[2023-03-16 12:48:16,863] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:48:16,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:48:16,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg366a9d9b-035c-48a6-884e-51cf39a1bdf7/dqc_reference
[2023-03-16 12:48:19,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:48:19,956] [INFO] Task started: Prodigal
[2023-03-16 12:48:19,957] [INFO] Running command: cat /var/lib/cwl/stgfa417aaf-ea28-4b22-9491-b2a6f02e1a56/OceanDNA-b3717.fa | prodigal -d OceanDNA-b3717/cds.fna -a OceanDNA-b3717/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:48:43,210] [INFO] Task succeeded: Prodigal
[2023-03-16 12:48:43,210] [INFO] Task started: HMMsearch
[2023-03-16 12:48:43,210] [INFO] Running command: hmmsearch --tblout OceanDNA-b3717/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg366a9d9b-035c-48a6-884e-51cf39a1bdf7/dqc_reference/reference_markers.hmm OceanDNA-b3717/protein.faa > /dev/null
[2023-03-16 12:48:43,424] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:48:43,425] [INFO] Found 6/6 markers.
[2023-03-16 12:48:43,455] [INFO] Query marker FASTA was written to OceanDNA-b3717/markers.fasta
[2023-03-16 12:48:43,457] [INFO] Task started: Blastn
[2023-03-16 12:48:43,457] [INFO] Running command: blastn -query OceanDNA-b3717/markers.fasta -db /var/lib/cwl/stg366a9d9b-035c-48a6-884e-51cf39a1bdf7/dqc_reference/reference_markers.fasta -out OceanDNA-b3717/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:48:44,030] [INFO] Task succeeded: Blastn
[2023-03-16 12:48:44,031] [INFO] Selected 30 target genomes.
[2023-03-16 12:48:44,031] [INFO] Target genome list was writen to OceanDNA-b3717/target_genomes.txt
[2023-03-16 12:48:44,051] [INFO] Task started: fastANI
[2023-03-16 12:48:44,051] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa417aaf-ea28-4b22-9491-b2a6f02e1a56/OceanDNA-b3717.fa --refList OceanDNA-b3717/target_genomes.txt --output OceanDNA-b3717/fastani_result.tsv --threads 1
[2023-03-16 12:49:18,589] [INFO] Task succeeded: fastANI
[2023-03-16 12:49:18,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg366a9d9b-035c-48a6-884e-51cf39a1bdf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:49:18,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg366a9d9b-035c-48a6-884e-51cf39a1bdf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:49:18,594] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:49:18,594] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 12:49:18,594] [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
Phaeodactylibacter xiamenensis	strain=KD52	GCA_000759025.1	1524460	1524460	type	True	78.6661	175	476	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 12:49:18,594] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3717/tc_result.tsv
[2023-03-16 12:49:18,594] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:49:18,594] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:49:18,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg366a9d9b-035c-48a6-884e-51cf39a1bdf7/dqc_reference/checkm_data
[2023-03-16 12:49:18,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:49:18,601] [INFO] Task started: CheckM
[2023-03-16 12:49:18,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3717/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3717/checkm_input OceanDNA-b3717/checkm_result
[2023-03-16 12:50:23,445] [INFO] Task succeeded: CheckM
[2023-03-16 12:50:23,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.69%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:50:23,449] [INFO] ===== Completeness check finished =====
[2023-03-16 12:50:23,449] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:50:23,450] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3717/markers.fasta)
[2023-03-16 12:50:23,451] [INFO] Task started: Blastn
[2023-03-16 12:50:23,451] [INFO] Running command: blastn -query OceanDNA-b3717/markers.fasta -db /var/lib/cwl/stg366a9d9b-035c-48a6-884e-51cf39a1bdf7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3717/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:50:24,383] [INFO] Task succeeded: Blastn
[2023-03-16 12:50:24,384] [INFO] Selected 39 target genomes.
[2023-03-16 12:50:24,384] [INFO] Target genome list was writen to OceanDNA-b3717/target_genomes_gtdb.txt
[2023-03-16 12:50:25,929] [INFO] Task started: fastANI
[2023-03-16 12:50:25,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa417aaf-ea28-4b22-9491-b2a6f02e1a56/OceanDNA-b3717.fa --refList OceanDNA-b3717/target_genomes_gtdb.txt --output OceanDNA-b3717/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:51:00,503] [INFO] Task succeeded: fastANI
[2023-03-16 12:51:00,505] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:51:00,505] [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
GCF_000759025.1	s__Phaeodactylibacter xiamenensis	78.637	174	476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:51:00,505] [INFO] GTDB search result was written to OceanDNA-b3717/result_gtdb.tsv
[2023-03-16 12:51:00,505] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:51:00,507] [INFO] DFAST_QC result json was written to OceanDNA-b3717/dqc_result.json
[2023-03-16 12:51:00,507] [INFO] DFAST_QC completed!
[2023-03-16 12:51:00,507] [INFO] Total running time: 0h2m44s