[2023-03-18 08:41:54,063] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:41:54,063] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:41:54,063] [INFO] DQC Reference Directory: /var/lib/cwl/stg153e1a18-5dac-4820-8478-0fbe88aabffe/dqc_reference
[2023-03-18 08:41:56,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:41:56,196] [INFO] Task started: Prodigal
[2023-03-18 08:41:56,196] [INFO] Running command: cat /var/lib/cwl/stg4693d20f-a47a-4ebc-9eec-dc269eaeae53/OceanDNA-b6227.fa | prodigal -d OceanDNA-b6227/cds.fna -a OceanDNA-b6227/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:42:08,723] [INFO] Task succeeded: Prodigal
[2023-03-18 08:42:08,723] [INFO] Task started: HMMsearch
[2023-03-18 08:42:08,723] [INFO] Running command: hmmsearch --tblout OceanDNA-b6227/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg153e1a18-5dac-4820-8478-0fbe88aabffe/dqc_reference/reference_markers.hmm OceanDNA-b6227/protein.faa > /dev/null
[2023-03-18 08:42:08,883] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:42:08,884] [INFO] Found 6/6 markers.
[2023-03-18 08:42:08,897] [INFO] Query marker FASTA was written to OceanDNA-b6227/markers.fasta
[2023-03-18 08:42:08,898] [INFO] Task started: Blastn
[2023-03-18 08:42:08,898] [INFO] Running command: blastn -query OceanDNA-b6227/markers.fasta -db /var/lib/cwl/stg153e1a18-5dac-4820-8478-0fbe88aabffe/dqc_reference/reference_markers.fasta -out OceanDNA-b6227/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:09,475] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:09,476] [INFO] Selected 29 target genomes.
[2023-03-18 08:42:09,476] [INFO] Target genome list was writen to OceanDNA-b6227/target_genomes.txt
[2023-03-18 08:42:09,490] [INFO] Task started: fastANI
[2023-03-18 08:42:09,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg4693d20f-a47a-4ebc-9eec-dc269eaeae53/OceanDNA-b6227.fa --refList OceanDNA-b6227/target_genomes.txt --output OceanDNA-b6227/fastani_result.tsv --threads 1
[2023-03-18 08:42:27,404] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:27,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg153e1a18-5dac-4820-8478-0fbe88aabffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:42:27,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg153e1a18-5dac-4820-8478-0fbe88aabffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:42:27,405] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:42:27,405] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:42:27,405] [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 08:42:27,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6227/tc_result.tsv
[2023-03-18 08:42:27,405] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:42:27,406] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:42:27,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg153e1a18-5dac-4820-8478-0fbe88aabffe/dqc_reference/checkm_data
[2023-03-18 08:42:27,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:42:27,421] [INFO] Task started: CheckM
[2023-03-18 08:42:27,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6227/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6227/checkm_input OceanDNA-b6227/checkm_result
[2023-03-18 08:43:02,647] [INFO] Task succeeded: CheckM
[2023-03-18 08:43:02,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:43:02,650] [INFO] ===== Completeness check finished =====
[2023-03-18 08:43:02,650] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:43:02,650] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6227/markers.fasta)
[2023-03-18 08:43:02,651] [INFO] Task started: Blastn
[2023-03-18 08:43:02,651] [INFO] Running command: blastn -query OceanDNA-b6227/markers.fasta -db /var/lib/cwl/stg153e1a18-5dac-4820-8478-0fbe88aabffe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6227/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:43:03,419] [INFO] Task succeeded: Blastn
[2023-03-18 08:43:03,420] [INFO] Selected 20 target genomes.
[2023-03-18 08:43:03,420] [INFO] Target genome list was writen to OceanDNA-b6227/target_genomes_gtdb.txt
[2023-03-18 08:43:03,433] [INFO] Task started: fastANI
[2023-03-18 08:43:03,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg4693d20f-a47a-4ebc-9eec-dc269eaeae53/OceanDNA-b6227.fa --refList OceanDNA-b6227/target_genomes_gtdb.txt --output OceanDNA-b6227/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:43:10,503] [INFO] Task succeeded: fastANI
[2023-03-18 08:43:10,509] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 08:43:10,509] [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_905182575.1	s__UBA8316 sp905182575	95.6448	498	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	95.72	95.72	0.87	0.87	2	inconclusive
GCA_017857815.1	s__UBA8316 sp017857815	95.0866	548	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_905182305.1	s__MS024-2A sp905182305	78.1853	64	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647605.1	s__UBA8316 sp018647605	76.7949	78	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390455.1	s__UBA8316 sp002390455	76.6567	70	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_009886625.1	s__MS024-2A sp009886625	76.3564	70	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	76.0607	64	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_002364535.1	s__UBA8316 sp002364535	76.0404	66	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:43:10,509] [INFO] GTDB search result was written to OceanDNA-b6227/result_gtdb.tsv
[2023-03-18 08:43:10,510] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:43:10,511] [INFO] DFAST_QC result json was written to OceanDNA-b6227/dqc_result.json
[2023-03-18 08:43:10,511] [INFO] DFAST_QC completed!
[2023-03-18 08:43:10,511] [INFO] Total running time: 0h1m16s