[2023-03-17 05:31:30,560] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:31:30,560] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:31:30,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg850a5381-207d-47ec-a242-998b30a927c1/dqc_reference
[2023-03-17 05:31:33,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:31:33,266] [INFO] Task started: Prodigal
[2023-03-17 05:31:33,266] [INFO] Running command: cat /var/lib/cwl/stgd552b09c-5841-4e73-baf8-8b638fec84ec/OceanDNA-b24886.fa | prodigal -d OceanDNA-b24886/cds.fna -a OceanDNA-b24886/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:31:43,838] [INFO] Task succeeded: Prodigal
[2023-03-17 05:31:43,838] [INFO] Task started: HMMsearch
[2023-03-17 05:31:43,838] [INFO] Running command: hmmsearch --tblout OceanDNA-b24886/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg850a5381-207d-47ec-a242-998b30a927c1/dqc_reference/reference_markers.hmm OceanDNA-b24886/protein.faa > /dev/null
[2023-03-17 05:31:44,004] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:31:44,004] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd552b09c-5841-4e73-baf8-8b638fec84ec/OceanDNA-b24886.fa]
[2023-03-17 05:31:44,022] [INFO] Query marker FASTA was written to OceanDNA-b24886/markers.fasta
[2023-03-17 05:31:44,023] [INFO] Task started: Blastn
[2023-03-17 05:31:44,023] [INFO] Running command: blastn -query OceanDNA-b24886/markers.fasta -db /var/lib/cwl/stg850a5381-207d-47ec-a242-998b30a927c1/dqc_reference/reference_markers.fasta -out OceanDNA-b24886/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:31:46,380] [INFO] Task succeeded: Blastn
[2023-03-17 05:31:46,381] [INFO] Selected 29 target genomes.
[2023-03-17 05:31:46,381] [INFO] Target genome list was writen to OceanDNA-b24886/target_genomes.txt
[2023-03-17 05:31:46,400] [INFO] Task started: fastANI
[2023-03-17 05:31:46,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgd552b09c-5841-4e73-baf8-8b638fec84ec/OceanDNA-b24886.fa --refList OceanDNA-b24886/target_genomes.txt --output OceanDNA-b24886/fastani_result.tsv --threads 1
[2023-03-17 05:32:03,316] [INFO] Task succeeded: fastANI
[2023-03-17 05:32:03,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg850a5381-207d-47ec-a242-998b30a927c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:32:03,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg850a5381-207d-47ec-a242-998b30a927c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:32:03,317] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:32:03,317] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:32:03,317] [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 05:32:03,317] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24886/tc_result.tsv
[2023-03-17 05:32:03,317] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:32:03,317] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:32:03,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg850a5381-207d-47ec-a242-998b30a927c1/dqc_reference/checkm_data
[2023-03-17 05:32:03,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:32:03,325] [INFO] Task started: CheckM
[2023-03-17 05:32:03,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24886/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24886/checkm_input OceanDNA-b24886/checkm_result
[2023-03-17 05:32:34,579] [INFO] Task succeeded: CheckM
[2023-03-17 05:32:34,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:32:34,581] [INFO] ===== Completeness check finished =====
[2023-03-17 05:32:34,581] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:32:34,582] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24886/markers.fasta)
[2023-03-17 05:32:34,583] [INFO] Task started: Blastn
[2023-03-17 05:32:34,583] [INFO] Running command: blastn -query OceanDNA-b24886/markers.fasta -db /var/lib/cwl/stg850a5381-207d-47ec-a242-998b30a927c1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24886/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:32:35,276] [INFO] Task succeeded: Blastn
[2023-03-17 05:32:35,277] [INFO] Selected 21 target genomes.
[2023-03-17 05:32:35,277] [INFO] Target genome list was writen to OceanDNA-b24886/target_genomes_gtdb.txt
[2023-03-17 05:32:35,292] [INFO] Task started: fastANI
[2023-03-17 05:32:35,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgd552b09c-5841-4e73-baf8-8b638fec84ec/OceanDNA-b24886.fa --refList OceanDNA-b24886/target_genomes_gtdb.txt --output OceanDNA-b24886/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:32:48,716] [INFO] Task succeeded: fastANI
[2023-03-17 05:32:48,720] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:32:48,720] [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_002746275.1	s__Mf105b01 sp002746275	77.3369	123	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003330885.1	s__Mf105b01 sp003330885	77.2466	93	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000509225.1	s__Mf105b01 sp000509225	77.0204	101	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	98.75	98.75	0.94	0.94	2	-
GCA_002695905.1	s__Mf105b01 sp002695905	76.9524	87	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	99.79	99.79	0.82	0.82	2	-
GCA_002715765.1	s__Mf105b01 sp002715765	76.3374	66	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	99.04	98.86	0.91	0.89	5	-
--------------------------------------------------------------------------------
[2023-03-17 05:32:48,720] [INFO] GTDB search result was written to OceanDNA-b24886/result_gtdb.tsv
[2023-03-17 05:32:48,721] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:32:48,721] [INFO] DFAST_QC result json was written to OceanDNA-b24886/dqc_result.json
[2023-03-17 05:32:48,721] [INFO] DFAST_QC completed!
[2023-03-17 05:32:48,721] [INFO] Total running time: 0h1m18s