[2023-03-16 09:53:50,307] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:53:50,308] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:53:50,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg32749a4b-9521-4524-a41d-058653fed155/dqc_reference
[2023-03-16 09:53:51,432] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:53:51,433] [INFO] Task started: Prodigal
[2023-03-16 09:53:51,433] [INFO] Running command: cat /var/lib/cwl/stg6710b028-5c6c-4083-958e-fa781d1179e6/OceanDNA-b37976.fa | prodigal -d OceanDNA-b37976/cds.fna -a OceanDNA-b37976/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:54:04,149] [INFO] Task succeeded: Prodigal
[2023-03-16 09:54:04,150] [INFO] Task started: HMMsearch
[2023-03-16 09:54:04,150] [INFO] Running command: hmmsearch --tblout OceanDNA-b37976/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32749a4b-9521-4524-a41d-058653fed155/dqc_reference/reference_markers.hmm OceanDNA-b37976/protein.faa > /dev/null
[2023-03-16 09:54:04,321] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:54:04,321] [INFO] Found 6/6 markers.
[2023-03-16 09:54:04,345] [INFO] Query marker FASTA was written to OceanDNA-b37976/markers.fasta
[2023-03-16 09:54:04,346] [INFO] Task started: Blastn
[2023-03-16 09:54:04,347] [INFO] Running command: blastn -query OceanDNA-b37976/markers.fasta -db /var/lib/cwl/stg32749a4b-9521-4524-a41d-058653fed155/dqc_reference/reference_markers.fasta -out OceanDNA-b37976/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:54:04,923] [INFO] Task succeeded: Blastn
[2023-03-16 09:54:04,924] [INFO] Selected 26 target genomes.
[2023-03-16 09:54:04,924] [INFO] Target genome list was writen to OceanDNA-b37976/target_genomes.txt
[2023-03-16 09:54:04,933] [INFO] Task started: fastANI
[2023-03-16 09:54:04,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg6710b028-5c6c-4083-958e-fa781d1179e6/OceanDNA-b37976.fa --refList OceanDNA-b37976/target_genomes.txt --output OceanDNA-b37976/fastani_result.tsv --threads 1
[2023-03-16 09:54:19,868] [INFO] Task succeeded: fastANI
[2023-03-16 09:54:19,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32749a4b-9521-4524-a41d-058653fed155/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:54:19,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32749a4b-9521-4524-a41d-058653fed155/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:54:19,873] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:54:19,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:54:19,874] [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
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.1616	57	633	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	75.751	54	633	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:54:19,874] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37976/tc_result.tsv
[2023-03-16 09:54:19,874] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:54:19,874] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:54:19,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32749a4b-9521-4524-a41d-058653fed155/dqc_reference/checkm_data
[2023-03-16 09:54:19,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:54:20,141] [INFO] Task started: CheckM
[2023-03-16 09:54:20,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37976/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37976/checkm_input OceanDNA-b37976/checkm_result
[2023-03-16 09:54:56,000] [INFO] Task succeeded: CheckM
[2023-03-16 09:54:56,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:54:56,011] [INFO] ===== Completeness check finished =====
[2023-03-16 09:54:56,011] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:54:56,011] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37976/markers.fasta)
[2023-03-16 09:54:56,012] [INFO] Task started: Blastn
[2023-03-16 09:54:56,012] [INFO] Running command: blastn -query OceanDNA-b37976/markers.fasta -db /var/lib/cwl/stg32749a4b-9521-4524-a41d-058653fed155/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37976/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:54:56,982] [INFO] Task succeeded: Blastn
[2023-03-16 09:54:56,985] [INFO] Selected 24 target genomes.
[2023-03-16 09:54:56,985] [INFO] Target genome list was writen to OceanDNA-b37976/target_genomes_gtdb.txt
[2023-03-16 09:54:57,012] [INFO] Task started: fastANI
[2023-03-16 09:54:57,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg6710b028-5c6c-4083-958e-fa781d1179e6/OceanDNA-b37976.fa --refList OceanDNA-b37976/target_genomes_gtdb.txt --output OceanDNA-b37976/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:55:11,442] [INFO] Task succeeded: fastANI
[2023-03-16 09:55:11,446] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:55:11,446] [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_012270045.1	s__Luminiphilus sp012270045	94.4208	555	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.26	98.26	0.90	0.90	2	-
GCA_000169115.1	s__Luminiphilus sp000169115	76.7043	59	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.96	96.76	0.93	0.91	5	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.0989	74	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	75.999	53	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:55:11,446] [INFO] GTDB search result was written to OceanDNA-b37976/result_gtdb.tsv
[2023-03-16 09:55:11,446] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:55:11,447] [INFO] DFAST_QC result json was written to OceanDNA-b37976/dqc_result.json
[2023-03-16 09:55:11,447] [INFO] DFAST_QC completed!
[2023-03-16 09:55:11,447] [INFO] Total running time: 0h1m21s