[2023-03-17 06:30:49,100] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,101] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg75c7a17b-14b3-4a28-8c2c-eeace80e1dec/dqc_reference
[2023-03-17 06:30:50,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,293] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stg44ced7cd-de49-45c6-9e5e-86e74bb7bbae/OceanDNA-b33386.fa | prodigal -d OceanDNA-b33386/cds.fna -a OceanDNA-b33386/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:03,892] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:03,892] [INFO] Task started: HMMsearch
[2023-03-17 06:31:03,892] [INFO] Running command: hmmsearch --tblout OceanDNA-b33386/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75c7a17b-14b3-4a28-8c2c-eeace80e1dec/dqc_reference/reference_markers.hmm OceanDNA-b33386/protein.faa > /dev/null
[2023-03-17 06:31:04,100] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:04,100] [INFO] Found 6/6 markers.
[2023-03-17 06:31:04,119] [INFO] Query marker FASTA was written to OceanDNA-b33386/markers.fasta
[2023-03-17 06:31:04,119] [INFO] Task started: Blastn
[2023-03-17 06:31:04,119] [INFO] Running command: blastn -query OceanDNA-b33386/markers.fasta -db /var/lib/cwl/stg75c7a17b-14b3-4a28-8c2c-eeace80e1dec/dqc_reference/reference_markers.fasta -out OceanDNA-b33386/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:04,836] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:04,837] [INFO] Selected 21 target genomes.
[2023-03-17 06:31:04,837] [INFO] Target genome list was writen to OceanDNA-b33386/target_genomes.txt
[2023-03-17 06:31:04,847] [INFO] Task started: fastANI
[2023-03-17 06:31:04,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ced7cd-de49-45c6-9e5e-86e74bb7bbae/OceanDNA-b33386.fa --refList OceanDNA-b33386/target_genomes.txt --output OceanDNA-b33386/fastani_result.tsv --threads 1
[2023-03-17 06:31:21,546] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:21,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75c7a17b-14b3-4a28-8c2c-eeace80e1dec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:21,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75c7a17b-14b3-4a28-8c2c-eeace80e1dec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:21,558] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:21,558] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:21,558] [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
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	84.3668	393	555	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	84.328	424	555	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	82.4122	358	555	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	79.1383	197	555	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	78.9112	231	555	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.5563	213	555	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	78.5474	244	555	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	78.5273	236	555	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	78.4881	213	555	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	78.4314	250	555	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.3335	249	555	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	78.227	180	555	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.1725	232	555	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	78.0386	204	555	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	77.9786	199	555	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	77.8816	199	555	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	77.8442	159	555	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	77.8055	180	555	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	77.7064	168	555	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	77.6187	145	555	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	77.6033	178	555	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:21,558] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33386/tc_result.tsv
[2023-03-17 06:31:21,558] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:21,558] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:21,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75c7a17b-14b3-4a28-8c2c-eeace80e1dec/dqc_reference/checkm_data
[2023-03-17 06:31:21,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:21,563] [INFO] Task started: CheckM
[2023-03-17 06:31:21,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33386/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33386/checkm_input OceanDNA-b33386/checkm_result
[2023-03-17 06:32:00,278] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:00,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:00,280] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:00,280] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:00,281] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33386/markers.fasta)
[2023-03-17 06:32:00,281] [INFO] Task started: Blastn
[2023-03-17 06:32:00,281] [INFO] Running command: blastn -query OceanDNA-b33386/markers.fasta -db /var/lib/cwl/stg75c7a17b-14b3-4a28-8c2c-eeace80e1dec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33386/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:01,561] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:01,562] [INFO] Selected 18 target genomes.
[2023-03-17 06:32:01,562] [INFO] Target genome list was writen to OceanDNA-b33386/target_genomes_gtdb.txt
[2023-03-17 06:32:01,814] [INFO] Task started: fastANI
[2023-03-17 06:32:01,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ced7cd-de49-45c6-9e5e-86e74bb7bbae/OceanDNA-b33386.fa --refList OceanDNA-b33386/target_genomes_gtdb.txt --output OceanDNA-b33386/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:12,973] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:12,983] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:12,983] [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_017848645.1	s__Limnohabitans_A sp017848645	86.6811	462	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.74	96.96	0.88	0.84	5	-
GCF_003063355.1	s__Limnohabitans_A sp003063355	85.9374	474	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063645.1	s__Limnohabitans_A sp003063645	85.7052	465	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412535.1	s__Limnohabitans_A sp001412535	85.462	453	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903932865.1	s__Limnohabitans_A sp903932865	85.3891	458	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.93	99.93	0.98	0.98	2	-
GCF_001269385.1	s__Limnohabitans_A sp001269385	85.0413	425	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063665.1	s__Limnohabitans_A sp003063665	84.9633	425	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	96.02	95.55	0.82	0.79	4	-
GCA_002256145.1	s__Limnohabitans_A sp002256145	84.7804	440	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269345.1	s__Limnohabitans_A sp001269345	84.6942	426	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903953985.1	s__Limnohabitans_A sp903953985	84.3675	375	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	98.68	98.68	0.76	0.76	2	-
GCF_003063455.1	s__Limnohabitans_A parvus	84.3668	393	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778285.1	s__Limnohabitans_A sp002778285	84.2458	425	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063505.1	s__Limnohabitans_A sp003063505	84.144	409	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894995.1	s__Limnohabitans_A sp903894995	84.0541	373	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.22	99.21	0.83	0.82	3	-
GCF_000293865.2	s__Limnohabitans_A sp000293865	83.7664	423	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063575.1	s__Limnohabitans_A sp003063575	83.6623	379	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657605.1	s__Limnohabitans_A sp015657605	83.4653	245	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017986605.1	s__Limnohabitans_A sp017986605	83.2125	314	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:12,983] [INFO] GTDB search result was written to OceanDNA-b33386/result_gtdb.tsv
[2023-03-17 06:32:12,984] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:12,986] [INFO] DFAST_QC result json was written to OceanDNA-b33386/dqc_result.json
[2023-03-17 06:32:12,986] [INFO] DFAST_QC completed!
[2023-03-17 06:32:12,986] [INFO] Total running time: 0h1m24s