[2023-03-15 08:12:33,752] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:12:33,753] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:12:33,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg10131228-05ea-4631-b82f-480904d62b2e/dqc_reference
[2023-03-15 08:12:34,977] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:12:34,977] [INFO] Task started: Prodigal
[2023-03-15 08:12:34,977] [INFO] Running command: cat /var/lib/cwl/stga0c3bb01-d8b0-42c0-b856-5e6cc44ea34a/OceanDNA-a3439.fa | prodigal -d OceanDNA-a3439/cds.fna -a OceanDNA-a3439/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:12:41,561] [INFO] Task succeeded: Prodigal
[2023-03-15 08:12:41,562] [INFO] Task started: HMMsearch
[2023-03-15 08:12:41,562] [INFO] Running command: hmmsearch --tblout OceanDNA-a3439/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10131228-05ea-4631-b82f-480904d62b2e/dqc_reference/reference_markers.hmm OceanDNA-a3439/protein.faa > /dev/null
[2023-03-15 08:12:41,768] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:12:41,768] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga0c3bb01-d8b0-42c0-b856-5e6cc44ea34a/OceanDNA-a3439.fa]
[2023-03-15 08:12:41,778] [INFO] Query marker FASTA was written to OceanDNA-a3439/markers.fasta
[2023-03-15 08:12:41,779] [INFO] Task started: Blastn
[2023-03-15 08:12:41,779] [INFO] Running command: blastn -query OceanDNA-a3439/markers.fasta -db /var/lib/cwl/stg10131228-05ea-4631-b82f-480904d62b2e/dqc_reference/reference_markers.fasta -out OceanDNA-a3439/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:12:42,352] [INFO] Task succeeded: Blastn
[2023-03-15 08:12:42,353] [INFO] Selected 4 target genomes.
[2023-03-15 08:12:42,354] [INFO] Target genome list was writen to OceanDNA-a3439/target_genomes.txt
[2023-03-15 08:12:42,359] [INFO] Task started: fastANI
[2023-03-15 08:12:42,359] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c3bb01-d8b0-42c0-b856-5e6cc44ea34a/OceanDNA-a3439.fa --refList OceanDNA-a3439/target_genomes.txt --output OceanDNA-a3439/fastani_result.tsv --threads 1
[2023-03-15 08:12:44,561] [INFO] Task succeeded: fastANI
[2023-03-15 08:12:44,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10131228-05ea-4631-b82f-480904d62b2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:12:44,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10131228-05ea-4631-b82f-480904d62b2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:12:44,562] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:12:44,562] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:12:44,562] [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
--------------------------------------------------------------------------------
[2023-03-15 08:12:44,563] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3439/tc_result.tsv
[2023-03-15 08:12:44,563] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:12:44,563] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:12:44,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10131228-05ea-4631-b82f-480904d62b2e/dqc_reference/checkm_data
[2023-03-15 08:12:44,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:12:44,569] [INFO] Task started: CheckM
[2023-03-15 08:12:44,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3439/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3439/checkm_input OceanDNA-a3439/checkm_result
[2023-03-15 08:13:07,267] [INFO] Task succeeded: CheckM
[2023-03-15 08:13:07,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:13:07,286] [INFO] ===== Completeness check finished =====
[2023-03-15 08:13:07,286] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:13:07,286] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3439/markers.fasta)
[2023-03-15 08:13:07,288] [INFO] Task started: Blastn
[2023-03-15 08:13:07,288] [INFO] Running command: blastn -query OceanDNA-a3439/markers.fasta -db /var/lib/cwl/stg10131228-05ea-4631-b82f-480904d62b2e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3439/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:13:08,013] [INFO] Task succeeded: Blastn
[2023-03-15 08:13:08,020] [INFO] Selected 7 target genomes.
[2023-03-15 08:13:08,020] [INFO] Target genome list was writen to OceanDNA-a3439/target_genomes_gtdb.txt
[2023-03-15 08:13:08,028] [INFO] Task started: fastANI
[2023-03-15 08:13:08,028] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c3bb01-d8b0-42c0-b856-5e6cc44ea34a/OceanDNA-a3439.fa --refList OceanDNA-a3439/target_genomes_gtdb.txt --output OceanDNA-a3439/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:13:09,726] [INFO] Task succeeded: fastANI
[2023-03-15 08:13:09,730] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:13:09,730] [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_002457555.1	s__MGIIb-O1 sp002457555	79.3667	223	379	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.79	99.79	0.86	0.86	2	-
GCA_002502175.1	s__MGIIb-O1 sp002502175	78.9563	214	379	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	98.79	95.28	0.87	0.80	11	-
GCA_002496905.1	s__MGIIb-O1 sp002496905	78.9277	192	379	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.08	98.67	0.77	0.73	3	-
GCA_002502365.1	s__MGIIb-O1 sp002502365	78.2922	100	379	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	96.24	96.24	0.82	0.82	2	-
GCA_002708385.1	s__MGIIb-O1 sp002708385	78.1657	118	379	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:13:09,736] [INFO] GTDB search result was written to OceanDNA-a3439/result_gtdb.tsv
[2023-03-15 08:13:09,736] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:13:09,740] [INFO] DFAST_QC result json was written to OceanDNA-a3439/dqc_result.json
[2023-03-15 08:13:09,740] [INFO] DFAST_QC completed!
[2023-03-15 08:13:09,740] [INFO] Total running time: 0h0m36s