[2023-03-16 17:54:39,652] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:54:39,652] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:54:39,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg81f23be1-f406-47ef-869c-9802973d9e0c/dqc_reference
[2023-03-16 17:54:42,307] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:54:42,307] [INFO] Task started: Prodigal
[2023-03-16 17:54:42,307] [INFO] Running command: cat /var/lib/cwl/stg4d259ec0-14b2-4d7b-a7f3-dae5412747cd/OceanDNA-b22373.fa | prodigal -d OceanDNA-b22373/cds.fna -a OceanDNA-b22373/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:55:08,556] [INFO] Task succeeded: Prodigal
[2023-03-16 17:55:08,556] [INFO] Task started: HMMsearch
[2023-03-16 17:55:08,556] [INFO] Running command: hmmsearch --tblout OceanDNA-b22373/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81f23be1-f406-47ef-869c-9802973d9e0c/dqc_reference/reference_markers.hmm OceanDNA-b22373/protein.faa > /dev/null
[2023-03-16 17:55:08,907] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:55:08,908] [INFO] Found 6/6 markers.
[2023-03-16 17:55:08,948] [INFO] Query marker FASTA was written to OceanDNA-b22373/markers.fasta
[2023-03-16 17:55:08,954] [INFO] Task started: Blastn
[2023-03-16 17:55:08,955] [INFO] Running command: blastn -query OceanDNA-b22373/markers.fasta -db /var/lib/cwl/stg81f23be1-f406-47ef-869c-9802973d9e0c/dqc_reference/reference_markers.fasta -out OceanDNA-b22373/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:55:09,825] [INFO] Task succeeded: Blastn
[2023-03-16 17:55:09,826] [INFO] Selected 14 target genomes.
[2023-03-16 17:55:09,827] [INFO] Target genome list was writen to OceanDNA-b22373/target_genomes.txt
[2023-03-16 17:55:09,837] [INFO] Task started: fastANI
[2023-03-16 17:55:09,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d259ec0-14b2-4d7b-a7f3-dae5412747cd/OceanDNA-b22373.fa --refList OceanDNA-b22373/target_genomes.txt --output OceanDNA-b22373/fastani_result.tsv --threads 1
[2023-03-16 17:55:16,497] [INFO] Task succeeded: fastANI
[2023-03-16 17:55:16,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81f23be1-f406-47ef-869c-9802973d9e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:55:16,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81f23be1-f406-47ef-869c-9802973d9e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:55:16,498] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:55:16,498] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:55:16,498] [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 17:55:16,499] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22373/tc_result.tsv
[2023-03-16 17:55:16,499] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:55:16,499] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:55:16,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81f23be1-f406-47ef-869c-9802973d9e0c/dqc_reference/checkm_data
[2023-03-16 17:55:16,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:55:16,510] [INFO] Task started: CheckM
[2023-03-16 17:55:16,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22373/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22373/checkm_input OceanDNA-b22373/checkm_result
[2023-03-16 17:56:17,244] [INFO] Task succeeded: CheckM
[2023-03-16 17:56:17,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 17:56:17,248] [INFO] ===== Completeness check finished =====
[2023-03-16 17:56:17,248] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:56:17,248] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22373/markers.fasta)
[2023-03-16 17:56:17,249] [INFO] Task started: Blastn
[2023-03-16 17:56:17,249] [INFO] Running command: blastn -query OceanDNA-b22373/markers.fasta -db /var/lib/cwl/stg81f23be1-f406-47ef-869c-9802973d9e0c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22373/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:56:18,230] [INFO] Task succeeded: Blastn
[2023-03-16 17:56:18,231] [INFO] Selected 11 target genomes.
[2023-03-16 17:56:18,231] [INFO] Target genome list was writen to OceanDNA-b22373/target_genomes_gtdb.txt
[2023-03-16 17:56:18,242] [INFO] Task started: fastANI
[2023-03-16 17:56:18,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d259ec0-14b2-4d7b-a7f3-dae5412747cd/OceanDNA-b22373.fa --refList OceanDNA-b22373/target_genomes_gtdb.txt --output OceanDNA-b22373/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:56:25,680] [INFO] Task succeeded: fastANI
[2023-03-16 17:56:25,683] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:56:25,683] [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_012965455.1	s__UBA721 sp012965455	86.1194	751	1215	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.43	99.43	0.81	0.81	2	-
GCA_018658605.1	s__UBA721 sp018658605	85.9766	851	1215	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660825.1	s__UBA721 sp018660825	84.4166	958	1215	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.75	99.55	0.94	0.93	7	-
--------------------------------------------------------------------------------
[2023-03-16 17:56:25,684] [INFO] GTDB search result was written to OceanDNA-b22373/result_gtdb.tsv
[2023-03-16 17:56:25,684] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:56:25,685] [INFO] DFAST_QC result json was written to OceanDNA-b22373/dqc_result.json
[2023-03-16 17:56:25,686] [INFO] DFAST_QC completed!
[2023-03-16 17:56:25,686] [INFO] Total running time: 0h1m46s