[2023-03-17 08:47:56,851] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:47:56,851] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:47:56,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg81a0e1c4-5a4d-49c1-95ec-703e7a6a16f3/dqc_reference
[2023-03-17 08:47:59,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:47:59,934] [INFO] Task started: Prodigal
[2023-03-17 08:47:59,935] [INFO] Running command: cat /var/lib/cwl/stgdd799219-67dc-4f36-b7e3-f9b917ce0378/OceanDNA-b142.fa | prodigal -d OceanDNA-b142/cds.fna -a OceanDNA-b142/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:48:13,203] [INFO] Task succeeded: Prodigal
[2023-03-17 08:48:13,203] [INFO] Task started: HMMsearch
[2023-03-17 08:48:13,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b142/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81a0e1c4-5a4d-49c1-95ec-703e7a6a16f3/dqc_reference/reference_markers.hmm OceanDNA-b142/protein.faa > /dev/null
[2023-03-17 08:48:13,384] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:48:13,385] [INFO] Found 6/6 markers.
[2023-03-17 08:48:13,406] [INFO] Query marker FASTA was written to OceanDNA-b142/markers.fasta
[2023-03-17 08:48:13,408] [INFO] Task started: Blastn
[2023-03-17 08:48:13,408] [INFO] Running command: blastn -query OceanDNA-b142/markers.fasta -db /var/lib/cwl/stg81a0e1c4-5a4d-49c1-95ec-703e7a6a16f3/dqc_reference/reference_markers.fasta -out OceanDNA-b142/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:48:13,943] [INFO] Task succeeded: Blastn
[2023-03-17 08:48:13,948] [INFO] Selected 23 target genomes.
[2023-03-17 08:48:13,948] [INFO] Target genome list was writen to OceanDNA-b142/target_genomes.txt
[2023-03-17 08:48:14,295] [INFO] Task started: fastANI
[2023-03-17 08:48:14,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd799219-67dc-4f36-b7e3-f9b917ce0378/OceanDNA-b142.fa --refList OceanDNA-b142/target_genomes.txt --output OceanDNA-b142/fastani_result.tsv --threads 1
[2023-03-17 08:48:31,616] [INFO] Task succeeded: fastANI
[2023-03-17 08:48:31,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81a0e1c4-5a4d-49c1-95ec-703e7a6a16f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:48:31,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81a0e1c4-5a4d-49c1-95ec-703e7a6a16f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:48:31,617] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:48:31,617] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:48:31,617] [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 08:48:31,619] [INFO] DFAST Taxonomy check result was written to OceanDNA-b142/tc_result.tsv
[2023-03-17 08:48:31,619] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:48:31,619] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:48:31,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81a0e1c4-5a4d-49c1-95ec-703e7a6a16f3/dqc_reference/checkm_data
[2023-03-17 08:48:31,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:48:31,628] [INFO] Task started: CheckM
[2023-03-17 08:48:31,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b142/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b142/checkm_input OceanDNA-b142/checkm_result
[2023-03-17 08:49:08,013] [INFO] Task succeeded: CheckM
[2023-03-17 08:49:08,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:49:08,028] [INFO] ===== Completeness check finished =====
[2023-03-17 08:49:08,028] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:49:08,029] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b142/markers.fasta)
[2023-03-17 08:49:08,030] [INFO] Task started: Blastn
[2023-03-17 08:49:08,030] [INFO] Running command: blastn -query OceanDNA-b142/markers.fasta -db /var/lib/cwl/stg81a0e1c4-5a4d-49c1-95ec-703e7a6a16f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b142/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:49:08,804] [INFO] Task succeeded: Blastn
[2023-03-17 08:49:08,807] [INFO] Selected 16 target genomes.
[2023-03-17 08:49:08,807] [INFO] Target genome list was writen to OceanDNA-b142/target_genomes_gtdb.txt
[2023-03-17 08:49:09,434] [INFO] Task started: fastANI
[2023-03-17 08:49:09,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd799219-67dc-4f36-b7e3-f9b917ce0378/OceanDNA-b142.fa --refList OceanDNA-b142/target_genomes_gtdb.txt --output OceanDNA-b142/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:49:17,158] [INFO] Task succeeded: fastANI
[2023-03-17 08:49:17,163] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:49:17,163] [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_002717745.1	s__UBA11600 sp002717745	97.5524	412	739	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA11600	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002730735.1	s__UBA11600 sp002730735	90.9742	389	739	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA11600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714165.1	s__UBA11600 sp002714165	90.06	563	739	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA11600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720285.1	s__UBA11600 sp002720285	89.0879	347	739	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA11600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296225.1	s__UBA823 sp002296225	79.747	263	739	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA823	95.0	99.57	99.38	0.83	0.81	4	-
GCA_002328835.1	s__UBA2161 sp002328835	76.2424	89	739	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_002730525.1	s__UBA2161 sp002730525	76.1648	83	739	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:49:17,167] [INFO] GTDB search result was written to OceanDNA-b142/result_gtdb.tsv
[2023-03-17 08:49:17,174] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:49:17,179] [INFO] DFAST_QC result json was written to OceanDNA-b142/dqc_result.json
[2023-03-17 08:49:17,179] [INFO] DFAST_QC completed!
[2023-03-17 08:49:17,179] [INFO] Total running time: 0h1m20s