[2023-03-18 22:44:57,814] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:57,815] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:57,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ae3d523-f4a6-4a3a-bd52-748e4e8f8935/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/stgc8a4adfc-f331-4a46-b539-3943e0574fcb/OceanDNA-b26240.fa | prodigal -d OceanDNA-b26240/cds.fna -a OceanDNA-b26240/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:10,395] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:10,395] [INFO] Task started: HMMsearch
[2023-03-18 22:45:10,395] [INFO] Running command: hmmsearch --tblout OceanDNA-b26240/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ae3d523-f4a6-4a3a-bd52-748e4e8f8935/dqc_reference/reference_markers.hmm OceanDNA-b26240/protein.faa > /dev/null
[2023-03-18 22:45:10,560] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:10,561] [INFO] Found 6/6 markers.
[2023-03-18 22:45:10,574] [INFO] Query marker FASTA was written to OceanDNA-b26240/markers.fasta
[2023-03-18 22:45:10,575] [INFO] Task started: Blastn
[2023-03-18 22:45:10,575] [INFO] Running command: blastn -query OceanDNA-b26240/markers.fasta -db /var/lib/cwl/stg5ae3d523-f4a6-4a3a-bd52-748e4e8f8935/dqc_reference/reference_markers.fasta -out OceanDNA-b26240/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:11,185] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:11,185] [INFO] Selected 32 target genomes.
[2023-03-18 22:45:11,186] [INFO] Target genome list was writen to OceanDNA-b26240/target_genomes.txt
[2023-03-18 22:45:11,205] [INFO] Task started: fastANI
[2023-03-18 22:45:11,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8a4adfc-f331-4a46-b539-3943e0574fcb/OceanDNA-b26240.fa --refList OceanDNA-b26240/target_genomes.txt --output OceanDNA-b26240/fastani_result.tsv --threads 1
[2023-03-18 22:45:33,792] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:33,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ae3d523-f4a6-4a3a-bd52-748e4e8f8935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:33,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ae3d523-f4a6-4a3a-bd52-748e4e8f8935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:33,792] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:33,792] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:45:33,793] [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 22:45:33,793] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26240/tc_result.tsv
[2023-03-18 22:45:33,793] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:33,793] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:33,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ae3d523-f4a6-4a3a-bd52-748e4e8f8935/dqc_reference/checkm_data
[2023-03-18 22:45:33,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:33,799] [INFO] Task started: CheckM
[2023-03-18 22:45:33,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26240/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26240/checkm_input OceanDNA-b26240/checkm_result
[2023-03-18 22:46:06,355] [INFO] Task succeeded: CheckM
[2023-03-18 22:46:06,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:46:06,357] [INFO] ===== Completeness check finished =====
[2023-03-18 22:46:06,357] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:46:06,357] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26240/markers.fasta)
[2023-03-18 22:46:06,359] [INFO] Task started: Blastn
[2023-03-18 22:46:06,359] [INFO] Running command: blastn -query OceanDNA-b26240/markers.fasta -db /var/lib/cwl/stg5ae3d523-f4a6-4a3a-bd52-748e4e8f8935/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26240/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:46:07,408] [INFO] Task succeeded: Blastn
[2023-03-18 22:46:07,409] [INFO] Selected 21 target genomes.
[2023-03-18 22:46:07,409] [INFO] Target genome list was writen to OceanDNA-b26240/target_genomes_gtdb.txt
[2023-03-18 22:46:07,459] [INFO] Task started: fastANI
[2023-03-18 22:46:07,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8a4adfc-f331-4a46-b539-3943e0574fcb/OceanDNA-b26240.fa --refList OceanDNA-b26240/target_genomes_gtdb.txt --output OceanDNA-b26240/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:46:15,914] [INFO] Task succeeded: fastANI
[2023-03-18 22:46:15,922] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:46:15,922] [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_905182545.1	s__UBA3439 sp905182545	77.5071	196	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009919335.1	s__UBA3439 sp009919335	77.4175	153	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.81	98.81	0.76	0.76	2	-
GCA_002378605.1	s__UBA3439 sp002378605	77.3863	167	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.28	99.28	0.80	0.80	2	-
GCA_017859295.1	s__UBA3439 sp017859295	77.3573	177	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.52	98.52	0.78	0.78	2	-
GCA_016778895.1	s__UBA3439 sp016778895	77.313	172	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.63	99.63	0.87	0.87	2	-
GCA_016778825.1	s__UBA3439 sp016778825	77.1039	105	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	77.0506	67	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_016780525.1	s__UBA3439 sp016780525	76.7518	104	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.22	99.22	0.71	0.71	2	-
GCA_009920665.1	s__UBA8309 sp009920665	76.5037	100	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	76.4296	100	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457745.1	s__UBA8309 sp002457745	76.281	66	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018668795.1	s__Puniceispirillum sp018668795	76.1034	78	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__Puniceispirillum	95.0	99.26	99.26	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:46:15,922] [INFO] GTDB search result was written to OceanDNA-b26240/result_gtdb.tsv
[2023-03-18 22:46:15,922] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:46:15,923] [INFO] DFAST_QC result json was written to OceanDNA-b26240/dqc_result.json
[2023-03-18 22:46:15,923] [INFO] DFAST_QC completed!
[2023-03-18 22:46:15,923] [INFO] Total running time: 0h1m18s