[2023-03-19 00:01:03,400] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,401] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bb5da6f-1cd2-41cd-8ff1-c7c17b96fe47/dqc_reference
[2023-03-19 00:01:04,603] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,603] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,603] [INFO] Running command: cat /var/lib/cwl/stg15f404ea-445c-4a72-8b97-e55ef34ea3a6/OceanDNA-b16283.fa | prodigal -d OceanDNA-b16283/cds.fna -a OceanDNA-b16283/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:12,044] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:12,045] [INFO] Task started: HMMsearch
[2023-03-19 00:01:12,045] [INFO] Running command: hmmsearch --tblout OceanDNA-b16283/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bb5da6f-1cd2-41cd-8ff1-c7c17b96fe47/dqc_reference/reference_markers.hmm OceanDNA-b16283/protein.faa > /dev/null
[2023-03-19 00:01:12,209] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:12,209] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg15f404ea-445c-4a72-8b97-e55ef34ea3a6/OceanDNA-b16283.fa]
[2023-03-19 00:01:12,218] [INFO] Query marker FASTA was written to OceanDNA-b16283/markers.fasta
[2023-03-19 00:01:12,218] [INFO] Task started: Blastn
[2023-03-19 00:01:12,218] [INFO] Running command: blastn -query OceanDNA-b16283/markers.fasta -db /var/lib/cwl/stg8bb5da6f-1cd2-41cd-8ff1-c7c17b96fe47/dqc_reference/reference_markers.fasta -out OceanDNA-b16283/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:12,650] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:12,651] [INFO] Selected 15 target genomes.
[2023-03-19 00:01:12,651] [INFO] Target genome list was writen to OceanDNA-b16283/target_genomes.txt
[2023-03-19 00:01:12,658] [INFO] Task started: fastANI
[2023-03-19 00:01:12,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg15f404ea-445c-4a72-8b97-e55ef34ea3a6/OceanDNA-b16283.fa --refList OceanDNA-b16283/target_genomes.txt --output OceanDNA-b16283/fastani_result.tsv --threads 1
[2023-03-19 00:01:18,209] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:18,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bb5da6f-1cd2-41cd-8ff1-c7c17b96fe47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:18,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bb5da6f-1cd2-41cd-8ff1-c7c17b96fe47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:18,210] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:18,210] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:01:18,210] [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
--------------------------------------------------------------------------------
[2023-03-19 00:01:18,210] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16283/tc_result.tsv
[2023-03-19 00:01:18,211] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:18,211] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:18,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bb5da6f-1cd2-41cd-8ff1-c7c17b96fe47/dqc_reference/checkm_data
[2023-03-19 00:01:18,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:18,216] [INFO] Task started: CheckM
[2023-03-19 00:01:18,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16283/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16283/checkm_input OceanDNA-b16283/checkm_result
[2023-03-19 00:01:42,250] [INFO] Task succeeded: CheckM
[2023-03-19 00:01:42,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:01:42,253] [INFO] ===== Completeness check finished =====
[2023-03-19 00:01:42,253] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:01:42,253] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16283/markers.fasta)
[2023-03-19 00:01:42,253] [INFO] Task started: Blastn
[2023-03-19 00:01:42,253] [INFO] Running command: blastn -query OceanDNA-b16283/markers.fasta -db /var/lib/cwl/stg8bb5da6f-1cd2-41cd-8ff1-c7c17b96fe47/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16283/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:42,710] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:42,711] [INFO] Selected 19 target genomes.
[2023-03-19 00:01:42,711] [INFO] Target genome list was writen to OceanDNA-b16283/target_genomes_gtdb.txt
[2023-03-19 00:01:42,737] [INFO] Task started: fastANI
[2023-03-19 00:01:42,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg15f404ea-445c-4a72-8b97-e55ef34ea3a6/OceanDNA-b16283.fa --refList OceanDNA-b16283/target_genomes_gtdb.txt --output OceanDNA-b16283/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:01:46,957] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:46,961] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:01:46,961] [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
GCF_000759855.1	s__Prochlorococcus_A marinus_N	76.6143	64	426	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	99.96	99.95	0.99	0.98	3	-
GCA_003212395.1	s__Prochlorococcus_A sp003212395	76.336	54	426	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003281335.1	s__Prochlorococcus_A sp003281335	76.206	60	426	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616385.1	s__Prochlorococcus_A sp902616385	76.0744	58	426	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003281185.1	s__Prochlorococcus_A sp003281185	76.0688	53	426	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017695975.1	s__Prochlorococcus_A marinus_AG	75.9477	65	426	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:01:46,961] [INFO] GTDB search result was written to OceanDNA-b16283/result_gtdb.tsv
[2023-03-19 00:01:46,962] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:01:46,962] [INFO] DFAST_QC result json was written to OceanDNA-b16283/dqc_result.json
[2023-03-19 00:01:46,962] [INFO] DFAST_QC completed!
[2023-03-19 00:01:46,962] [INFO] Total running time: 0h0m44s