[2023-03-16 16:35:56,430] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:35:56,430] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:35:56,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg95e7d313-ab40-484e-8015-34d2d5dda974/dqc_reference
[2023-03-16 16:35:57,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:35:57,561] [INFO] Task started: Prodigal
[2023-03-16 16:35:57,561] [INFO] Running command: cat /var/lib/cwl/stg3b0b7ae6-007c-4acf-ab11-898c7471bbac/OceanDNA-b30642.fa | prodigal -d OceanDNA-b30642/cds.fna -a OceanDNA-b30642/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:36:10,341] [INFO] Task succeeded: Prodigal
[2023-03-16 16:36:10,342] [INFO] Task started: HMMsearch
[2023-03-16 16:36:10,342] [INFO] Running command: hmmsearch --tblout OceanDNA-b30642/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95e7d313-ab40-484e-8015-34d2d5dda974/dqc_reference/reference_markers.hmm OceanDNA-b30642/protein.faa > /dev/null
[2023-03-16 16:36:10,509] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:36:10,509] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3b0b7ae6-007c-4acf-ab11-898c7471bbac/OceanDNA-b30642.fa]
[2023-03-16 16:36:10,528] [INFO] Query marker FASTA was written to OceanDNA-b30642/markers.fasta
[2023-03-16 16:36:10,528] [INFO] Task started: Blastn
[2023-03-16 16:36:10,528] [INFO] Running command: blastn -query OceanDNA-b30642/markers.fasta -db /var/lib/cwl/stg95e7d313-ab40-484e-8015-34d2d5dda974/dqc_reference/reference_markers.fasta -out OceanDNA-b30642/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:36:11,348] [INFO] Task succeeded: Blastn
[2023-03-16 16:36:11,349] [INFO] Selected 25 target genomes.
[2023-03-16 16:36:11,350] [INFO] Target genome list was writen to OceanDNA-b30642/target_genomes.txt
[2023-03-16 16:36:11,366] [INFO] Task started: fastANI
[2023-03-16 16:36:11,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b0b7ae6-007c-4acf-ab11-898c7471bbac/OceanDNA-b30642.fa --refList OceanDNA-b30642/target_genomes.txt --output OceanDNA-b30642/fastani_result.tsv --threads 1
[2023-03-16 16:36:35,958] [INFO] Task succeeded: fastANI
[2023-03-16 16:36:35,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95e7d313-ab40-484e-8015-34d2d5dda974/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:36:35,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95e7d313-ab40-484e-8015-34d2d5dda974/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:36:35,963] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:36:35,963] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:36:35,963] [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
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	77.2139	72	284	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:36:35,963] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30642/tc_result.tsv
[2023-03-16 16:36:35,963] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:36:35,963] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:36:35,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95e7d313-ab40-484e-8015-34d2d5dda974/dqc_reference/checkm_data
[2023-03-16 16:36:35,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:36:35,968] [INFO] Task started: CheckM
[2023-03-16 16:36:35,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30642/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30642/checkm_input OceanDNA-b30642/checkm_result
[2023-03-16 16:37:03,353] [INFO] Task succeeded: CheckM
[2023-03-16 16:37:03,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:37:03,356] [INFO] ===== Completeness check finished =====
[2023-03-16 16:37:03,356] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:37:03,356] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30642/markers.fasta)
[2023-03-16 16:37:03,357] [INFO] Task started: Blastn
[2023-03-16 16:37:03,357] [INFO] Running command: blastn -query OceanDNA-b30642/markers.fasta -db /var/lib/cwl/stg95e7d313-ab40-484e-8015-34d2d5dda974/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30642/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:37:04,213] [INFO] Task succeeded: Blastn
[2023-03-16 16:37:04,442] [INFO] Selected 29 target genomes.
[2023-03-16 16:37:04,443] [INFO] Target genome list was writen to OceanDNA-b30642/target_genomes_gtdb.txt
[2023-03-16 16:37:04,815] [INFO] Task started: fastANI
[2023-03-16 16:37:04,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b0b7ae6-007c-4acf-ab11-898c7471bbac/OceanDNA-b30642.fa --refList OceanDNA-b30642/target_genomes_gtdb.txt --output OceanDNA-b30642/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:37:20,503] [INFO] Task succeeded: fastANI
[2023-03-16 16:37:20,505] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:37:20,506] [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
GCF_014199395.1	s__Yoonia ponticola	77.2139	72	284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:37:20,506] [INFO] GTDB search result was written to OceanDNA-b30642/result_gtdb.tsv
[2023-03-16 16:37:20,506] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:37:20,506] [INFO] DFAST_QC result json was written to OceanDNA-b30642/dqc_result.json
[2023-03-16 16:37:20,506] [INFO] DFAST_QC completed!
[2023-03-16 16:37:20,507] [INFO] Total running time: 0h1m24s