[2023-03-19 05:19:33,745] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,746] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,746] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b74b5ea-b7e6-465f-ba9c-2b529a59d009/dqc_reference
[2023-03-19 05:19:35,400] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,400] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,401] [INFO] Running command: cat /var/lib/cwl/stg8692f4a9-c138-4573-bbe9-7695f921dfac/OceanDNA-a4774.fa | prodigal -d OceanDNA-a4774/cds.fna -a OceanDNA-a4774/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:41,104] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:41,105] [INFO] Task started: HMMsearch
[2023-03-19 05:19:41,105] [INFO] Running command: hmmsearch --tblout OceanDNA-a4774/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b74b5ea-b7e6-465f-ba9c-2b529a59d009/dqc_reference/reference_markers.hmm OceanDNA-a4774/protein.faa > /dev/null
[2023-03-19 05:19:41,258] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:41,259] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8692f4a9-c138-4573-bbe9-7695f921dfac/OceanDNA-a4774.fa]
[2023-03-19 05:19:41,269] [INFO] Query marker FASTA was written to OceanDNA-a4774/markers.fasta
[2023-03-19 05:19:41,269] [INFO] Task started: Blastn
[2023-03-19 05:19:41,269] [INFO] Running command: blastn -query OceanDNA-a4774/markers.fasta -db /var/lib/cwl/stg6b74b5ea-b7e6-465f-ba9c-2b529a59d009/dqc_reference/reference_markers.fasta -out OceanDNA-a4774/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:41,701] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:41,702] [INFO] Selected 1 target genomes.
[2023-03-19 05:19:41,702] [INFO] Target genome list was writen to OceanDNA-a4774/target_genomes.txt
[2023-03-19 05:19:41,703] [INFO] Task started: fastANI
[2023-03-19 05:19:41,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg8692f4a9-c138-4573-bbe9-7695f921dfac/OceanDNA-a4774.fa --refList OceanDNA-a4774/target_genomes.txt --output OceanDNA-a4774/fastani_result.tsv --threads 1
[2023-03-19 05:19:42,340] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:42,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b74b5ea-b7e6-465f-ba9c-2b529a59d009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:42,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b74b5ea-b7e6-465f-ba9c-2b529a59d009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:19:42,341] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:19:42,341] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:19:42,341] [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
--------------------------------------------------------------------------------
[2023-03-19 05:19:42,341] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4774/tc_result.tsv
[2023-03-19 05:19:42,341] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:19:42,342] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:42,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b74b5ea-b7e6-465f-ba9c-2b529a59d009/dqc_reference/checkm_data
[2023-03-19 05:19:42,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:42,347] [INFO] Task started: CheckM
[2023-03-19 05:19:42,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4774/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4774/checkm_input OceanDNA-a4774/checkm_result
[2023-03-19 05:20:03,318] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:03,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:03,320] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:03,320] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:03,320] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4774/markers.fasta)
[2023-03-19 05:20:03,321] [INFO] Task started: Blastn
[2023-03-19 05:20:03,321] [INFO] Running command: blastn -query OceanDNA-a4774/markers.fasta -db /var/lib/cwl/stg6b74b5ea-b7e6-465f-ba9c-2b529a59d009/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4774/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:03,884] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:03,885] [INFO] Selected 9 target genomes.
[2023-03-19 05:20:03,885] [INFO] Target genome list was writen to OceanDNA-a4774/target_genomes_gtdb.txt
[2023-03-19 05:20:03,981] [INFO] Task started: fastANI
[2023-03-19 05:20:03,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg8692f4a9-c138-4573-bbe9-7695f921dfac/OceanDNA-a4774.fa --refList OceanDNA-a4774/target_genomes_gtdb.txt --output OceanDNA-a4774/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:06,629] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:06,631] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:20:06,631] [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_002498455.1	s__MGIIb-P sp002498455	76.8678	53	261	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	98.13	97.46	0.87	0.81	6	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:06,631] [INFO] GTDB search result was written to OceanDNA-a4774/result_gtdb.tsv
[2023-03-19 05:20:06,631] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:06,632] [INFO] DFAST_QC result json was written to OceanDNA-a4774/dqc_result.json
[2023-03-19 05:20:06,632] [INFO] DFAST_QC completed!
[2023-03-19 05:20:06,632] [INFO] Total running time: 0h0m33s