[2023-03-17 05:16:58,086] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:58,086] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:58,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg6aad1b50-da53-4e0e-afc2-d9f5d3cdb7e1/dqc_reference
[2023-03-17 05:16:59,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,895] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,896] [INFO] Running command: cat /var/lib/cwl/stgae6c4479-44da-446c-85da-4c4e461ea994/OceanDNA-b3582.fa | prodigal -d OceanDNA-b3582/cds.fna -a OceanDNA-b3582/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:19,230] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:19,231] [INFO] Task started: HMMsearch
[2023-03-17 05:17:19,231] [INFO] Running command: hmmsearch --tblout OceanDNA-b3582/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6aad1b50-da53-4e0e-afc2-d9f5d3cdb7e1/dqc_reference/reference_markers.hmm OceanDNA-b3582/protein.faa > /dev/null
[2023-03-17 05:17:19,442] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:19,443] [INFO] Found 6/6 markers.
[2023-03-17 05:17:19,461] [INFO] Query marker FASTA was written to OceanDNA-b3582/markers.fasta
[2023-03-17 05:17:19,462] [INFO] Task started: Blastn
[2023-03-17 05:17:19,462] [INFO] Running command: blastn -query OceanDNA-b3582/markers.fasta -db /var/lib/cwl/stg6aad1b50-da53-4e0e-afc2-d9f5d3cdb7e1/dqc_reference/reference_markers.fasta -out OceanDNA-b3582/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:19,991] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:19,992] [INFO] Selected 30 target genomes.
[2023-03-17 05:17:19,992] [INFO] Target genome list was writen to OceanDNA-b3582/target_genomes.txt
[2023-03-17 05:17:20,211] [INFO] Task started: fastANI
[2023-03-17 05:17:20,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgae6c4479-44da-446c-85da-4c4e461ea994/OceanDNA-b3582.fa --refList OceanDNA-b3582/target_genomes.txt --output OceanDNA-b3582/fastani_result.tsv --threads 1
[2023-03-17 05:17:37,508] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:37,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6aad1b50-da53-4e0e-afc2-d9f5d3cdb7e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:37,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6aad1b50-da53-4e0e-afc2-d9f5d3cdb7e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:37,508] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:37,509] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:17:37,509] [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
--------------------------------------------------------------------------------
[2023-03-17 05:17:37,509] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3582/tc_result.tsv
[2023-03-17 05:17:37,509] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:37,509] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:37,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6aad1b50-da53-4e0e-afc2-d9f5d3cdb7e1/dqc_reference/checkm_data
[2023-03-17 05:17:37,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:37,516] [INFO] Task started: CheckM
[2023-03-17 05:17:37,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3582/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3582/checkm_input OceanDNA-b3582/checkm_result
[2023-03-17 05:18:28,185] [INFO] Task succeeded: CheckM
[2023-03-17 05:18:28,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:18:28,188] [INFO] ===== Completeness check finished =====
[2023-03-17 05:18:28,189] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:18:28,189] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3582/markers.fasta)
[2023-03-17 05:18:28,190] [INFO] Task started: Blastn
[2023-03-17 05:18:28,190] [INFO] Running command: blastn -query OceanDNA-b3582/markers.fasta -db /var/lib/cwl/stg6aad1b50-da53-4e0e-afc2-d9f5d3cdb7e1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3582/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:18:28,920] [INFO] Task succeeded: Blastn
[2023-03-17 05:18:28,922] [INFO] Selected 32 target genomes.
[2023-03-17 05:18:28,922] [INFO] Target genome list was writen to OceanDNA-b3582/target_genomes_gtdb.txt
[2023-03-17 05:18:29,157] [INFO] Task started: fastANI
[2023-03-17 05:18:29,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgae6c4479-44da-446c-85da-4c4e461ea994/OceanDNA-b3582.fa --refList OceanDNA-b3582/target_genomes_gtdb.txt --output OceanDNA-b3582/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:18:45,928] [INFO] Task succeeded: fastANI
[2023-03-17 05:18:45,931] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:18:45,931] [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_015493685.1	s__4572-112 sp015493685	76.7684	104	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1556;g__4572-112	95.0	98.88	98.75	0.82	0.82	4	-
GCA_002254285.1	s__4572-112 sp002254285	76.6279	64	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1556;g__4572-112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003648395.1	s__4572-112 sp003648395	76.246	105	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1556;g__4572-112	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:18:45,931] [INFO] GTDB search result was written to OceanDNA-b3582/result_gtdb.tsv
[2023-03-17 05:18:45,932] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:18:45,933] [INFO] DFAST_QC result json was written to OceanDNA-b3582/dqc_result.json
[2023-03-17 05:18:45,933] [INFO] DFAST_QC completed!
[2023-03-17 05:18:45,933] [INFO] Total running time: 0h1m48s