[2023-03-18 09:58:36,592] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:58:36,593] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:58:36,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg7697e2f0-6b0d-4a14-82be-3ff6ff0af13a/dqc_reference
[2023-03-18 09:58:38,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:58:38,401] [INFO] Task started: Prodigal
[2023-03-18 09:58:38,402] [INFO] Running command: cat /var/lib/cwl/stg5b497e50-7091-46b6-84d2-969da4750f5d/OceanDNA-b33116.fa | prodigal -d OceanDNA-b33116/cds.fna -a OceanDNA-b33116/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:58:51,863] [INFO] Task succeeded: Prodigal
[2023-03-18 09:58:51,863] [INFO] Task started: HMMsearch
[2023-03-18 09:58:51,863] [INFO] Running command: hmmsearch --tblout OceanDNA-b33116/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7697e2f0-6b0d-4a14-82be-3ff6ff0af13a/dqc_reference/reference_markers.hmm OceanDNA-b33116/protein.faa > /dev/null
[2023-03-18 09:58:52,094] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:58:52,094] [INFO] Found 6/6 markers.
[2023-03-18 09:58:52,112] [INFO] Query marker FASTA was written to OceanDNA-b33116/markers.fasta
[2023-03-18 09:58:52,113] [INFO] Task started: Blastn
[2023-03-18 09:58:52,114] [INFO] Running command: blastn -query OceanDNA-b33116/markers.fasta -db /var/lib/cwl/stg7697e2f0-6b0d-4a14-82be-3ff6ff0af13a/dqc_reference/reference_markers.fasta -out OceanDNA-b33116/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:58:52,680] [INFO] Task succeeded: Blastn
[2023-03-18 09:58:52,681] [INFO] Selected 26 target genomes.
[2023-03-18 09:58:52,681] [INFO] Target genome list was writen to OceanDNA-b33116/target_genomes.txt
[2023-03-18 09:58:52,704] [INFO] Task started: fastANI
[2023-03-18 09:58:52,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b497e50-7091-46b6-84d2-969da4750f5d/OceanDNA-b33116.fa --refList OceanDNA-b33116/target_genomes.txt --output OceanDNA-b33116/fastani_result.tsv --threads 1
[2023-03-18 09:59:05,721] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:05,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7697e2f0-6b0d-4a14-82be-3ff6ff0af13a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:59:05,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7697e2f0-6b0d-4a14-82be-3ff6ff0af13a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:59:05,722] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:59:05,722] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:59:05,722] [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
--------------------------------------------------------------------------------
[2023-03-18 09:59:05,723] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33116/tc_result.tsv
[2023-03-18 09:59:05,723] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:59:05,723] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:59:05,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7697e2f0-6b0d-4a14-82be-3ff6ff0af13a/dqc_reference/checkm_data
[2023-03-18 09:59:05,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:59:05,730] [INFO] Task started: CheckM
[2023-03-18 09:59:05,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33116/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33116/checkm_input OceanDNA-b33116/checkm_result
[2023-03-18 09:59:42,824] [INFO] Task succeeded: CheckM
[2023-03-18 09:59:42,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:59:42,827] [INFO] ===== Completeness check finished =====
[2023-03-18 09:59:42,827] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:59:42,827] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33116/markers.fasta)
[2023-03-18 09:59:42,828] [INFO] Task started: Blastn
[2023-03-18 09:59:42,828] [INFO] Running command: blastn -query OceanDNA-b33116/markers.fasta -db /var/lib/cwl/stg7697e2f0-6b0d-4a14-82be-3ff6ff0af13a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33116/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:59:43,713] [INFO] Task succeeded: Blastn
[2023-03-18 09:59:43,714] [INFO] Selected 22 target genomes.
[2023-03-18 09:59:43,714] [INFO] Target genome list was writen to OceanDNA-b33116/target_genomes_gtdb.txt
[2023-03-18 09:59:43,744] [INFO] Task started: fastANI
[2023-03-18 09:59:43,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b497e50-7091-46b6-84d2-969da4750f5d/OceanDNA-b33116.fa --refList OceanDNA-b33116/target_genomes_gtdb.txt --output OceanDNA-b33116/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:59:53,456] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:53,459] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:59:53,459] [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_002711555.1	s__UBA8366 sp002711555	90.0887	666	795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA8366	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718015.1	s__UBA8366 sp002718015	87.9306	504	795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA8366	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:59:53,459] [INFO] GTDB search result was written to OceanDNA-b33116/result_gtdb.tsv
[2023-03-18 09:59:53,459] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:59:53,460] [INFO] DFAST_QC result json was written to OceanDNA-b33116/dqc_result.json
[2023-03-18 09:59:53,460] [INFO] DFAST_QC completed!
[2023-03-18 09:59:53,460] [INFO] Total running time: 0h1m17s