[2023-03-16 00:33:46,711] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:33:46,711] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:33:46,711] [INFO] DQC Reference Directory: /var/lib/cwl/stgf26c206e-e377-4a86-8736-e182e7217ae9/dqc_reference
[2023-03-16 00:33:47,829] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:33:47,829] [INFO] Task started: Prodigal
[2023-03-16 00:33:47,830] [INFO] Running command: cat /var/lib/cwl/stg92c1c93b-77dd-47ae-8eb4-e0fd7a8a17dd/OceanDNA-b11272.fa | prodigal -d OceanDNA-b11272/cds.fna -a OceanDNA-b11272/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:33:56,405] [INFO] Task succeeded: Prodigal
[2023-03-16 00:33:56,406] [INFO] Task started: HMMsearch
[2023-03-16 00:33:56,406] [INFO] Running command: hmmsearch --tblout OceanDNA-b11272/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf26c206e-e377-4a86-8736-e182e7217ae9/dqc_reference/reference_markers.hmm OceanDNA-b11272/protein.faa > /dev/null
[2023-03-16 00:33:56,590] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:33:56,591] [INFO] Found 6/6 markers.
[2023-03-16 00:33:56,604] [INFO] Query marker FASTA was written to OceanDNA-b11272/markers.fasta
[2023-03-16 00:33:56,606] [INFO] Task started: Blastn
[2023-03-16 00:33:56,606] [INFO] Running command: blastn -query OceanDNA-b11272/markers.fasta -db /var/lib/cwl/stgf26c206e-e377-4a86-8736-e182e7217ae9/dqc_reference/reference_markers.fasta -out OceanDNA-b11272/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:33:57,218] [INFO] Task succeeded: Blastn
[2023-03-16 00:33:57,219] [INFO] Selected 31 target genomes.
[2023-03-16 00:33:57,219] [INFO] Target genome list was writen to OceanDNA-b11272/target_genomes.txt
[2023-03-16 00:33:57,520] [INFO] Task started: fastANI
[2023-03-16 00:33:57,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c1c93b-77dd-47ae-8eb4-e0fd7a8a17dd/OceanDNA-b11272.fa --refList OceanDNA-b11272/target_genomes.txt --output OceanDNA-b11272/fastani_result.tsv --threads 1
[2023-03-16 00:34:14,371] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:14,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf26c206e-e377-4a86-8736-e182e7217ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:34:14,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf26c206e-e377-4a86-8736-e182e7217ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:34:14,372] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:34:14,372] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:34:14,372] [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
--------------------------------------------------------------------------------
[2023-03-16 00:34:14,373] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11272/tc_result.tsv
[2023-03-16 00:34:14,373] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:34:14,373] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:34:14,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf26c206e-e377-4a86-8736-e182e7217ae9/dqc_reference/checkm_data
[2023-03-16 00:34:14,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:34:14,475] [INFO] Task started: CheckM
[2023-03-16 00:34:14,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11272/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11272/checkm_input OceanDNA-b11272/checkm_result
[2023-03-16 00:34:41,042] [INFO] Task succeeded: CheckM
[2023-03-16 00:34:41,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:34:41,050] [INFO] ===== Completeness check finished =====
[2023-03-16 00:34:41,050] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:34:41,051] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11272/markers.fasta)
[2023-03-16 00:34:41,052] [INFO] Task started: Blastn
[2023-03-16 00:34:41,052] [INFO] Running command: blastn -query OceanDNA-b11272/markers.fasta -db /var/lib/cwl/stgf26c206e-e377-4a86-8736-e182e7217ae9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11272/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:34:42,020] [INFO] Task succeeded: Blastn
[2023-03-16 00:34:42,021] [INFO] Selected 15 target genomes.
[2023-03-16 00:34:42,022] [INFO] Target genome list was writen to OceanDNA-b11272/target_genomes_gtdb.txt
[2023-03-16 00:34:42,063] [INFO] Task started: fastANI
[2023-03-16 00:34:42,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c1c93b-77dd-47ae-8eb4-e0fd7a8a17dd/OceanDNA-b11272.fa --refList OceanDNA-b11272/target_genomes_gtdb.txt --output OceanDNA-b11272/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:34:48,505] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:48,510] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:34:48,510] [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_902584445.1	s__UBA8316 sp902584445	95.1059	303	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902515395.1	s__UBA8316 sp902515395	93.1182	301	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	96.55	96.55	0.73	0.73	2	-
GCA_902590705.1	s__UBA8316 sp902590705	91.9169	329	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.92	99.92	0.88	0.88	2	-
GCA_002171295.2	s__UBA8316 sp002171295	85.0665	212	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695445.1	s__UBA8316 sp002695445	80.7141	208	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	97.71	97.71	0.68	0.68	2	-
--------------------------------------------------------------------------------
[2023-03-16 00:34:48,510] [INFO] GTDB search result was written to OceanDNA-b11272/result_gtdb.tsv
[2023-03-16 00:34:48,510] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:34:48,511] [INFO] DFAST_QC result json was written to OceanDNA-b11272/dqc_result.json
[2023-03-16 00:34:48,511] [INFO] DFAST_QC completed!
[2023-03-16 00:34:48,511] [INFO] Total running time: 0h1m2s