[2023-03-15 21:01:44,380] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,380] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,380] [INFO] DQC Reference Directory: /var/lib/cwl/stgde000d53-4b41-491d-827a-4fd5458d2a7f/dqc_reference
[2023-03-15 21:01:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stg687bade3-4ac5-4607-a944-b9d545a2f77c/OceanDNA-b22228.fa | prodigal -d OceanDNA-b22228/cds.fna -a OceanDNA-b22228/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:03,726] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:03,726] [INFO] Task started: HMMsearch
[2023-03-15 21:02:03,726] [INFO] Running command: hmmsearch --tblout OceanDNA-b22228/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde000d53-4b41-491d-827a-4fd5458d2a7f/dqc_reference/reference_markers.hmm OceanDNA-b22228/protein.faa > /dev/null
[2023-03-15 21:02:03,918] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:03,919] [INFO] Found 6/6 markers.
[2023-03-15 21:02:03,937] [INFO] Query marker FASTA was written to OceanDNA-b22228/markers.fasta
[2023-03-15 21:02:03,937] [INFO] Task started: Blastn
[2023-03-15 21:02:03,937] [INFO] Running command: blastn -query OceanDNA-b22228/markers.fasta -db /var/lib/cwl/stgde000d53-4b41-491d-827a-4fd5458d2a7f/dqc_reference/reference_markers.fasta -out OceanDNA-b22228/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:04,454] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:04,455] [INFO] Selected 17 target genomes.
[2023-03-15 21:02:04,455] [INFO] Target genome list was writen to OceanDNA-b22228/target_genomes.txt
[2023-03-15 21:02:04,467] [INFO] Task started: fastANI
[2023-03-15 21:02:04,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg687bade3-4ac5-4607-a944-b9d545a2f77c/OceanDNA-b22228.fa --refList OceanDNA-b22228/target_genomes.txt --output OceanDNA-b22228/fastani_result.tsv --threads 1
[2023-03-15 21:02:15,472] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:15,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde000d53-4b41-491d-827a-4fd5458d2a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:15,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde000d53-4b41-491d-827a-4fd5458d2a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:15,473] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:15,473] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:02:15,473] [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
--------------------------------------------------------------------------------
[2023-03-15 21:02:15,473] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22228/tc_result.tsv
[2023-03-15 21:02:15,473] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:15,473] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:15,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde000d53-4b41-491d-827a-4fd5458d2a7f/dqc_reference/checkm_data
[2023-03-15 21:02:15,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:15,481] [INFO] Task started: CheckM
[2023-03-15 21:02:15,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22228/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22228/checkm_input OceanDNA-b22228/checkm_result
[2023-03-15 21:03:12,218] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:12,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:12,221] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:12,221] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:12,221] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22228/markers.fasta)
[2023-03-15 21:03:12,221] [INFO] Task started: Blastn
[2023-03-15 21:03:12,221] [INFO] Running command: blastn -query OceanDNA-b22228/markers.fasta -db /var/lib/cwl/stgde000d53-4b41-491d-827a-4fd5458d2a7f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22228/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:12,923] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:12,924] [INFO] Selected 22 target genomes.
[2023-03-15 21:03:12,924] [INFO] Target genome list was writen to OceanDNA-b22228/target_genomes_gtdb.txt
[2023-03-15 21:03:13,565] [INFO] Task started: fastANI
[2023-03-15 21:03:13,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg687bade3-4ac5-4607-a944-b9d545a2f77c/OceanDNA-b22228.fa --refList OceanDNA-b22228/target_genomes_gtdb.txt --output OceanDNA-b22228/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:23,979] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:23,983] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:03:23,983] [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_002717655.1	s__UBA1668 sp002717655	99.9148	902	945	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002702575.1	s__UBA1668 sp002702575	77.2985	204	945	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	99.83	99.83	0.97	0.97	3	-
GCA_002716385.1	s__UBA1668 sp002716385	77.2235	166	945	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364555.1	s__UBA1668 sp002364555	76.8965	158	945	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:23,983] [INFO] GTDB search result was written to OceanDNA-b22228/result_gtdb.tsv
[2023-03-15 21:03:23,983] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:23,984] [INFO] DFAST_QC result json was written to OceanDNA-b22228/dqc_result.json
[2023-03-15 21:03:23,984] [INFO] DFAST_QC completed!
[2023-03-15 21:03:23,984] [INFO] Total running time: 0h1m40s