[2023-03-15 17:46:31,715] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,715] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,715] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcb5b83b-697c-41b3-a6cc-3465609dc468/dqc_reference
[2023-03-15 17:46:32,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,798] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,798] [INFO] Running command: cat /var/lib/cwl/stg45182777-bf60-409e-a2c4-a0c749e09662/OceanDNA-b11477.fa | prodigal -d OceanDNA-b11477/cds.fna -a OceanDNA-b11477/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:48,149] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:48,149] [INFO] Task started: HMMsearch
[2023-03-15 17:46:48,149] [INFO] Running command: hmmsearch --tblout OceanDNA-b11477/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcb5b83b-697c-41b3-a6cc-3465609dc468/dqc_reference/reference_markers.hmm OceanDNA-b11477/protein.faa > /dev/null
[2023-03-15 17:46:48,347] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:48,347] [INFO] Found 6/6 markers.
[2023-03-15 17:46:48,369] [INFO] Query marker FASTA was written to OceanDNA-b11477/markers.fasta
[2023-03-15 17:46:48,370] [INFO] Task started: Blastn
[2023-03-15 17:46:48,370] [INFO] Running command: blastn -query OceanDNA-b11477/markers.fasta -db /var/lib/cwl/stgbcb5b83b-697c-41b3-a6cc-3465609dc468/dqc_reference/reference_markers.fasta -out OceanDNA-b11477/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:48,912] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:48,915] [INFO] Selected 43 target genomes.
[2023-03-15 17:46:48,916] [INFO] Target genome list was writen to OceanDNA-b11477/target_genomes.txt
[2023-03-15 17:46:48,942] [INFO] Task started: fastANI
[2023-03-15 17:46:48,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg45182777-bf60-409e-a2c4-a0c749e09662/OceanDNA-b11477.fa --refList OceanDNA-b11477/target_genomes.txt --output OceanDNA-b11477/fastani_result.tsv --threads 1
[2023-03-15 17:47:14,277] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:14,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcb5b83b-697c-41b3-a6cc-3465609dc468/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:47:14,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcb5b83b-697c-41b3-a6cc-3465609dc468/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:47:14,278] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:47:14,278] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:47:14,278] [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 17:47:14,359] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11477/tc_result.tsv
[2023-03-15 17:47:14,362] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:47:14,362] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:47:14,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcb5b83b-697c-41b3-a6cc-3465609dc468/dqc_reference/checkm_data
[2023-03-15 17:47:14,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:47:14,388] [INFO] Task started: CheckM
[2023-03-15 17:47:14,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11477/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11477/checkm_input OceanDNA-b11477/checkm_result
[2023-03-15 17:47:55,199] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:55,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:55,202] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:55,202] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:55,202] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11477/markers.fasta)
[2023-03-15 17:47:55,203] [INFO] Task started: Blastn
[2023-03-15 17:47:55,203] [INFO] Running command: blastn -query OceanDNA-b11477/markers.fasta -db /var/lib/cwl/stgbcb5b83b-697c-41b3-a6cc-3465609dc468/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11477/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:55,974] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:55,975] [INFO] Selected 42 target genomes.
[2023-03-15 17:47:55,975] [INFO] Target genome list was writen to OceanDNA-b11477/target_genomes_gtdb.txt
[2023-03-15 17:47:56,079] [INFO] Task started: fastANI
[2023-03-15 17:47:56,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg45182777-bf60-409e-a2c4-a0c749e09662/OceanDNA-b11477.fa --refList OceanDNA-b11477/target_genomes_gtdb.txt --output OceanDNA-b11477/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:48:18,029] [INFO] Task succeeded: fastANI
[2023-03-15 17:48:18,032] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:48:18,032] [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_905182585.1	s__GCA-002722245 sp905182585	77.3208	81	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722245.1	s__GCA-002722245 sp002722245	76.2793	57	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717515.1	s__GCA-002722245 sp002717515	75.7506	63	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	99.42	99.42	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:48:18,032] [INFO] GTDB search result was written to OceanDNA-b11477/result_gtdb.tsv
[2023-03-15 17:48:18,032] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:48:18,032] [INFO] DFAST_QC result json was written to OceanDNA-b11477/dqc_result.json
[2023-03-15 17:48:18,033] [INFO] DFAST_QC completed!
[2023-03-15 17:48:18,033] [INFO] Total running time: 0h1m46s