[2023-03-15 20:34:26,716] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,716] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,716] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf07c1a0-e0d6-4408-8fa2-ab2b4e8b3a16/dqc_reference
[2023-03-15 20:34:28,458] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,458] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,458] [INFO] Running command: cat /var/lib/cwl/stgc9529068-b9a3-4114-a4b8-a47683dc9430/OceanDNA-b11288.fa | prodigal -d OceanDNA-b11288/cds.fna -a OceanDNA-b11288/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:43,000] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:43,001] [INFO] Task started: HMMsearch
[2023-03-15 20:34:43,001] [INFO] Running command: hmmsearch --tblout OceanDNA-b11288/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf07c1a0-e0d6-4408-8fa2-ab2b4e8b3a16/dqc_reference/reference_markers.hmm OceanDNA-b11288/protein.faa > /dev/null
[2023-03-15 20:34:43,186] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:43,187] [INFO] Found 6/6 markers.
[2023-03-15 20:34:43,200] [INFO] Query marker FASTA was written to OceanDNA-b11288/markers.fasta
[2023-03-15 20:34:43,200] [INFO] Task started: Blastn
[2023-03-15 20:34:43,200] [INFO] Running command: blastn -query OceanDNA-b11288/markers.fasta -db /var/lib/cwl/stgdf07c1a0-e0d6-4408-8fa2-ab2b4e8b3a16/dqc_reference/reference_markers.fasta -out OceanDNA-b11288/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:43,735] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:43,735] [INFO] Selected 36 target genomes.
[2023-03-15 20:34:43,736] [INFO] Target genome list was writen to OceanDNA-b11288/target_genomes.txt
[2023-03-15 20:34:43,755] [INFO] Task started: fastANI
[2023-03-15 20:34:43,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9529068-b9a3-4114-a4b8-a47683dc9430/OceanDNA-b11288.fa --refList OceanDNA-b11288/target_genomes.txt --output OceanDNA-b11288/fastani_result.tsv --threads 1
[2023-03-15 20:35:06,193] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:06,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf07c1a0-e0d6-4408-8fa2-ab2b4e8b3a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:35:06,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf07c1a0-e0d6-4408-8fa2-ab2b4e8b3a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:35:06,194] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:35:06,194] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:35:06,194] [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 20:35:06,316] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11288/tc_result.tsv
[2023-03-15 20:35:06,316] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:35:06,317] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:35:06,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf07c1a0-e0d6-4408-8fa2-ab2b4e8b3a16/dqc_reference/checkm_data
[2023-03-15 20:35:06,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:35:06,407] [INFO] Task started: CheckM
[2023-03-15 20:35:06,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11288/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11288/checkm_input OceanDNA-b11288/checkm_result
[2023-03-15 20:35:46,530] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:46,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:46,532] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:46,532] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:46,533] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11288/markers.fasta)
[2023-03-15 20:35:46,534] [INFO] Task started: Blastn
[2023-03-15 20:35:46,534] [INFO] Running command: blastn -query OceanDNA-b11288/markers.fasta -db /var/lib/cwl/stgdf07c1a0-e0d6-4408-8fa2-ab2b4e8b3a16/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11288/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:47,275] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:47,276] [INFO] Selected 13 target genomes.
[2023-03-15 20:35:47,276] [INFO] Target genome list was writen to OceanDNA-b11288/target_genomes_gtdb.txt
[2023-03-15 20:35:47,547] [INFO] Task started: fastANI
[2023-03-15 20:35:47,547] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9529068-b9a3-4114-a4b8-a47683dc9430/OceanDNA-b11288.fa --refList OceanDNA-b11288/target_genomes_gtdb.txt --output OceanDNA-b11288/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:51,630] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:51,637] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:35:51,637] [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_002390455.1	s__UBA8316 sp002390455	99.7898	478	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	conclusive
GCA_009936675.1	s__UBA8316 sp009936675	87.5684	387	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_018623955.1	s__UBA8316 sp018623955	81.8794	203	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364535.1	s__UBA8316 sp002364535	81.3807	425	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_002687665.1	s__UBA8316 sp002687665	79.6189	224	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619315.1	s__UBA8316 sp902619315	78.942	234	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647605.1	s__UBA8316 sp018647605	78.8819	268	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336305.1	s__UBA8316 sp002336305	78.5647	239	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538555.1	s__UBA8316 sp003538555	77.1664	100	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	98.54	98.54	0.88	0.88	2	-
GCA_017857815.1	s__UBA8316 sp017857815	76.6534	78	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182575.1	s__UBA8316 sp905182575	76.5503	77	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	95.72	95.72	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:51,637] [INFO] GTDB search result was written to OceanDNA-b11288/result_gtdb.tsv
[2023-03-15 20:35:51,637] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:51,638] [INFO] DFAST_QC result json was written to OceanDNA-b11288/dqc_result.json
[2023-03-15 20:35:51,638] [INFO] DFAST_QC completed!
[2023-03-15 20:35:51,638] [INFO] Total running time: 0h1m25s