[2023-03-18 20:13:32,797] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg28bd14d4-bd16-4b5e-aa28-2f8fc1dbb03e/dqc_reference
[2023-03-18 20:13:34,556] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:34,556] [INFO] Task started: Prodigal
[2023-03-18 20:13:34,557] [INFO] Running command: cat /var/lib/cwl/stgac5b8cc9-e47d-436a-964d-3496efea16ad/OceanDNA-b33569.fa | prodigal -d OceanDNA-b33569/cds.fna -a OceanDNA-b33569/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:41,903] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:41,903] [INFO] Task started: HMMsearch
[2023-03-18 20:13:41,903] [INFO] Running command: hmmsearch --tblout OceanDNA-b33569/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28bd14d4-bd16-4b5e-aa28-2f8fc1dbb03e/dqc_reference/reference_markers.hmm OceanDNA-b33569/protein.faa > /dev/null
[2023-03-18 20:13:42,038] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:42,039] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgac5b8cc9-e47d-436a-964d-3496efea16ad/OceanDNA-b33569.fa]
[2023-03-18 20:13:42,048] [INFO] Query marker FASTA was written to OceanDNA-b33569/markers.fasta
[2023-03-18 20:13:42,049] [INFO] Task started: Blastn
[2023-03-18 20:13:42,049] [INFO] Running command: blastn -query OceanDNA-b33569/markers.fasta -db /var/lib/cwl/stg28bd14d4-bd16-4b5e-aa28-2f8fc1dbb03e/dqc_reference/reference_markers.fasta -out OceanDNA-b33569/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:42,482] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:42,483] [INFO] Selected 18 target genomes.
[2023-03-18 20:13:42,483] [INFO] Target genome list was writen to OceanDNA-b33569/target_genomes.txt
[2023-03-18 20:13:42,492] [INFO] Task started: fastANI
[2023-03-18 20:13:42,493] [INFO] Running command: fastANI --query /var/lib/cwl/stgac5b8cc9-e47d-436a-964d-3496efea16ad/OceanDNA-b33569.fa --refList OceanDNA-b33569/target_genomes.txt --output OceanDNA-b33569/fastani_result.tsv --threads 1
[2023-03-18 20:13:54,099] [INFO] Task succeeded: fastANI
[2023-03-18 20:13:54,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28bd14d4-bd16-4b5e-aa28-2f8fc1dbb03e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:13:54,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28bd14d4-bd16-4b5e-aa28-2f8fc1dbb03e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:13:54,100] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:13:54,100] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:13:54,100] [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
--------------------------------------------------------------------------------
[2023-03-18 20:13:54,100] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33569/tc_result.tsv
[2023-03-18 20:13:54,101] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:13:54,101] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:13:54,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28bd14d4-bd16-4b5e-aa28-2f8fc1dbb03e/dqc_reference/checkm_data
[2023-03-18 20:13:54,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:13:54,106] [INFO] Task started: CheckM
[2023-03-18 20:13:54,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33569/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33569/checkm_input OceanDNA-b33569/checkm_result
[2023-03-18 20:14:17,672] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:17,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:17,674] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:17,674] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:17,674] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33569/markers.fasta)
[2023-03-18 20:14:17,674] [INFO] Task started: Blastn
[2023-03-18 20:14:17,674] [INFO] Running command: blastn -query OceanDNA-b33569/markers.fasta -db /var/lib/cwl/stg28bd14d4-bd16-4b5e-aa28-2f8fc1dbb03e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33569/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:18,105] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:18,106] [INFO] Selected 14 target genomes.
[2023-03-18 20:14:18,106] [INFO] Target genome list was writen to OceanDNA-b33569/target_genomes_gtdb.txt
[2023-03-18 20:14:18,594] [INFO] Task started: fastANI
[2023-03-18 20:14:18,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgac5b8cc9-e47d-436a-964d-3496efea16ad/OceanDNA-b33569.fa --refList OceanDNA-b33569/target_genomes_gtdb.txt --output OceanDNA-b33569/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:14:25,896] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:25,900] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:14:25,900] [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_900299025.1	s__UBA3064 sp005787245	99.0537	345	398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	98.97	98.30	0.89	0.84	12	conclusive
GCA_016868095.1	s__UBA3064 sp016868095	92.1482	266	398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359635.1	s__UBA3064 sp002359635	79.4566	146	398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	99.69	99.55	0.89	0.78	24	-
GCA_002342365.1	s__UBA3064 sp002342365	76.8788	93	398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	99.81	99.60	0.94	0.90	39	-
--------------------------------------------------------------------------------
[2023-03-18 20:14:25,900] [INFO] GTDB search result was written to OceanDNA-b33569/result_gtdb.tsv
[2023-03-18 20:14:25,900] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:14:25,901] [INFO] DFAST_QC result json was written to OceanDNA-b33569/dqc_result.json
[2023-03-18 20:14:25,901] [INFO] DFAST_QC completed!
[2023-03-18 20:14:25,901] [INFO] Total running time: 0h0m53s