[2023-03-18 22:44:57,806] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:57,806] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:57,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg981545d8-1036-4bd2-91c6-6397a9b550bf/dqc_reference
[2023-03-18 22:44:58,938] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:58,938] [INFO] Task started: Prodigal
[2023-03-18 22:44:58,938] [INFO] Running command: cat /var/lib/cwl/stg1ffd6ede-5ee9-4078-ad4a-94a58ae53b1c/OceanDNA-b6616.fa | prodigal -d OceanDNA-b6616/cds.fna -a OceanDNA-b6616/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:13,634] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:13,634] [INFO] Task started: HMMsearch
[2023-03-18 22:45:13,634] [INFO] Running command: hmmsearch --tblout OceanDNA-b6616/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg981545d8-1036-4bd2-91c6-6397a9b550bf/dqc_reference/reference_markers.hmm OceanDNA-b6616/protein.faa > /dev/null
[2023-03-18 22:45:13,822] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:13,823] [INFO] Found 6/6 markers.
[2023-03-18 22:45:13,835] [INFO] Query marker FASTA was written to OceanDNA-b6616/markers.fasta
[2023-03-18 22:45:13,837] [INFO] Task started: Blastn
[2023-03-18 22:45:13,837] [INFO] Running command: blastn -query OceanDNA-b6616/markers.fasta -db /var/lib/cwl/stg981545d8-1036-4bd2-91c6-6397a9b550bf/dqc_reference/reference_markers.fasta -out OceanDNA-b6616/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:14,383] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:14,384] [INFO] Selected 33 target genomes.
[2023-03-18 22:45:14,384] [INFO] Target genome list was writen to OceanDNA-b6616/target_genomes.txt
[2023-03-18 22:45:14,402] [INFO] Task started: fastANI
[2023-03-18 22:45:14,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ffd6ede-5ee9-4078-ad4a-94a58ae53b1c/OceanDNA-b6616.fa --refList OceanDNA-b6616/target_genomes.txt --output OceanDNA-b6616/fastani_result.tsv --threads 1
[2023-03-18 22:45:31,842] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:31,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg981545d8-1036-4bd2-91c6-6397a9b550bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:31,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg981545d8-1036-4bd2-91c6-6397a9b550bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:31,846] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:31,846] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:45:31,846] [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
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	77.5022	54	614	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:45:31,847] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6616/tc_result.tsv
[2023-03-18 22:45:31,847] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:31,847] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:31,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg981545d8-1036-4bd2-91c6-6397a9b550bf/dqc_reference/checkm_data
[2023-03-18 22:45:31,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:31,851] [INFO] Task started: CheckM
[2023-03-18 22:45:31,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6616/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6616/checkm_input OceanDNA-b6616/checkm_result
[2023-03-18 22:46:12,283] [INFO] Task succeeded: CheckM
[2023-03-18 22:46:12,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:46:12,285] [INFO] ===== Completeness check finished =====
[2023-03-18 22:46:12,285] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:46:12,286] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6616/markers.fasta)
[2023-03-18 22:46:12,287] [INFO] Task started: Blastn
[2023-03-18 22:46:12,287] [INFO] Running command: blastn -query OceanDNA-b6616/markers.fasta -db /var/lib/cwl/stg981545d8-1036-4bd2-91c6-6397a9b550bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6616/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:46:13,051] [INFO] Task succeeded: Blastn
[2023-03-18 22:46:13,440] [INFO] Selected 25 target genomes.
[2023-03-18 22:46:13,440] [INFO] Target genome list was writen to OceanDNA-b6616/target_genomes_gtdb.txt
[2023-03-18 22:46:13,524] [INFO] Task started: fastANI
[2023-03-18 22:46:13,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ffd6ede-5ee9-4078-ad4a-94a58ae53b1c/OceanDNA-b6616.fa --refList OceanDNA-b6616/target_genomes_gtdb.txt --output OceanDNA-b6616/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:46:26,192] [INFO] Task succeeded: fastANI
[2023-03-18 22:46:26,197] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:46:26,198] [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_002384055.1	s__BACL21 sp002384055	99.8247	581	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	99.79	99.68	0.93	0.91	4	conclusive
GCA_002707025.1	s__IN17 sp002707025	77.2347	54	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	-
GCA_900299425.1	s__BACL21 sp900299425	77.2023	84	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694465.1	s__IN17 sp002694465	77.1086	58	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCA_011525065.1	s__BACL21 sp011525065	76.8345	50	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009921505.1	s__BACL21 sp009921505	76.6141	85	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	97.10	97.10	0.82	0.82	2	-
GCA_002335345.1	s__BACL21 sp002335345	76.2774	60	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	98.72	98.64	0.77	0.75	3	-
--------------------------------------------------------------------------------
[2023-03-18 22:46:26,198] [INFO] GTDB search result was written to OceanDNA-b6616/result_gtdb.tsv
[2023-03-18 22:46:26,198] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:46:26,199] [INFO] DFAST_QC result json was written to OceanDNA-b6616/dqc_result.json
[2023-03-18 22:46:26,199] [INFO] DFAST_QC completed!
[2023-03-18 22:46:26,199] [INFO] Total running time: 0h1m28s