95.27	0.88	0.88	2	-
GCA_002796995.1	s__Allorhizobium sp002796995	78.7414	425	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
GCF_902706095.1	s__Allorhizobium sp902706095	78.7372	385	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912145.1	s__Allorhizobium rhizophilum	78.7067	351	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.70	95.70	0.88	0.88	2	-
GCF_000247475.1	s__Allorhizobium sp000247475	78.6696	380	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470155.1	s__Allorhizobium sp900470155	78.6232	406	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912135.1	s__Allorhizobium rosettiformans	78.5892	369	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCF_002600635.1	s__Allorhizobium sp002600635	78.5742	391	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205195.1	s__Allorhizobium wuzhouense	78.5172	378	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.59	97.59	0.92	0.92	2	-
GCF_014280875.1	s__Allorhizobium daejeonense	78.471	354	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	3	-
GCA_003248775.1	s__Allorhizobium sp003248775	78.4446	352	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473805.1	s__Allorhizobium sp900473805	78.3013	356	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.45	97.28	0.98	0.92	6	-
GCF_014237835.1	s__Allorhizobium sp014237835	78.2725	345	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877135.1	s__Rhizobium_A galegae_A	78.1315	326	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014126615.1	s__Allorhizobium thiooxidans	78.0635	321	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466005.1	s__Allorhizobium sp900466005	78.0454	315	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.03	99.00	0.93	0.93	3	-
GCA_900471515.1	s__Rhizobium sp900471515	78.0353	318	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	98.55	0.92	0.91	6	-
GCF_000271845.1	s__Rhizobium leguminosarum_G	77.9411	319	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000985875.1	s__Neorhizobium galegae_C	77.9228	308	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCF_002531935.1	s__Rhizobium chutanense	77.9123	324	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.76	96.76	0.89	0.89	2	-
GCF_011046245.1	s__Rhizobium_A pseudoryzae	77.7718	317	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211285.1	s__Rhizobium sp002211285	77.7682	309	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003985145.1	s__Rhizobium anhuiense	77.6759	313	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.85	98.46	0.91	0.88	19	-
--------------------------------------------------------------------------------
[2023-03-14 11:19:14,955] [INFO] GTDB search result was written to OceanDNA-b26794/result_gtdb.tsv
[2023-03-14 11:19:14,958] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:19:14,962] [INFO] DFAST_QC result json was written to OceanDNA-b26794/dqc_result.json
[2023-03-14 11:19:14,962] [INFO] DFAST_QC completed!
[2023-03-14 11:19:14,962] [INFO] Total running time: 0h1m47s