[2023-03-14 11:36:02,657] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:36:02,660] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:36:02,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ee07280-7f36-4d8a-bf41-2c8e5a944c58/dqc_reference
[2023-03-14 11:36:04,413] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:36:04,414] [INFO] Task started: Prodigal
[2023-03-14 11:36:04,414] [INFO] Running command: cat /var/lib/cwl/stg6a97cfc3-e9bb-4a40-89de-af82edf63879/OceanDNA-b26955.fa | prodigal -d OceanDNA-b26955/cds.fna -a OceanDNA-b26955/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:36:09,807] [INFO] Task succeeded: Prodigal
[2023-03-14 11:36:09,807] [INFO] Task started: HMMsearch
[2023-03-14 11:36:09,807] [INFO] Running command: hmmsearch --tblout OceanDNA-b26955/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ee07280-7f36-4d8a-bf41-2c8e5a944c58/dqc_reference/reference_markers.hmm OceanDNA-b26955/protein.faa > /dev/null
[2023-03-14 11:36:09,972] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:36:09,973] [INFO] Found 6/6 markers.
[2023-03-14 11:36:09,984] [INFO] Query marker FASTA was written to OceanDNA-b26955/markers.fasta
[2023-03-14 11:36:09,985] [INFO] Task started: Blastn
[2023-03-14 11:36:09,985] [INFO] Running command: blastn -query OceanDNA-b26955/markers.fasta -db /var/lib/cwl/stg7ee07280-7f36-4d8a-bf41-2c8e5a944c58/dqc_reference/reference_markers.fasta -out OceanDNA-b26955/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:10,539] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:10,540] [INFO] Selected 25 target genomes.
[2023-03-14 11:36:10,540] [INFO] Target genome list was writen to OceanDNA-b26955/target_genomes.txt
[2023-03-14 11:36:10,550] [INFO] Task started: fastANI
[2023-03-14 11:36:10,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a97cfc3-e9bb-4a40-89de-af82edf63879/OceanDNA-b26955.fa --refList OceanDNA-b26955/target_genomes.txt --output OceanDNA-b26955/fastani_result.tsv --threads 1
[2023-03-14 11:36:21,802] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:21,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ee07280-7f36-4d8a-bf41-2c8e5a944c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:36:21,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ee07280-7f36-4d8a-bf41-2c8e5a944c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:36:21,803] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:36:21,803] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:36:21,803] [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
--------------------------------------------------------------------------------
[2023-03-14 11:36:21,804] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26955/tc_result.tsv
[2023-03-14 11:36:21,804] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:36:21,804] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:36:21,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ee07280-7f36-4d8a-bf41-2c8e5a944c58/dqc_reference/checkm_data
[2023-03-14 11:36:21,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:36:21,815] [INFO] Task started: CheckM
[2023-03-14 11:36:21,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26955/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26955/checkm_input OceanDNA-b26955/checkm_result
[2023-03-14 11:36:40,983] [INFO] Task succeeded: CheckM
[2023-03-14 11:36:40,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:36:40,985] [INFO] ===== Completeness check finished =====
[2023-03-14 11:36:40,985] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:36:40,986] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26955/markers.fasta)
[2023-03-14 11:36:40,987] [INFO] Task started: Blastn
[2023-03-14 11:36:40,987] [INFO] Running command: blastn -query OceanDNA-b26955/markers.fasta -db /var/lib/cwl/stg7ee07280-7f36-4d8a-bf41-2c8e5a944c58/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26955/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:41,901] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:41,901] [INFO] Selected 11 target genomes.
[2023-03-14 11:36:41,901] [INFO] Target genome list was writen to OceanDNA-b26955/target_genomes_gtdb.txt
[2023-03-14 11:36:41,988] [INFO] Task started: fastANI
[2023-03-14 11:36:41,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a97cfc3-e9bb-4a40-89de-af82edf63879/OceanDNA-b26955.fa --refList OceanDNA-b26955/target_genomes_gtdb.txt --output OceanDNA-b26955/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:36:44,846] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:44,852] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:36:44,852] [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_002728335.1	s__AG-430-B22 sp002728335	88.0214	226	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	97.53	96.38	0.78	0.71	4	-
GCA_003209955.1	s__AG-430-B22 sp003209955	81.848	219	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003212795.1	s__AG-430-B22 sp003212795	81.8077	272	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.52	95.66	0.95	0.87	7	-
GCA_002726005.1	s__AG-430-B22 sp002726005	81.7785	214	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.76	98.76	0.74	0.74	2	-
GCA_902609025.1	s__AG-430-B22 sp902609025	81.7456	156	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608415.1	s__AG-430-B22 sp902608415	81.7011	196	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902533755.1	s__AG-430-B22 sp902533755	81.4467	201	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	99.48	99.48	0.87	0.87	3	-
GCA_003278145.1	s__MED-G09 sp003278145	76.0445	50	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	98.26	96.25	0.89	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-14 11:36:44,852] [INFO] GTDB search result was written to OceanDNA-b26955/result_gtdb.tsv
[2023-03-14 11:36:44,852] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:36:44,853] [INFO] DFAST_QC result json was written to OceanDNA-b26955/dqc_result.json
[2023-03-14 11:36:44,853] [INFO] DFAST_QC completed!
[2023-03-14 11:36:44,853] [INFO] Total running time: 0h0m42s