[2023-03-18 21:15:29,381] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,383] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg208162d2-bfda-41e9-91c7-057869606e5e/dqc_reference
[2023-03-18 21:15:31,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,044] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,044] [INFO] Running command: cat /var/lib/cwl/stgdddb8f80-5f9f-4b1e-9f64-08fa39aa7375/OceanDNA-b25027.fa | prodigal -d OceanDNA-b25027/cds.fna -a OceanDNA-b25027/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:36,257] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:36,258] [INFO] Task started: HMMsearch
[2023-03-18 21:15:36,258] [INFO] Running command: hmmsearch --tblout OceanDNA-b25027/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg208162d2-bfda-41e9-91c7-057869606e5e/dqc_reference/reference_markers.hmm OceanDNA-b25027/protein.faa > /dev/null
[2023-03-18 21:15:36,417] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:36,418] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdddb8f80-5f9f-4b1e-9f64-08fa39aa7375/OceanDNA-b25027.fa]
[2023-03-18 21:15:36,432] [INFO] Query marker FASTA was written to OceanDNA-b25027/markers.fasta
[2023-03-18 21:15:36,433] [INFO] Task started: Blastn
[2023-03-18 21:15:36,433] [INFO] Running command: blastn -query OceanDNA-b25027/markers.fasta -db /var/lib/cwl/stg208162d2-bfda-41e9-91c7-057869606e5e/dqc_reference/reference_markers.fasta -out OceanDNA-b25027/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:37,203] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:37,204] [INFO] Selected 34 target genomes.
[2023-03-18 21:15:37,205] [INFO] Target genome list was writen to OceanDNA-b25027/target_genomes.txt
[2023-03-18 21:15:37,227] [INFO] Task started: fastANI
[2023-03-18 21:15:37,227] [INFO] Running command: fastANI --query /var/lib/cwl/stgdddb8f80-5f9f-4b1e-9f64-08fa39aa7375/OceanDNA-b25027.fa --refList OceanDNA-b25027/target_genomes.txt --output OceanDNA-b25027/fastani_result.tsv --threads 1
[2023-03-18 21:15:56,270] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:56,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg208162d2-bfda-41e9-91c7-057869606e5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:56,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg208162d2-bfda-41e9-91c7-057869606e5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:56,271] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:56,271] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:15:56,271] [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 21:15:56,272] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25027/tc_result.tsv
[2023-03-18 21:15:56,272] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:56,272] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:56,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg208162d2-bfda-41e9-91c7-057869606e5e/dqc_reference/checkm_data
[2023-03-18 21:15:56,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:56,279] [INFO] Task started: CheckM
[2023-03-18 21:15:56,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25027/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25027/checkm_input OceanDNA-b25027/checkm_result
[2023-03-18 21:16:15,806] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:15,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.09%
Contamintation: 6.92%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-18 21:16:15,814] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:15,814] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:15,814] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25027/markers.fasta)
[2023-03-18 21:16:15,816] [INFO] Task started: Blastn
[2023-03-18 21:16:15,816] [INFO] Running command: blastn -query OceanDNA-b25027/markers.fasta -db /var/lib/cwl/stg208162d2-bfda-41e9-91c7-057869606e5e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25027/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:16,652] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:16,654] [INFO] Selected 22 target genomes.
[2023-03-18 21:16:16,654] [INFO] Target genome list was writen to OceanDNA-b25027/target_genomes_gtdb.txt
[2023-03-18 21:16:16,700] [INFO] Task started: fastANI
[2023-03-18 21:16:16,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgdddb8f80-5f9f-4b1e-9f64-08fa39aa7375/OceanDNA-b25027.fa --refList OceanDNA-b25027/target_genomes_gtdb.txt --output OceanDNA-b25027/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:27,048] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:27,052] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:16:27,052] [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_002689195.1	s__UBA7378 sp002689195	94.8226	126	184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	98.73	98.05	0.85	0.80	4	-
GCA_902624095.1	s__UBA7378 sp902624095	83.2986	134	184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469805.1	s__UBA7378 sp002469805	78.4885	86	184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	99.20	98.74	0.81	0.77	5	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:27,052] [INFO] GTDB search result was written to OceanDNA-b25027/result_gtdb.tsv
[2023-03-18 21:16:27,053] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:27,054] [INFO] DFAST_QC result json was written to OceanDNA-b25027/dqc_result.json
[2023-03-18 21:16:27,055] [INFO] DFAST_QC completed!
[2023-03-18 21:16:27,055] [INFO] Total running time: 0h0m58s