[2023-03-17 23:01:26,541] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:01:26,543] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:01:26,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg24c5673d-3727-4574-8296-18f3e392fa57/dqc_reference
[2023-03-17 23:01:28,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:01:28,781] [INFO] Task started: Prodigal
[2023-03-17 23:01:28,781] [INFO] Running command: cat /var/lib/cwl/stg5286bdee-5641-4a90-9d74-dde11e6d6648/OceanDNA-b31504.fa | prodigal -d OceanDNA-b31504/cds.fna -a OceanDNA-b31504/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:01:40,492] [INFO] Task succeeded: Prodigal
[2023-03-17 23:01:40,493] [INFO] Task started: HMMsearch
[2023-03-17 23:01:40,493] [INFO] Running command: hmmsearch --tblout OceanDNA-b31504/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24c5673d-3727-4574-8296-18f3e392fa57/dqc_reference/reference_markers.hmm OceanDNA-b31504/protein.faa > /dev/null
[2023-03-17 23:01:40,677] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:01:40,677] [INFO] Found 6/6 markers.
[2023-03-17 23:01:40,691] [INFO] Query marker FASTA was written to OceanDNA-b31504/markers.fasta
[2023-03-17 23:01:40,693] [INFO] Task started: Blastn
[2023-03-17 23:01:40,693] [INFO] Running command: blastn -query OceanDNA-b31504/markers.fasta -db /var/lib/cwl/stg24c5673d-3727-4574-8296-18f3e392fa57/dqc_reference/reference_markers.fasta -out OceanDNA-b31504/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:01:41,297] [INFO] Task succeeded: Blastn
[2023-03-17 23:01:41,297] [INFO] Selected 24 target genomes.
[2023-03-17 23:01:41,298] [INFO] Target genome list was writen to OceanDNA-b31504/target_genomes.txt
[2023-03-17 23:01:41,315] [INFO] Task started: fastANI
[2023-03-17 23:01:41,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg5286bdee-5641-4a90-9d74-dde11e6d6648/OceanDNA-b31504.fa --refList OceanDNA-b31504/target_genomes.txt --output OceanDNA-b31504/fastani_result.tsv --threads 1
[2023-03-17 23:01:53,275] [INFO] Task succeeded: fastANI
[2023-03-17 23:01:53,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24c5673d-3727-4574-8296-18f3e392fa57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:01:53,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24c5673d-3727-4574-8296-18f3e392fa57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:01:53,286] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:01:53,286] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:01:53,287] [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
Pseudemcibacter aquimaris	strain=Y4	GCA_020748165.1	2857064	2857064	type	True	77.0381	72	712	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:01:53,290] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31504/tc_result.tsv
[2023-03-17 23:01:53,291] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:01:53,291] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:01:53,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24c5673d-3727-4574-8296-18f3e392fa57/dqc_reference/checkm_data
[2023-03-17 23:01:53,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:01:53,446] [INFO] Task started: CheckM
[2023-03-17 23:01:53,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31504/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31504/checkm_input OceanDNA-b31504/checkm_result
[2023-03-17 23:02:26,616] [INFO] Task succeeded: CheckM
[2023-03-17 23:02:26,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:02:26,631] [INFO] ===== Completeness check finished =====
[2023-03-17 23:02:26,632] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:02:26,632] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31504/markers.fasta)
[2023-03-17 23:02:26,633] [INFO] Task started: Blastn
[2023-03-17 23:02:26,633] [INFO] Running command: blastn -query OceanDNA-b31504/markers.fasta -db /var/lib/cwl/stg24c5673d-3727-4574-8296-18f3e392fa57/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31504/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:02:27,737] [INFO] Task succeeded: Blastn
[2023-03-17 23:02:27,743] [INFO] Selected 17 target genomes.
[2023-03-17 23:02:27,743] [INFO] Target genome list was writen to OceanDNA-b31504/target_genomes_gtdb.txt
[2023-03-17 23:02:27,766] [INFO] Task started: fastANI
[2023-03-17 23:02:27,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg5286bdee-5641-4a90-9d74-dde11e6d6648/OceanDNA-b31504.fa --refList OceanDNA-b31504/target_genomes_gtdb.txt --output OceanDNA-b31504/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:02:35,067] [INFO] Task succeeded: fastANI
[2023-03-17 23:02:35,071] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:02:35,071] [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_018675425.1	s__UBA4441 sp018675425	98.8209	623	712	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.54	99.14	0.91	0.86	6	conclusive
GCA_905612225.1	s__UBA4441 sp905612225	88.4253	325	712	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390425.1	s__UBA4441 sp002390425	77.6057	117	712	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.08	99.08	0.89	0.89	2	-
GCA_018660225.1	s__UBA4441 sp018660225	77.145	130	712	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.68	99.64	0.89	0.88	3	-
GCA_016763335.1	s__UBA4441 sp016763335	77.073	99	712	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699075.1	s__UBA4441 sp018699075	76.3337	97	712	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.25	99.25	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:02:35,072] [INFO] GTDB search result was written to OceanDNA-b31504/result_gtdb.tsv
[2023-03-17 23:02:35,072] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:02:35,073] [INFO] DFAST_QC result json was written to OceanDNA-b31504/dqc_result.json
[2023-03-17 23:02:35,073] [INFO] DFAST_QC completed!
[2023-03-17 23:02:35,073] [INFO] Total running time: 0h1m9s