[2023-03-17 00:45:47,092] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,092] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,092] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b6a2c58-8897-4519-bc53-74920c8be792/dqc_reference
[2023-03-17 00:45:48,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,284] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,284] [INFO] Running command: cat /var/lib/cwl/stgc23c1755-1072-428b-9ee4-831e9625767e/OceanDNA-b11649.fa | prodigal -d OceanDNA-b11649/cds.fna -a OceanDNA-b11649/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:02,234] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:02,234] [INFO] Task started: HMMsearch
[2023-03-17 00:46:02,234] [INFO] Running command: hmmsearch --tblout OceanDNA-b11649/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b6a2c58-8897-4519-bc53-74920c8be792/dqc_reference/reference_markers.hmm OceanDNA-b11649/protein.faa > /dev/null
[2023-03-17 00:46:02,417] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:02,418] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc23c1755-1072-428b-9ee4-831e9625767e/OceanDNA-b11649.fa]
[2023-03-17 00:46:02,431] [INFO] Query marker FASTA was written to OceanDNA-b11649/markers.fasta
[2023-03-17 00:46:02,432] [INFO] Task started: Blastn
[2023-03-17 00:46:02,432] [INFO] Running command: blastn -query OceanDNA-b11649/markers.fasta -db /var/lib/cwl/stg9b6a2c58-8897-4519-bc53-74920c8be792/dqc_reference/reference_markers.fasta -out OceanDNA-b11649/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:02,949] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:02,950] [INFO] Selected 21 target genomes.
[2023-03-17 00:46:02,950] [INFO] Target genome list was writen to OceanDNA-b11649/target_genomes.txt
[2023-03-17 00:46:03,015] [INFO] Task started: fastANI
[2023-03-17 00:46:03,016] [INFO] Running command: fastANI --query /var/lib/cwl/stgc23c1755-1072-428b-9ee4-831e9625767e/OceanDNA-b11649.fa --refList OceanDNA-b11649/target_genomes.txt --output OceanDNA-b11649/fastani_result.tsv --threads 1
[2023-03-17 00:46:15,555] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:15,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b6a2c58-8897-4519-bc53-74920c8be792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:15,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b6a2c58-8897-4519-bc53-74920c8be792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:15,556] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:15,556] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:15,556] [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
--------------------------------------------------------------------------------
[2023-03-17 00:46:15,557] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11649/tc_result.tsv
[2023-03-17 00:46:15,557] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:15,557] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:15,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b6a2c58-8897-4519-bc53-74920c8be792/dqc_reference/checkm_data
[2023-03-17 00:46:15,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:15,621] [INFO] Task started: CheckM
[2023-03-17 00:46:15,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11649/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11649/checkm_input OceanDNA-b11649/checkm_result
[2023-03-17 00:46:53,211] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:53,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:53,230] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:53,230] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:53,231] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11649/markers.fasta)
[2023-03-17 00:46:53,232] [INFO] Task started: Blastn
[2023-03-17 00:46:53,232] [INFO] Running command: blastn -query OceanDNA-b11649/markers.fasta -db /var/lib/cwl/stg9b6a2c58-8897-4519-bc53-74920c8be792/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11649/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:53,958] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:53,959] [INFO] Selected 15 target genomes.
[2023-03-17 00:46:53,960] [INFO] Target genome list was writen to OceanDNA-b11649/target_genomes_gtdb.txt
[2023-03-17 00:46:54,148] [INFO] Task started: fastANI
[2023-03-17 00:46:54,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgc23c1755-1072-428b-9ee4-831e9625767e/OceanDNA-b11649.fa --refList OceanDNA-b11649/target_genomes_gtdb.txt --output OceanDNA-b11649/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:03,225] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:03,228] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:47:03,228] [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_002336675.1	s__ASP10-05a sp002336675	99.753	662	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__ASP10-05a	95.0	99.85	99.85	0.92	0.92	2	conclusive
GCA_000981645.1	s__ASP10-05a sp000981645	90.7617	679	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__ASP10-05a	95.0	99.43	99.38	0.95	0.94	4	-
GCA_905182895.1	s__ASP10-05a sp905182895	90.3897	384	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__ASP10-05a	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:03,229] [INFO] GTDB search result was written to OceanDNA-b11649/result_gtdb.tsv
[2023-03-17 00:47:03,229] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:03,230] [INFO] DFAST_QC result json was written to OceanDNA-b11649/dqc_result.json
[2023-03-17 00:47:03,230] [INFO] DFAST_QC completed!
[2023-03-17 00:47:03,230] [INFO] Total running time: 0h1m16s