[2023-03-18 05:27:36,797] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:27:36,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:27:36,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a426f0c-fede-4d83-8cbe-c9b27b2c480e/dqc_reference
[2023-03-18 05:27:37,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:27:37,952] [INFO] Task started: Prodigal
[2023-03-18 05:27:37,952] [INFO] Running command: cat /var/lib/cwl/stg15791246-2095-4cae-9e9f-1f6c32f253e1/OceanDNA-b25417.fa | prodigal -d OceanDNA-b25417/cds.fna -a OceanDNA-b25417/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:27:41,970] [INFO] Task succeeded: Prodigal
[2023-03-18 05:27:41,971] [INFO] Task started: HMMsearch
[2023-03-18 05:27:41,971] [INFO] Running command: hmmsearch --tblout OceanDNA-b25417/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a426f0c-fede-4d83-8cbe-c9b27b2c480e/dqc_reference/reference_markers.hmm OceanDNA-b25417/protein.faa > /dev/null
[2023-03-18 05:27:42,106] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:27:42,107] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg15791246-2095-4cae-9e9f-1f6c32f253e1/OceanDNA-b25417.fa]
[2023-03-18 05:27:42,116] [INFO] Query marker FASTA was written to OceanDNA-b25417/markers.fasta
[2023-03-18 05:27:42,118] [INFO] Task started: Blastn
[2023-03-18 05:27:42,118] [INFO] Running command: blastn -query OceanDNA-b25417/markers.fasta -db /var/lib/cwl/stg8a426f0c-fede-4d83-8cbe-c9b27b2c480e/dqc_reference/reference_markers.fasta -out OceanDNA-b25417/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:27:42,676] [INFO] Task succeeded: Blastn
[2023-03-18 05:27:42,677] [INFO] Selected 12 target genomes.
[2023-03-18 05:27:42,677] [INFO] Target genome list was writen to OceanDNA-b25417/target_genomes.txt
[2023-03-18 05:27:42,685] [INFO] Task started: fastANI
[2023-03-18 05:27:42,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg15791246-2095-4cae-9e9f-1f6c32f253e1/OceanDNA-b25417.fa --refList OceanDNA-b25417/target_genomes.txt --output OceanDNA-b25417/fastani_result.tsv --threads 1
[2023-03-18 05:27:47,823] [INFO] Task succeeded: fastANI
[2023-03-18 05:27:47,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a426f0c-fede-4d83-8cbe-c9b27b2c480e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:27:47,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a426f0c-fede-4d83-8cbe-c9b27b2c480e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:27:47,825] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:27:47,825] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:27:47,825] [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 05:27:47,825] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25417/tc_result.tsv
[2023-03-18 05:27:47,825] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:27:47,825] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:27:47,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a426f0c-fede-4d83-8cbe-c9b27b2c480e/dqc_reference/checkm_data
[2023-03-18 05:27:47,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:27:47,840] [INFO] Task started: CheckM
[2023-03-18 05:27:47,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25417/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25417/checkm_input OceanDNA-b25417/checkm_result
[2023-03-18 05:28:05,175] [INFO] Task succeeded: CheckM
[2023-03-18 05:28:05,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 05:28:05,177] [INFO] ===== Completeness check finished =====
[2023-03-18 05:28:05,177] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:28:05,177] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25417/markers.fasta)
[2023-03-18 05:28:05,179] [INFO] Task started: Blastn
[2023-03-18 05:28:05,179] [INFO] Running command: blastn -query OceanDNA-b25417/markers.fasta -db /var/lib/cwl/stg8a426f0c-fede-4d83-8cbe-c9b27b2c480e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25417/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:28:06,087] [INFO] Task succeeded: Blastn
[2023-03-18 05:28:06,088] [INFO] Selected 19 target genomes.
[2023-03-18 05:28:06,088] [INFO] Target genome list was writen to OceanDNA-b25417/target_genomes_gtdb.txt
[2023-03-18 05:28:06,117] [INFO] Task started: fastANI
[2023-03-18 05:28:06,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg15791246-2095-4cae-9e9f-1f6c32f253e1/OceanDNA-b25417.fa --refList OceanDNA-b25417/target_genomes_gtdb.txt --output OceanDNA-b25417/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:28:09,198] [INFO] Task succeeded: fastANI
[2023-03-18 05:28:09,205] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:28:09,205] [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_016764285.1	s__AG-414-E02 sp016764285	97.7884	117	135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902607625.1	s__AG-414-E02 sp902607625	81.5169	77	135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211695.1	s__AAA240-E13 sp003211695	80.5913	57	135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902607585.1	s__AG-414-E02 sp902607585	80.4001	64	135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000504625.1	s__AAA240-E13 sp000504625	79.8612	54	135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588335.1	s__AG-414-E02 sp902588335	79.3769	65	135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606835.1	s__AG-414-E02 sp902606835	79.0478	66	135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902561465.1	s__AG-414-E02 sp902561465	78.2255	53	135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902567945.1	s__AG-414-E02 sp902567945	78.0634	60	135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:28:09,205] [INFO] GTDB search result was written to OceanDNA-b25417/result_gtdb.tsv
[2023-03-18 05:28:09,205] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:28:09,206] [INFO] DFAST_QC result json was written to OceanDNA-b25417/dqc_result.json
[2023-03-18 05:28:09,206] [INFO] DFAST_QC completed!
[2023-03-18 05:28:09,206] [INFO] Total running time: 0h0m32s