[2023-03-17 11:25:36,999] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:37,002] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:37,002] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcada599-00dd-4deb-b6f4-bd57a3f9ee1e/dqc_reference
[2023-03-17 11:25:38,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,114] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,114] [INFO] Running command: cat /var/lib/cwl/stg782884aa-966a-4ddc-8d1c-89032e54a377/OceanDNA-b297.fa | prodigal -d OceanDNA-b297/cds.fna -a OceanDNA-b297/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:25:58,722] [INFO] Task succeeded: Prodigal
[2023-03-17 11:25:58,723] [INFO] Task started: HMMsearch
[2023-03-17 11:25:58,723] [INFO] Running command: hmmsearch --tblout OceanDNA-b297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcada599-00dd-4deb-b6f4-bd57a3f9ee1e/dqc_reference/reference_markers.hmm OceanDNA-b297/protein.faa > /dev/null
[2023-03-17 11:25:58,933] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:25:58,933] [INFO] Found 6/6 markers.
[2023-03-17 11:25:58,961] [INFO] Query marker FASTA was written to OceanDNA-b297/markers.fasta
[2023-03-17 11:25:58,962] [INFO] Task started: Blastn
[2023-03-17 11:25:58,962] [INFO] Running command: blastn -query OceanDNA-b297/markers.fasta -db /var/lib/cwl/stgbcada599-00dd-4deb-b6f4-bd57a3f9ee1e/dqc_reference/reference_markers.fasta -out OceanDNA-b297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:25:59,472] [INFO] Task succeeded: Blastn
[2023-03-17 11:25:59,484] [INFO] Selected 19 target genomes.
[2023-03-17 11:25:59,484] [INFO] Target genome list was writen to OceanDNA-b297/target_genomes.txt
[2023-03-17 11:25:59,496] [INFO] Task started: fastANI
[2023-03-17 11:25:59,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg782884aa-966a-4ddc-8d1c-89032e54a377/OceanDNA-b297.fa --refList OceanDNA-b297/target_genomes.txt --output OceanDNA-b297/fastani_result.tsv --threads 1
[2023-03-17 11:26:10,535] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:10,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcada599-00dd-4deb-b6f4-bd57a3f9ee1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:26:10,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcada599-00dd-4deb-b6f4-bd57a3f9ee1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:26:10,535] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:26:10,535] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:26:10,535] [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 11:26:10,541] [INFO] DFAST Taxonomy check result was written to OceanDNA-b297/tc_result.tsv
[2023-03-17 11:26:10,549] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:26:10,549] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:26:10,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcada599-00dd-4deb-b6f4-bd57a3f9ee1e/dqc_reference/checkm_data
[2023-03-17 11:26:10,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:26:10,561] [INFO] Task started: CheckM
[2023-03-17 11:26:10,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b297/checkm_input OceanDNA-b297/checkm_result
[2023-03-17 11:27:02,918] [INFO] Task succeeded: CheckM
[2023-03-17 11:27:02,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:27:03,017] [INFO] ===== Completeness check finished =====
[2023-03-17 11:27:03,018] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:27:03,018] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b297/markers.fasta)
[2023-03-17 11:27:03,019] [INFO] Task started: Blastn
[2023-03-17 11:27:03,019] [INFO] Running command: blastn -query OceanDNA-b297/markers.fasta -db /var/lib/cwl/stgbcada599-00dd-4deb-b6f4-bd57a3f9ee1e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:27:03,718] [INFO] Task succeeded: Blastn
[2023-03-17 11:27:03,723] [INFO] Selected 26 target genomes.
[2023-03-17 11:27:03,723] [INFO] Target genome list was writen to OceanDNA-b297/target_genomes_gtdb.txt
[2023-03-17 11:27:03,752] [INFO] Task started: fastANI
[2023-03-17 11:27:03,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg782884aa-966a-4ddc-8d1c-89032e54a377/OceanDNA-b297.fa --refList OceanDNA-b297/target_genomes_gtdb.txt --output OceanDNA-b297/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:27:16,860] [INFO] Task succeeded: fastANI
[2023-03-17 11:27:16,862] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:27:16,862] [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_002347025.1	s__UBA2990 sp002347025	99.9599	1051	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2990	95.0	99.94	99.92	0.88	0.83	3	conclusive
GCA_002726085.1	s__NP936 sp002726085	76.0124	53	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:27:16,866] [INFO] GTDB search result was written to OceanDNA-b297/result_gtdb.tsv
[2023-03-17 11:27:16,868] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:27:16,874] [INFO] DFAST_QC result json was written to OceanDNA-b297/dqc_result.json
[2023-03-17 11:27:16,874] [INFO] DFAST_QC completed!
[2023-03-17 11:27:16,874] [INFO] Total running time: 0h1m40s