[2023-03-16 20:47:10,534] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:47:10,534] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:47:10,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c9aa9cd-aa11-444b-b13d-e51cae61dc0d/dqc_reference
[2023-03-16 20:47:11,625] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:47:11,626] [INFO] Task started: Prodigal
[2023-03-16 20:47:11,627] [INFO] Running command: cat /var/lib/cwl/stg855f47da-f800-41bf-be48-b5288a0f55f0/OceanDNA-b40797.fa | prodigal -d OceanDNA-b40797/cds.fna -a OceanDNA-b40797/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:47:26,825] [INFO] Task succeeded: Prodigal
[2023-03-16 20:47:26,825] [INFO] Task started: HMMsearch
[2023-03-16 20:47:26,826] [INFO] Running command: hmmsearch --tblout OceanDNA-b40797/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c9aa9cd-aa11-444b-b13d-e51cae61dc0d/dqc_reference/reference_markers.hmm OceanDNA-b40797/protein.faa > /dev/null
[2023-03-16 20:47:27,041] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:47:27,042] [INFO] Found 6/6 markers.
[2023-03-16 20:47:27,060] [INFO] Query marker FASTA was written to OceanDNA-b40797/markers.fasta
[2023-03-16 20:47:27,061] [INFO] Task started: Blastn
[2023-03-16 20:47:27,061] [INFO] Running command: blastn -query OceanDNA-b40797/markers.fasta -db /var/lib/cwl/stg3c9aa9cd-aa11-444b-b13d-e51cae61dc0d/dqc_reference/reference_markers.fasta -out OceanDNA-b40797/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:27,651] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:27,651] [INFO] Selected 32 target genomes.
[2023-03-16 20:47:27,652] [INFO] Target genome list was writen to OceanDNA-b40797/target_genomes.txt
[2023-03-16 20:47:27,671] [INFO] Task started: fastANI
[2023-03-16 20:47:27,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg855f47da-f800-41bf-be48-b5288a0f55f0/OceanDNA-b40797.fa --refList OceanDNA-b40797/target_genomes.txt --output OceanDNA-b40797/fastani_result.tsv --threads 1
[2023-03-16 20:47:50,303] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:50,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c9aa9cd-aa11-444b-b13d-e51cae61dc0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:47:50,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c9aa9cd-aa11-444b-b13d-e51cae61dc0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:47:50,303] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:47:50,303] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 20:47:50,303] [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
--------------------------------------------------------------------------------
[2023-03-16 20:47:50,304] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40797/tc_result.tsv
[2023-03-16 20:47:50,304] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:47:50,304] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:47:50,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c9aa9cd-aa11-444b-b13d-e51cae61dc0d/dqc_reference/checkm_data
[2023-03-16 20:47:50,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:47:50,311] [INFO] Task started: CheckM
[2023-03-16 20:47:50,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40797/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40797/checkm_input OceanDNA-b40797/checkm_result
[2023-03-16 20:48:44,916] [INFO] Task succeeded: CheckM
[2023-03-16 20:48:44,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 20:48:44,919] [INFO] ===== Completeness check finished =====
[2023-03-16 20:48:44,919] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:48:44,919] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40797/markers.fasta)
[2023-03-16 20:48:44,921] [INFO] Task started: Blastn
[2023-03-16 20:48:44,921] [INFO] Running command: blastn -query OceanDNA-b40797/markers.fasta -db /var/lib/cwl/stg3c9aa9cd-aa11-444b-b13d-e51cae61dc0d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40797/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:48:46,128] [INFO] Task succeeded: Blastn
[2023-03-16 20:48:46,129] [INFO] Selected 21 target genomes.
[2023-03-16 20:48:46,129] [INFO] Target genome list was writen to OceanDNA-b40797/target_genomes_gtdb.txt
[2023-03-16 20:48:46,168] [INFO] Task started: fastANI
[2023-03-16 20:48:46,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg855f47da-f800-41bf-be48-b5288a0f55f0/OceanDNA-b40797.fa --refList OceanDNA-b40797/target_genomes_gtdb.txt --output OceanDNA-b40797/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:49:06,595] [INFO] Task succeeded: fastANI
[2023-03-16 20:49:06,598] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:49:06,598] [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_002684935.1	s__UBA9145 sp002684935	98.3997	767	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.47	98.41	0.83	0.81	3	conclusive
GCA_002477465.1	s__UBA9145 sp002477465	91.8648	804	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	-
GCA_002730035.1	s__UBA9145 sp002730035	75.9699	54	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.69	99.69	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-16 20:49:06,599] [INFO] GTDB search result was written to OceanDNA-b40797/result_gtdb.tsv
[2023-03-16 20:49:06,599] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:49:06,600] [INFO] DFAST_QC result json was written to OceanDNA-b40797/dqc_result.json
[2023-03-16 20:49:06,600] [INFO] DFAST_QC completed!
[2023-03-16 20:49:06,600] [INFO] Total running time: 0h1m56s