[2023-03-18 23:45:35,839] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:45:35,839] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:45:35,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg33495e48-512c-4776-9e15-b1b6a23e2ece/dqc_reference
[2023-03-18 23:45:37,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:45:37,733] [INFO] Task started: Prodigal
[2023-03-18 23:45:37,733] [INFO] Running command: cat /var/lib/cwl/stg8f8162ce-8269-4020-8420-42526ab130cb/OceanDNA-b33314.fa | prodigal -d OceanDNA-b33314/cds.fna -a OceanDNA-b33314/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:45:53,111] [INFO] Task succeeded: Prodigal
[2023-03-18 23:45:53,111] [INFO] Task started: HMMsearch
[2023-03-18 23:45:53,111] [INFO] Running command: hmmsearch --tblout OceanDNA-b33314/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33495e48-512c-4776-9e15-b1b6a23e2ece/dqc_reference/reference_markers.hmm OceanDNA-b33314/protein.faa > /dev/null
[2023-03-18 23:45:53,330] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:45:53,331] [INFO] Found 6/6 markers.
[2023-03-18 23:45:53,360] [INFO] Query marker FASTA was written to OceanDNA-b33314/markers.fasta
[2023-03-18 23:45:53,361] [INFO] Task started: Blastn
[2023-03-18 23:45:53,361] [INFO] Running command: blastn -query OceanDNA-b33314/markers.fasta -db /var/lib/cwl/stg33495e48-512c-4776-9e15-b1b6a23e2ece/dqc_reference/reference_markers.fasta -out OceanDNA-b33314/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:54,209] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:54,209] [INFO] Selected 12 target genomes.
[2023-03-18 23:45:54,210] [INFO] Target genome list was writen to OceanDNA-b33314/target_genomes.txt
[2023-03-18 23:45:54,216] [INFO] Task started: fastANI
[2023-03-18 23:45:54,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f8162ce-8269-4020-8420-42526ab130cb/OceanDNA-b33314.fa --refList OceanDNA-b33314/target_genomes.txt --output OceanDNA-b33314/fastani_result.tsv --threads 1
[2023-03-18 23:46:04,128] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:04,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33495e48-512c-4776-9e15-b1b6a23e2ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:46:04,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33495e48-512c-4776-9e15-b1b6a23e2ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:46:04,136] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:46:04,136] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:46:04,137] [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
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	91.9091	488	601	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	91.9059	492	601	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	91.8947	499	601	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	89.1956	451	601	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	86.0215	423	601	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.3323	265	601	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.8364	274	601	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.5382	284	601	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	79.4935	238	601	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	78.374	184	601	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	78.1735	155	601	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.0806	243	601	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:46:04,137] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33314/tc_result.tsv
[2023-03-18 23:46:04,137] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:46:04,137] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:46:04,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33495e48-512c-4776-9e15-b1b6a23e2ece/dqc_reference/checkm_data
[2023-03-18 23:46:04,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:46:04,236] [INFO] Task started: CheckM
[2023-03-18 23:46:04,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33314/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33314/checkm_input OceanDNA-b33314/checkm_result
[2023-03-18 23:46:45,125] [INFO] Task succeeded: CheckM
[2023-03-18 23:46:45,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.63%
Contamintation: 5.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:46:45,128] [INFO] ===== Completeness check finished =====
[2023-03-18 23:46:45,128] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:46:45,128] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33314/markers.fasta)
[2023-03-18 23:46:45,129] [INFO] Task started: Blastn
[2023-03-18 23:46:45,129] [INFO] Running command: blastn -query OceanDNA-b33314/markers.fasta -db /var/lib/cwl/stg33495e48-512c-4776-9e15-b1b6a23e2ece/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33314/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:46:46,866] [INFO] Task succeeded: Blastn
[2023-03-18 23:46:46,867] [INFO] Selected 8 target genomes.
[2023-03-18 23:46:46,867] [INFO] Target genome list was writen to OceanDNA-b33314/target_genomes_gtdb.txt
[2023-03-18 23:46:46,873] [INFO] Task started: fastANI
[2023-03-18 23:46:46,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f8162ce-8269-4020-8420-42526ab130cb/OceanDNA-b33314.fa --refList OceanDNA-b33314/target_genomes_gtdb.txt --output OceanDNA-b33314/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:46:52,421] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:52,427] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:46:52,427] [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_011772445.1	s__Hydrogenophaga sp011772445	92.0794	479	601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	9	-
GCF_000723405.1	s__Hydrogenophaga intermedia	91.8947	499	601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.52	98.31	0.93	0.83	5	-
GCF_003417535.1	s__Hydrogenophaga borbori	89.1955	451	601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.89	96.31	0.93	0.91	7	-
GCA_016741995.1	s__Hydrogenophaga sp016741995	86.2055	350	601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	86.0317	423	601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	82.4119	280	601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823485.1	s__Hydrogenophaga sp013823485	81.5783	261	601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	98.29	98.29	0.80	0.80	2	-
GCA_001724785.1	s__Giesbergeria sp001724785	79.8772	172	601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:46:52,427] [INFO] GTDB search result was written to OceanDNA-b33314/result_gtdb.tsv
[2023-03-18 23:46:52,427] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:46:52,429] [INFO] DFAST_QC result json was written to OceanDNA-b33314/dqc_result.json
[2023-03-18 23:46:52,429] [INFO] DFAST_QC completed!
[2023-03-18 23:46:52,429] [INFO] Total running time: 0h1m17s