[2023-03-18 21:43:12,584] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:43:12,584] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:43:12,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg936adce1-6df9-4111-a565-bff1550b4744/dqc_reference
[2023-03-18 21:43:13,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:43:13,685] [INFO] Task started: Prodigal
[2023-03-18 21:43:13,686] [INFO] Running command: cat /var/lib/cwl/stg81fad002-44b2-46aa-9a2b-46530bad8b19/OceanDNA-b37641.fa | prodigal -d OceanDNA-b37641/cds.fna -a OceanDNA-b37641/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:43:33,016] [INFO] Task succeeded: Prodigal
[2023-03-18 21:43:33,016] [INFO] Task started: HMMsearch
[2023-03-18 21:43:33,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b37641/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg936adce1-6df9-4111-a565-bff1550b4744/dqc_reference/reference_markers.hmm OceanDNA-b37641/protein.faa > /dev/null
[2023-03-18 21:43:33,214] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:43:33,214] [INFO] Found 6/6 markers.
[2023-03-18 21:43:33,235] [INFO] Query marker FASTA was written to OceanDNA-b37641/markers.fasta
[2023-03-18 21:43:33,236] [INFO] Task started: Blastn
[2023-03-18 21:43:33,236] [INFO] Running command: blastn -query OceanDNA-b37641/markers.fasta -db /var/lib/cwl/stg936adce1-6df9-4111-a565-bff1550b4744/dqc_reference/reference_markers.fasta -out OceanDNA-b37641/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:43:33,759] [INFO] Task succeeded: Blastn
[2023-03-18 21:43:33,760] [INFO] Selected 31 target genomes.
[2023-03-18 21:43:33,760] [INFO] Target genome list was writen to OceanDNA-b37641/target_genomes.txt
[2023-03-18 21:43:33,776] [INFO] Task started: fastANI
[2023-03-18 21:43:33,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg81fad002-44b2-46aa-9a2b-46530bad8b19/OceanDNA-b37641.fa --refList OceanDNA-b37641/target_genomes.txt --output OceanDNA-b37641/fastani_result.tsv --threads 1
[2023-03-18 21:43:50,969] [INFO] Task succeeded: fastANI
[2023-03-18 21:43:50,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg936adce1-6df9-4111-a565-bff1550b4744/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:43:50,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg936adce1-6df9-4111-a565-bff1550b4744/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:43:50,975] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:43:50,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:43:50,975] [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
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	76.5522	52	1063	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.2811	54	1063	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.2524	55	1063	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.2257	56	1063	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.1817	62	1063	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:43:50,975] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37641/tc_result.tsv
[2023-03-18 21:43:50,975] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:43:50,975] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:43:50,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg936adce1-6df9-4111-a565-bff1550b4744/dqc_reference/checkm_data
[2023-03-18 21:43:50,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:43:50,981] [INFO] Task started: CheckM
[2023-03-18 21:43:50,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37641/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37641/checkm_input OceanDNA-b37641/checkm_result
[2023-03-18 21:44:40,152] [INFO] Task succeeded: CheckM
[2023-03-18 21:44:40,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:44:40,155] [INFO] ===== Completeness check finished =====
[2023-03-18 21:44:40,156] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:44:40,156] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37641/markers.fasta)
[2023-03-18 21:44:40,157] [INFO] Task started: Blastn
[2023-03-18 21:44:40,157] [INFO] Running command: blastn -query OceanDNA-b37641/markers.fasta -db /var/lib/cwl/stg936adce1-6df9-4111-a565-bff1550b4744/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37641/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:44:40,884] [INFO] Task succeeded: Blastn
[2023-03-18 21:44:40,885] [INFO] Selected 34 target genomes.
[2023-03-18 21:44:40,885] [INFO] Target genome list was writen to OceanDNA-b37641/target_genomes_gtdb.txt
[2023-03-18 21:44:40,930] [INFO] Task started: fastANI
[2023-03-18 21:44:40,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg81fad002-44b2-46aa-9a2b-46530bad8b19/OceanDNA-b37641.fa --refList OceanDNA-b37641/target_genomes_gtdb.txt --output OceanDNA-b37641/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:45:02,207] [INFO] Task succeeded: fastANI
[2023-03-18 21:45:02,213] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:45:02,213] [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_002862465.1	s__Halioglobus sp002862465	81.4472	694	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705825.1	s__Halioglobus japonicus_A	76.7363	162	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646415.1	s__Halioglobus sp003646415	76.7034	69	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	76.5612	59	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	76.5522	52	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_003719295.1	s__Haliea alexandrii	76.1817	62	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.1766	55	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	76.1494	61	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646405.1	s__Halioglobus sp003646405	75.8735	79	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:45:02,213] [INFO] GTDB search result was written to OceanDNA-b37641/result_gtdb.tsv
[2023-03-18 21:45:02,213] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:45:02,214] [INFO] DFAST_QC result json was written to OceanDNA-b37641/dqc_result.json
[2023-03-18 21:45:02,214] [INFO] DFAST_QC completed!
[2023-03-18 21:45:02,214] [INFO] Total running time: 0h1m50s