[2023-03-17 02:42:34,227] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:42:34,227] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:42:34,227] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6ec8b93-2484-4a6f-ab99-f5441dad871f/dqc_reference
[2023-03-17 02:42:35,367] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:42:35,368] [INFO] Task started: Prodigal
[2023-03-17 02:42:35,368] [INFO] Running command: cat /var/lib/cwl/stgf2e14387-fa4b-46b1-a426-e44a134ea175/OceanDNA-b26971.fa | prodigal -d OceanDNA-b26971/cds.fna -a OceanDNA-b26971/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:42:38,737] [INFO] Task succeeded: Prodigal
[2023-03-17 02:42:38,737] [INFO] Task started: HMMsearch
[2023-03-17 02:42:38,737] [INFO] Running command: hmmsearch --tblout OceanDNA-b26971/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6ec8b93-2484-4a6f-ab99-f5441dad871f/dqc_reference/reference_markers.hmm OceanDNA-b26971/protein.faa > /dev/null
[2023-03-17 02:42:38,890] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:42:38,891] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf2e14387-fa4b-46b1-a426-e44a134ea175/OceanDNA-b26971.fa]
[2023-03-17 02:42:38,897] [INFO] Query marker FASTA was written to OceanDNA-b26971/markers.fasta
[2023-03-17 02:42:38,899] [INFO] Task started: Blastn
[2023-03-17 02:42:38,899] [INFO] Running command: blastn -query OceanDNA-b26971/markers.fasta -db /var/lib/cwl/stgf6ec8b93-2484-4a6f-ab99-f5441dad871f/dqc_reference/reference_markers.fasta -out OceanDNA-b26971/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:42:39,391] [INFO] Task succeeded: Blastn
[2023-03-17 02:42:39,392] [INFO] Selected 20 target genomes.
[2023-03-17 02:42:39,392] [INFO] Target genome list was writen to OceanDNA-b26971/target_genomes.txt
[2023-03-17 02:42:39,451] [INFO] Task started: fastANI
[2023-03-17 02:42:39,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e14387-fa4b-46b1-a426-e44a134ea175/OceanDNA-b26971.fa --refList OceanDNA-b26971/target_genomes.txt --output OceanDNA-b26971/fastani_result.tsv --threads 1
[2023-03-17 02:42:46,109] [INFO] Task succeeded: fastANI
[2023-03-17 02:42:46,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6ec8b93-2484-4a6f-ab99-f5441dad871f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:42:46,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6ec8b93-2484-4a6f-ab99-f5441dad871f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:42:46,110] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:42:46,110] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:42:46,110] [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
--------------------------------------------------------------------------------
[2023-03-17 02:42:46,110] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26971/tc_result.tsv
[2023-03-17 02:42:46,110] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:42:46,110] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:42:46,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6ec8b93-2484-4a6f-ab99-f5441dad871f/dqc_reference/checkm_data
[2023-03-17 02:42:46,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:42:46,143] [INFO] Task started: CheckM
[2023-03-17 02:42:46,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26971/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26971/checkm_input OceanDNA-b26971/checkm_result
[2023-03-17 02:43:00,944] [INFO] Task succeeded: CheckM
[2023-03-17 02:43:00,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.44%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 02:43:00,946] [INFO] ===== Completeness check finished =====
[2023-03-17 02:43:00,946] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:43:00,946] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26971/markers.fasta)
[2023-03-17 02:43:00,947] [INFO] Task started: Blastn
[2023-03-17 02:43:00,947] [INFO] Running command: blastn -query OceanDNA-b26971/markers.fasta -db /var/lib/cwl/stgf6ec8b93-2484-4a6f-ab99-f5441dad871f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26971/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:43:01,676] [INFO] Task succeeded: Blastn
[2023-03-17 02:43:01,676] [INFO] Selected 7 target genomes.
[2023-03-17 02:43:01,677] [INFO] Target genome list was writen to OceanDNA-b26971/target_genomes_gtdb.txt
[2023-03-17 02:43:01,685] [INFO] Task started: fastANI
[2023-03-17 02:43:01,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e14387-fa4b-46b1-a426-e44a134ea175/OceanDNA-b26971.fa --refList OceanDNA-b26971/target_genomes_gtdb.txt --output OceanDNA-b26971/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:43:03,123] [INFO] Task succeeded: fastANI
[2023-03-17 02:43:03,127] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:43:03,128] [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_002726005.1	s__AG-430-B22 sp002726005	99.0568	199	225	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	conclusive
GCA_902608415.1	s__AG-430-B22 sp902608415	92.5343	169	225	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_003212795.1	s__AG-430-B22 sp003212795	91.9487	219	225	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_902533755.1	s__AG-430-B22 sp902533755	91.4897	145	225	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_902609025.1	s__AG-430-B22 sp902609025	91.2972	134	225	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_003209955.1	s__AG-430-B22 sp003209955	90.3622	176	225	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_002728335.1	s__AG-430-B22 sp002728335	82.6063	170	225	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	-
--------------------------------------------------------------------------------
[2023-03-17 02:43:03,128] [INFO] GTDB search result was written to OceanDNA-b26971/result_gtdb.tsv
[2023-03-17 02:43:03,128] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:43:03,129] [INFO] DFAST_QC result json was written to OceanDNA-b26971/dqc_result.json
[2023-03-17 02:43:03,129] [INFO] DFAST_QC completed!
[2023-03-17 02:43:03,129] [INFO] Total running time: 0h0m29s