[2023-03-15 09:48:16,566] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,566] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,566] [INFO] DQC Reference Directory: /var/lib/cwl/stge4ca3b38-9804-45a1-be30-5de21fff8614/dqc_reference
[2023-03-15 09:48:18,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,228] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,229] [INFO] Running command: cat /var/lib/cwl/stg616c55e8-3cf2-474e-81de-1c9de34b1b91/OceanDNA-b12166.fa | prodigal -d OceanDNA-b12166/cds.fna -a OceanDNA-b12166/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:26,456] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:26,457] [INFO] Task started: HMMsearch
[2023-03-15 09:48:26,457] [INFO] Running command: hmmsearch --tblout OceanDNA-b12166/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4ca3b38-9804-45a1-be30-5de21fff8614/dqc_reference/reference_markers.hmm OceanDNA-b12166/protein.faa > /dev/null
[2023-03-15 09:48:26,617] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:26,617] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg616c55e8-3cf2-474e-81de-1c9de34b1b91/OceanDNA-b12166.fa]
[2023-03-15 09:48:26,631] [INFO] Query marker FASTA was written to OceanDNA-b12166/markers.fasta
[2023-03-15 09:48:26,631] [INFO] Task started: Blastn
[2023-03-15 09:48:26,631] [INFO] Running command: blastn -query OceanDNA-b12166/markers.fasta -db /var/lib/cwl/stge4ca3b38-9804-45a1-be30-5de21fff8614/dqc_reference/reference_markers.fasta -out OceanDNA-b12166/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:27,193] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:27,194] [INFO] Selected 24 target genomes.
[2023-03-15 09:48:27,194] [INFO] Target genome list was writen to OceanDNA-b12166/target_genomes.txt
[2023-03-15 09:48:27,210] [INFO] Task started: fastANI
[2023-03-15 09:48:27,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg616c55e8-3cf2-474e-81de-1c9de34b1b91/OceanDNA-b12166.fa --refList OceanDNA-b12166/target_genomes.txt --output OceanDNA-b12166/fastani_result.tsv --threads 1
[2023-03-15 09:48:40,361] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:40,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4ca3b38-9804-45a1-be30-5de21fff8614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:40,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4ca3b38-9804-45a1-be30-5de21fff8614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:40,362] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:40,362] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:40,362] [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 09:48:40,362] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12166/tc_result.tsv
[2023-03-15 09:48:40,362] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:40,362] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:40,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4ca3b38-9804-45a1-be30-5de21fff8614/dqc_reference/checkm_data
[2023-03-15 09:48:40,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:40,368] [INFO] Task started: CheckM
[2023-03-15 09:48:40,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12166/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12166/checkm_input OceanDNA-b12166/checkm_result
[2023-03-15 09:49:06,479] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:06,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.55%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 09:49:06,481] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:06,482] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:06,482] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12166/markers.fasta)
[2023-03-15 09:49:06,482] [INFO] Task started: Blastn
[2023-03-15 09:49:06,482] [INFO] Running command: blastn -query OceanDNA-b12166/markers.fasta -db /var/lib/cwl/stge4ca3b38-9804-45a1-be30-5de21fff8614/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12166/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:07,498] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:07,499] [INFO] Selected 19 target genomes.
[2023-03-15 09:49:07,500] [INFO] Target genome list was writen to OceanDNA-b12166/target_genomes_gtdb.txt
[2023-03-15 09:49:07,997] [INFO] Task started: fastANI
[2023-03-15 09:49:07,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg616c55e8-3cf2-474e-81de-1c9de34b1b91/OceanDNA-b12166.fa --refList OceanDNA-b12166/target_genomes_gtdb.txt --output OceanDNA-b12166/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:14,867] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:14,871] [INFO] Found 4 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-15 09:49:14,871] [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_002694645.1	s__GCA-002727735 sp002694645	97.6874	144	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-002727735	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902536695.1	s__GCA-002727735 sp902536695	97.3643	216	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-002727735	95.0	97.41	97.41	0.52	0.52	2	inconclusive
GCA_002691605.1	s__MED-G20 sp002691605	76.2916	50	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.19	95.12	0.79	0.76	3	-
GCA_002723085.1	s__GCA-2723085 sp002723085	76.1576	54	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2723085	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:14,872] [INFO] GTDB search result was written to OceanDNA-b12166/result_gtdb.tsv
[2023-03-15 09:49:14,872] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:14,872] [INFO] DFAST_QC result json was written to OceanDNA-b12166/dqc_result.json
[2023-03-15 09:49:14,872] [INFO] DFAST_QC completed!
[2023-03-15 09:49:14,872] [INFO] Total running time: 0h0m58s