[2023-03-17 07:47:46,518] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:47:46,518] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:47:46,519] [INFO] DQC Reference Directory: /var/lib/cwl/stge6e06874-272d-457a-a212-6e8f824224cb/dqc_reference
[2023-03-17 07:47:47,611] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:47:47,611] [INFO] Task started: Prodigal
[2023-03-17 07:47:47,611] [INFO] Running command: cat /var/lib/cwl/stg03c14634-9669-427d-9b88-b1bb1284b825/OceanDNA-b36732.fa | prodigal -d OceanDNA-b36732/cds.fna -a OceanDNA-b36732/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:48:01,738] [INFO] Task succeeded: Prodigal
[2023-03-17 07:48:01,738] [INFO] Task started: HMMsearch
[2023-03-17 07:48:01,738] [INFO] Running command: hmmsearch --tblout OceanDNA-b36732/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6e06874-272d-457a-a212-6e8f824224cb/dqc_reference/reference_markers.hmm OceanDNA-b36732/protein.faa > /dev/null
[2023-03-17 07:48:01,926] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:48:01,927] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg03c14634-9669-427d-9b88-b1bb1284b825/OceanDNA-b36732.fa]
[2023-03-17 07:48:01,952] [INFO] Query marker FASTA was written to OceanDNA-b36732/markers.fasta
[2023-03-17 07:48:01,952] [INFO] Task started: Blastn
[2023-03-17 07:48:01,952] [INFO] Running command: blastn -query OceanDNA-b36732/markers.fasta -db /var/lib/cwl/stge6e06874-272d-457a-a212-6e8f824224cb/dqc_reference/reference_markers.fasta -out OceanDNA-b36732/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:48:02,415] [INFO] Task succeeded: Blastn
[2023-03-17 07:48:02,416] [INFO] Selected 20 target genomes.
[2023-03-17 07:48:02,416] [INFO] Target genome list was writen to OceanDNA-b36732/target_genomes.txt
[2023-03-17 07:48:02,426] [INFO] Task started: fastANI
[2023-03-17 07:48:02,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg03c14634-9669-427d-9b88-b1bb1284b825/OceanDNA-b36732.fa --refList OceanDNA-b36732/target_genomes.txt --output OceanDNA-b36732/fastani_result.tsv --threads 1
[2023-03-17 07:48:15,956] [INFO] Task succeeded: fastANI
[2023-03-17 07:48:15,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6e06874-272d-457a-a212-6e8f824224cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:48:15,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6e06874-272d-457a-a212-6e8f824224cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:48:15,960] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:48:15,960] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:48:15,960] [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
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.7544	52	671	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.7471	51	671	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	75.2068	50	671	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:48:15,960] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36732/tc_result.tsv
[2023-03-17 07:48:15,960] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:48:15,961] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:48:15,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6e06874-272d-457a-a212-6e8f824224cb/dqc_reference/checkm_data
[2023-03-17 07:48:15,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:48:15,966] [INFO] Task started: CheckM
[2023-03-17 07:48:15,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36732/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36732/checkm_input OceanDNA-b36732/checkm_result
[2023-03-17 07:48:53,546] [INFO] Task succeeded: CheckM
[2023-03-17 07:48:53,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:48:53,549] [INFO] ===== Completeness check finished =====
[2023-03-17 07:48:53,549] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:48:53,549] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36732/markers.fasta)
[2023-03-17 07:48:53,550] [INFO] Task started: Blastn
[2023-03-17 07:48:53,550] [INFO] Running command: blastn -query OceanDNA-b36732/markers.fasta -db /var/lib/cwl/stge6e06874-272d-457a-a212-6e8f824224cb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36732/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:48:54,059] [INFO] Task succeeded: Blastn
[2023-03-17 07:48:54,060] [INFO] Selected 18 target genomes.
[2023-03-17 07:48:54,060] [INFO] Target genome list was writen to OceanDNA-b36732/target_genomes_gtdb.txt
[2023-03-17 07:48:54,213] [INFO] Task started: fastANI
[2023-03-17 07:48:54,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg03c14634-9669-427d-9b88-b1bb1284b825/OceanDNA-b36732.fa --refList OceanDNA-b36732/target_genomes_gtdb.txt --output OceanDNA-b36732/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:49:05,348] [INFO] Task succeeded: fastANI
[2023-03-17 07:49:05,353] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:49:05,353] [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_007122315.1	s__SLTB01 sp007122315	76.4762	104	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	99.34	99.17	0.86	0.79	4	-
GCA_007694905.1	s__SLTB01 sp007694905	76.4713	96	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131295.1	s__SLTB01 sp007131295	76.3031	88	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	99.75	99.70	0.93	0.92	5	-
GCA_007130155.1	s__SLTB01 sp007130155	76.3005	64	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	99.66	99.66	0.93	0.93	2	-
GCF_900103845.1	s__Pseudomonas jinjuensis	75.3824	57	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002879645.1	s__Halomonas heilongjiangensis	75.2068	50	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 07:49:05,353] [INFO] GTDB search result was written to OceanDNA-b36732/result_gtdb.tsv
[2023-03-17 07:49:05,353] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:49:05,354] [INFO] DFAST_QC result json was written to OceanDNA-b36732/dqc_result.json
[2023-03-17 07:49:05,354] [INFO] DFAST_QC completed!
[2023-03-17 07:49:05,354] [INFO] Total running time: 0h1m19s