[2023-03-15 05:29:10,773] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:10,784] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:10,784] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d6e1b22-fd4d-4f30-8ea9-4842fdb6636e/dqc_reference
[2023-03-15 05:29:12,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:12,382] [INFO] Task started: Prodigal
[2023-03-15 05:29:12,382] [INFO] Running command: cat /var/lib/cwl/stg47ff144c-f389-428f-b7f9-ec964509afe8/OceanDNA-b33443.fa | prodigal -d OceanDNA-b33443/cds.fna -a OceanDNA-b33443/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:29,741] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:29,741] [INFO] Task started: HMMsearch
[2023-03-15 05:29:29,741] [INFO] Running command: hmmsearch --tblout OceanDNA-b33443/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d6e1b22-fd4d-4f30-8ea9-4842fdb6636e/dqc_reference/reference_markers.hmm OceanDNA-b33443/protein.faa > /dev/null
[2023-03-15 05:29:29,988] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:29,988] [INFO] Found 6/6 markers.
[2023-03-15 05:29:30,005] [INFO] Query marker FASTA was written to OceanDNA-b33443/markers.fasta
[2023-03-15 05:29:30,006] [INFO] Task started: Blastn
[2023-03-15 05:29:30,006] [INFO] Running command: blastn -query OceanDNA-b33443/markers.fasta -db /var/lib/cwl/stg6d6e1b22-fd4d-4f30-8ea9-4842fdb6636e/dqc_reference/reference_markers.fasta -out OceanDNA-b33443/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:30,633] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:30,633] [INFO] Selected 23 target genomes.
[2023-03-15 05:29:30,634] [INFO] Target genome list was writen to OceanDNA-b33443/target_genomes.txt
[2023-03-15 05:29:30,647] [INFO] Task started: fastANI
[2023-03-15 05:29:30,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ff144c-f389-428f-b7f9-ec964509afe8/OceanDNA-b33443.fa --refList OceanDNA-b33443/target_genomes.txt --output OceanDNA-b33443/fastani_result.tsv --threads 1
[2023-03-15 05:29:45,554] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:45,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d6e1b22-fd4d-4f30-8ea9-4842fdb6636e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:45,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d6e1b22-fd4d-4f30-8ea9-4842fdb6636e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:45,563] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:45,563] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:45,563] [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 planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	76.3929	114	839	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	76.3518	75	839	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.3145	89	839	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.1677	65	839	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	76.166	62	839	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	76.1311	112	839	95	below_threshold
Serpentinimonas raichei	strain=A1	GCA_000828895.1	1458425	1458425	type	True	76.1286	56	839	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	76.0387	75	839	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	75.9479	73	839	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	75.852	82	839	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	75.6799	67	839	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	75.5031	64	839	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	75.4855	65	839	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:45,563] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33443/tc_result.tsv
[2023-03-15 05:29:45,563] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:45,563] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:45,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d6e1b22-fd4d-4f30-8ea9-4842fdb6636e/dqc_reference/checkm_data
[2023-03-15 05:29:45,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:45,568] [INFO] Task started: CheckM
[2023-03-15 05:29:45,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33443/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33443/checkm_input OceanDNA-b33443/checkm_result
[2023-03-15 05:30:31,442] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:31,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:31,445] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:31,445] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:31,445] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33443/markers.fasta)
[2023-03-15 05:30:31,445] [INFO] Task started: Blastn
[2023-03-15 05:30:31,445] [INFO] Running command: blastn -query OceanDNA-b33443/markers.fasta -db /var/lib/cwl/stg6d6e1b22-fd4d-4f30-8ea9-4842fdb6636e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33443/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:32,524] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:32,525] [INFO] Selected 27 target genomes.
[2023-03-15 05:30:32,525] [INFO] Target genome list was writen to OceanDNA-b33443/target_genomes_gtdb.txt
[2023-03-15 05:30:32,547] [INFO] Task started: fastANI
[2023-03-15 05:30:32,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ff144c-f389-428f-b7f9-ec964509afe8/OceanDNA-b33443.fa --refList OceanDNA-b33443/target_genomes_gtdb.txt --output OceanDNA-b33443/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:48,062] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:48,076] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:30:48,076] [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_000496475.1	s__RS62 sp000496475	98.6114	789	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	98.53	98.53	0.95	0.95	2	conclusive
GCA_018607835.1	s__RS62 sp002340675	77.4485	135	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	99.19	98.96	0.91	0.88	5	-
GCA_903892175.1	s__Limnohabitans sp903892175	76.6689	93	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.61	96.75	0.84	0.82	4	-
GCF_003063265.1	s__Limnohabitans_A sp003063265	76.6071	93	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.80	97.80	0.90	0.90	2	-
GCF_018474005.1	s__Rhodoferax sp018474005	76.565	83	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903952885.1	s__Limnohabitans sp903952885	76.4398	68	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.13	99.13	0.83	0.83	2	-
GCA_009693505.1	s__Limnohabitans_A sp009693505	76.3602	90	839	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_003063335.1	s__Limnohabitans_A sp003063335	76.2865	102	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.88	99.88	0.96	0.96	2	-
GCF_010020825.1	s__Giesbergeria sp010020825	76.2722	68	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.40	98.40	0.98	0.98	2	-
GCF_900111115.1	s__Giesbergeria anulus	76.2719	70	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903880855.1	s__Limnohabitans sp903880855	76.2109	76	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.14	98.09	0.92	0.91	4	-
GCF_001428625.1	s__Hydrogenophaga sp001428625	76.1991	100	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517545.1	s__Limnohabitans_A sp001517545	76.1121	121	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	96.89	95.29	0.97	0.96	4	-
GCF_000828895.1	s__Serpentinomonas raichei	76.0825	55	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163715.1	s__Rhodoferax sp002163715	76.0665	86	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	97.64	97.64	0.97	0.97	2	-
GCF_003669015.1	s__Acidovorax sp002754495	76.0537	82	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.04	96.96	0.91	0.90	3	-
GCF_005876985.1	s__Rhodoferax bucti	76.0143	88	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903961095.1	s__Limnohabitans_A sp903961095	76.0009	79	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.26	99.25	0.86	0.84	3	-
GCA_003268905.1	s__Acidovorax defluvii	75.9743	71	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.35	96.64	0.82	0.75	12	-
GCA_018882835.1	s__Limnohabitans sp018882835	75.9509	96	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256145.1	s__Limnohabitans_A sp002256145	75.9419	104	839	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_001713375.1	s__Hydrogenophaga sp001713375	75.9223	107	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837135.1	s__Macromonas bipunctata	75.8181	77	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011772445.1	s__Hydrogenophaga sp011772445	75.6896	72	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	9	-
GCF_000211835.1	s__Hylemonella gracilis	75.5487	50	839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:48,076] [INFO] GTDB search result was written to OceanDNA-b33443/result_gtdb.tsv
[2023-03-15 05:30:48,076] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:48,078] [INFO] DFAST_QC result json was written to OceanDNA-b33443/dqc_result.json
[2023-03-15 05:30:48,078] [INFO] DFAST_QC completed!
[2023-03-15 05:30:48,079] [INFO] Total running time: 0h1m37s