[2023-03-15 10:34:47,893] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:34:47,896] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:34:47,896] [INFO] DQC Reference Directory: /var/lib/cwl/stge23c8b7f-f83a-49a8-900e-953ad953b6ae/dqc_reference
[2023-03-15 10:34:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:34:49,423] [INFO] Task started: Prodigal
[2023-03-15 10:34:49,423] [INFO] Running command: cat /var/lib/cwl/stg2776dd3e-f03f-4df7-b0f9-68beaaded4a4/OceanDNA-b17550.fa | prodigal -d OceanDNA-b17550/cds.fna -a OceanDNA-b17550/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:34:55,695] [INFO] Task succeeded: Prodigal
[2023-03-15 10:34:55,695] [INFO] Task started: HMMsearch
[2023-03-15 10:34:55,695] [INFO] Running command: hmmsearch --tblout OceanDNA-b17550/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge23c8b7f-f83a-49a8-900e-953ad953b6ae/dqc_reference/reference_markers.hmm OceanDNA-b17550/protein.faa > /dev/null
[2023-03-15 10:34:55,844] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:34:55,844] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2776dd3e-f03f-4df7-b0f9-68beaaded4a4/OceanDNA-b17550.fa]
[2023-03-15 10:34:55,866] [INFO] Query marker FASTA was written to OceanDNA-b17550/markers.fasta
[2023-03-15 10:34:55,867] [INFO] Task started: Blastn
[2023-03-15 10:34:55,867] [INFO] Running command: blastn -query OceanDNA-b17550/markers.fasta -db /var/lib/cwl/stge23c8b7f-f83a-49a8-900e-953ad953b6ae/dqc_reference/reference_markers.fasta -out OceanDNA-b17550/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:34:56,351] [INFO] Task succeeded: Blastn
[2023-03-15 10:34:56,352] [INFO] Selected 7 target genomes.
[2023-03-15 10:34:56,352] [INFO] Target genome list was writen to OceanDNA-b17550/target_genomes.txt
[2023-03-15 10:34:56,355] [INFO] Task started: fastANI
[2023-03-15 10:34:56,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg2776dd3e-f03f-4df7-b0f9-68beaaded4a4/OceanDNA-b17550.fa --refList OceanDNA-b17550/target_genomes.txt --output OceanDNA-b17550/fastani_result.tsv --threads 1
[2023-03-15 10:35:01,195] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:01,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge23c8b7f-f83a-49a8-900e-953ad953b6ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:35:01,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge23c8b7f-f83a-49a8-900e-953ad953b6ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:35:01,196] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:35:01,196] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:35:01,196] [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 10:35:01,199] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17550/tc_result.tsv
[2023-03-15 10:35:01,202] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:35:01,202] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:35:01,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge23c8b7f-f83a-49a8-900e-953ad953b6ae/dqc_reference/checkm_data
[2023-03-15 10:35:01,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:35:01,233] [INFO] Task started: CheckM
[2023-03-15 10:35:01,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17550/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17550/checkm_input OceanDNA-b17550/checkm_result
[2023-03-15 10:35:23,591] [INFO] Task succeeded: CheckM
[2023-03-15 10:35:23,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.81%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:35:23,891] [INFO] ===== Completeness check finished =====
[2023-03-15 10:35:23,891] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:35:23,891] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17550/markers.fasta)
[2023-03-15 10:35:23,892] [INFO] Task started: Blastn
[2023-03-15 10:35:23,892] [INFO] Running command: blastn -query OceanDNA-b17550/markers.fasta -db /var/lib/cwl/stge23c8b7f-f83a-49a8-900e-953ad953b6ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17550/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:24,519] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:24,522] [INFO] Selected 15 target genomes.
[2023-03-15 10:35:24,522] [INFO] Target genome list was writen to OceanDNA-b17550/target_genomes_gtdb.txt
[2023-03-15 10:35:25,088] [INFO] Task started: fastANI
[2023-03-15 10:35:25,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg2776dd3e-f03f-4df7-b0f9-68beaaded4a4/OceanDNA-b17550.fa --refList OceanDNA-b17550/target_genomes_gtdb.txt --output OceanDNA-b17550/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:35:32,396] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:32,398] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:35:32,398] [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_012965445.1	s__DTSJ01 sp012965445	96.2254	148	226	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__GCA-2746185;g__DTSJ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-15 10:35:32,401] [INFO] GTDB search result was written to OceanDNA-b17550/result_gtdb.tsv
[2023-03-15 10:35:32,402] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:35:32,404] [INFO] DFAST_QC result json was written to OceanDNA-b17550/dqc_result.json
[2023-03-15 10:35:32,404] [INFO] DFAST_QC completed!
[2023-03-15 10:35:32,404] [INFO] Total running time: 0h0m45s