[2023-03-15 05:29:12,494] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:12,494] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:12,494] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc423b04-a147-41e4-9e9a-59a8862be23e/dqc_reference
[2023-03-15 05:29:13,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:13,781] [INFO] Task started: Prodigal
[2023-03-15 05:29:13,781] [INFO] Running command: cat /var/lib/cwl/stg249470d6-c798-438b-98a6-ed6baea0e5e9/OceanDNA-b23839.fa | prodigal -d OceanDNA-b23839/cds.fna -a OceanDNA-b23839/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:30,126] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:30,126] [INFO] Task started: HMMsearch
[2023-03-15 05:29:30,126] [INFO] Running command: hmmsearch --tblout OceanDNA-b23839/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc423b04-a147-41e4-9e9a-59a8862be23e/dqc_reference/reference_markers.hmm OceanDNA-b23839/protein.faa > /dev/null
[2023-03-15 05:29:30,348] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:30,349] [INFO] Found 6/6 markers.
[2023-03-15 05:29:30,365] [INFO] Query marker FASTA was written to OceanDNA-b23839/markers.fasta
[2023-03-15 05:29:30,366] [INFO] Task started: Blastn
[2023-03-15 05:29:30,366] [INFO] Running command: blastn -query OceanDNA-b23839/markers.fasta -db /var/lib/cwl/stgfc423b04-a147-41e4-9e9a-59a8862be23e/dqc_reference/reference_markers.fasta -out OceanDNA-b23839/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:30,997] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:30,998] [INFO] Selected 25 target genomes.
[2023-03-15 05:29:30,998] [INFO] Target genome list was writen to OceanDNA-b23839/target_genomes.txt
[2023-03-15 05:29:31,010] [INFO] Task started: fastANI
[2023-03-15 05:29:31,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg249470d6-c798-438b-98a6-ed6baea0e5e9/OceanDNA-b23839.fa --refList OceanDNA-b23839/target_genomes.txt --output OceanDNA-b23839/fastani_result.tsv --threads 1
[2023-03-15 05:29:47,071] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:47,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc423b04-a147-41e4-9e9a-59a8862be23e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:47,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc423b04-a147-41e4-9e9a-59a8862be23e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:47,075] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:47,076] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:47,076] [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
Litorimonas taeanensis	strain=DSM 22008	GCA_003634015.1	568099	568099	type	True	77.377	106	919	95	below_threshold
Hellea balneolensis	strain=DSM 19091	GCA_000428525.1	287478	287478	type	True	76.7886	97	919	95	below_threshold
Algimonas arctica	strain=KCTC 32513	GCA_014652695.1	1479486	1479486	type	True	76.3734	59	919	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:47,076] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23839/tc_result.tsv
[2023-03-15 05:29:47,076] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:47,076] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:47,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc423b04-a147-41e4-9e9a-59a8862be23e/dqc_reference/checkm_data
[2023-03-15 05:29:47,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:47,082] [INFO] Task started: CheckM
[2023-03-15 05:29:47,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23839/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23839/checkm_input OceanDNA-b23839/checkm_result
[2023-03-15 05:30:30,017] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:30,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:30,020] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:30,020] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:30,020] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23839/markers.fasta)
[2023-03-15 05:30:30,020] [INFO] Task started: Blastn
[2023-03-15 05:30:30,020] [INFO] Running command: blastn -query OceanDNA-b23839/markers.fasta -db /var/lib/cwl/stgfc423b04-a147-41e4-9e9a-59a8862be23e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23839/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:31,068] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:31,069] [INFO] Selected 29 target genomes.
[2023-03-15 05:30:31,069] [INFO] Target genome list was writen to OceanDNA-b23839/target_genomes_gtdb.txt
[2023-03-15 05:30:31,090] [INFO] Task started: fastANI
[2023-03-15 05:30:31,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg249470d6-c798-438b-98a6-ed6baea0e5e9/OceanDNA-b23839.fa --refList OceanDNA-b23839/target_genomes_gtdb.txt --output OceanDNA-b23839/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:47,144] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:47,148] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:30:47,148] [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_003634015.1	s__Litorimonas taeanensis	77.377	106	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428525.1	s__Hellea balneolensis	76.8115	96	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hellea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002305.1	s__JACOMS01 sp013002305	76.5567	58	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__JACOMS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238285.1	s__JACOMS01 sp014238285	76.4059	53	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__JACOMS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652695.1	s__Litorimonas arctica	76.3734	59	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000365025.1	s__Robiginitomaculum antarcticum	75.9603	76	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Robiginitomaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:47,149] [INFO] GTDB search result was written to OceanDNA-b23839/result_gtdb.tsv
[2023-03-15 05:30:47,149] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:47,150] [INFO] DFAST_QC result json was written to OceanDNA-b23839/dqc_result.json
[2023-03-15 05:30:47,150] [INFO] DFAST_QC completed!
[2023-03-15 05:30:47,150] [INFO] Total running time: 0h1m35s