[2023-03-15 04:45:00,980] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:00,981] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:00,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d565fa6-d1cc-442a-8190-bf634708bbd7/dqc_reference
[2023-03-15 04:45:02,125] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:02,126] [INFO] Task started: Prodigal
[2023-03-15 04:45:02,126] [INFO] Running command: cat /var/lib/cwl/stg5c6698e1-07e7-4759-9c5c-901ff01cf6bd/OceanDNA-b278.fa | prodigal -d OceanDNA-b278/cds.fna -a OceanDNA-b278/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:45:16,179] [INFO] Task succeeded: Prodigal
[2023-03-15 04:45:16,180] [INFO] Task started: HMMsearch
[2023-03-15 04:45:16,180] [INFO] Running command: hmmsearch --tblout OceanDNA-b278/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d565fa6-d1cc-442a-8190-bf634708bbd7/dqc_reference/reference_markers.hmm OceanDNA-b278/protein.faa > /dev/null
[2023-03-15 04:45:16,373] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:45:16,373] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5c6698e1-07e7-4759-9c5c-901ff01cf6bd/OceanDNA-b278.fa]
[2023-03-15 04:45:16,413] [INFO] Query marker FASTA was written to OceanDNA-b278/markers.fasta
[2023-03-15 04:45:16,415] [INFO] Task started: Blastn
[2023-03-15 04:45:16,415] [INFO] Running command: blastn -query OceanDNA-b278/markers.fasta -db /var/lib/cwl/stg4d565fa6-d1cc-442a-8190-bf634708bbd7/dqc_reference/reference_markers.fasta -out OceanDNA-b278/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:45:16,989] [INFO] Task succeeded: Blastn
[2023-03-15 04:45:16,994] [INFO] Selected 12 target genomes.
[2023-03-15 04:45:16,995] [INFO] Target genome list was writen to OceanDNA-b278/target_genomes.txt
[2023-03-15 04:45:17,004] [INFO] Task started: fastANI
[2023-03-15 04:45:17,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c6698e1-07e7-4759-9c5c-901ff01cf6bd/OceanDNA-b278.fa --refList OceanDNA-b278/target_genomes.txt --output OceanDNA-b278/fastani_result.tsv --threads 1
[2023-03-15 04:45:24,984] [INFO] Task succeeded: fastANI
[2023-03-15 04:45:24,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d565fa6-d1cc-442a-8190-bf634708bbd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:45:24,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d565fa6-d1cc-442a-8190-bf634708bbd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:45:24,985] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:45:24,985] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:45:24,985] [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 04:45:24,987] [INFO] DFAST Taxonomy check result was written to OceanDNA-b278/tc_result.tsv
[2023-03-15 04:45:24,990] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:45:24,990] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:45:24,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d565fa6-d1cc-442a-8190-bf634708bbd7/dqc_reference/checkm_data
[2023-03-15 04:45:25,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:45:25,007] [INFO] Task started: CheckM
[2023-03-15 04:45:25,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b278/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b278/checkm_input OceanDNA-b278/checkm_result
[2023-03-15 04:46:03,906] [INFO] Task succeeded: CheckM
[2023-03-15 04:46:03,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.98%
Contamintation: 1.88%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 04:46:03,964] [INFO] ===== Completeness check finished =====
[2023-03-15 04:46:03,964] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:46:03,964] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b278/markers.fasta)
[2023-03-15 04:46:03,966] [INFO] Task started: Blastn
[2023-03-15 04:46:03,966] [INFO] Running command: blastn -query OceanDNA-b278/markers.fasta -db /var/lib/cwl/stg4d565fa6-d1cc-442a-8190-bf634708bbd7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b278/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:04,966] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:04,972] [INFO] Selected 13 target genomes.
[2023-03-15 04:46:04,973] [INFO] Target genome list was writen to OceanDNA-b278/target_genomes_gtdb.txt
[2023-03-15 04:46:04,991] [INFO] Task started: fastANI
[2023-03-15 04:46:04,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c6698e1-07e7-4759-9c5c-901ff01cf6bd/OceanDNA-b278.fa --refList OceanDNA-b278/target_genomes_gtdb.txt --output OceanDNA-b278/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:46:14,252] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:14,256] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:46:14,256] [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_003533545.1	s__UBA9620 sp003533545	89.7295	538	755	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA9620	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712885.1	s__UBA8438 sp002712885	76.9672	143	755	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015659035.1	s__NP936 sp015659035	76.6964	138	755	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	76.6123	157	755	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346545.1	s__UBA2994 sp002346545	76.0956	103	755	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:46:14,259] [INFO] GTDB search result was written to OceanDNA-b278/result_gtdb.tsv
[2023-03-15 04:46:14,262] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:46:14,267] [INFO] DFAST_QC result json was written to OceanDNA-b278/dqc_result.json
[2023-03-15 04:46:14,267] [INFO] DFAST_QC completed!
[2023-03-15 04:46:14,267] [INFO] Total running time: 0h1m13s