[2023-03-15 13:03:53,445] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,445] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg40e8623a-5a0b-4faa-9328-523ad0b75e8d/dqc_reference
[2023-03-15 13:03:54,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,580] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,580] [INFO] Running command: cat /var/lib/cwl/stge5b228ce-5308-46c1-b1f7-e214d45ac4e9/OceanDNA-b11602.fa | prodigal -d OceanDNA-b11602/cds.fna -a OceanDNA-b11602/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:02,273] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:02,274] [INFO] Task started: HMMsearch
[2023-03-15 13:04:02,274] [INFO] Running command: hmmsearch --tblout OceanDNA-b11602/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40e8623a-5a0b-4faa-9328-523ad0b75e8d/dqc_reference/reference_markers.hmm OceanDNA-b11602/protein.faa > /dev/null
[2023-03-15 13:04:02,508] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:02,509] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge5b228ce-5308-46c1-b1f7-e214d45ac4e9/OceanDNA-b11602.fa]
[2023-03-15 13:04:02,519] [INFO] Query marker FASTA was written to OceanDNA-b11602/markers.fasta
[2023-03-15 13:04:02,519] [INFO] Task started: Blastn
[2023-03-15 13:04:02,519] [INFO] Running command: blastn -query OceanDNA-b11602/markers.fasta -db /var/lib/cwl/stg40e8623a-5a0b-4faa-9328-523ad0b75e8d/dqc_reference/reference_markers.fasta -out OceanDNA-b11602/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:03,071] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:03,072] [INFO] Selected 22 target genomes.
[2023-03-15 13:04:03,072] [INFO] Target genome list was writen to OceanDNA-b11602/target_genomes.txt
[2023-03-15 13:04:03,088] [INFO] Task started: fastANI
[2023-03-15 13:04:03,089] [INFO] Running command: fastANI --query /var/lib/cwl/stge5b228ce-5308-46c1-b1f7-e214d45ac4e9/OceanDNA-b11602.fa --refList OceanDNA-b11602/target_genomes.txt --output OceanDNA-b11602/fastani_result.tsv --threads 1
[2023-03-15 13:04:16,449] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:16,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40e8623a-5a0b-4faa-9328-523ad0b75e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:16,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40e8623a-5a0b-4faa-9328-523ad0b75e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:16,450] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:16,450] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:04:16,450] [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 13:04:16,450] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11602/tc_result.tsv
[2023-03-15 13:04:16,450] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:16,450] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:16,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40e8623a-5a0b-4faa-9328-523ad0b75e8d/dqc_reference/checkm_data
[2023-03-15 13:04:16,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:16,455] [INFO] Task started: CheckM
[2023-03-15 13:04:16,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11602/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11602/checkm_input OceanDNA-b11602/checkm_result
[2023-03-15 13:04:41,691] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:41,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:41,693] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:41,693] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:41,693] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11602/markers.fasta)
[2023-03-15 13:04:41,694] [INFO] Task started: Blastn
[2023-03-15 13:04:41,694] [INFO] Running command: blastn -query OceanDNA-b11602/markers.fasta -db /var/lib/cwl/stg40e8623a-5a0b-4faa-9328-523ad0b75e8d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11602/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:42,628] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:42,630] [INFO] Selected 25 target genomes.
[2023-03-15 13:04:42,630] [INFO] Target genome list was writen to OceanDNA-b11602/target_genomes_gtdb.txt
[2023-03-15 13:04:42,789] [INFO] Task started: fastANI
[2023-03-15 13:04:42,789] [INFO] Running command: fastANI --query /var/lib/cwl/stge5b228ce-5308-46c1-b1f7-e214d45ac4e9/OceanDNA-b11602.fa --refList OceanDNA-b11602/target_genomes_gtdb.txt --output OceanDNA-b11602/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:04:50,267] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:50,271] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:04:50,271] [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_002863085.1	s__GCA-2863085 sp002863085	93.3799	309	405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2863085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171975.2	s__GCA-2696965 sp002171975	76.8199	80	405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713285.1	s__SP256 sp002713285	76.1025	60	405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714185.1	s__SP256 sp002714185	75.864	65	405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707245.1	s__GCA-002707245 sp002707245	75.5124	52	405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:04:50,271] [INFO] GTDB search result was written to OceanDNA-b11602/result_gtdb.tsv
[2023-03-15 13:04:50,316] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:04:50,317] [INFO] DFAST_QC result json was written to OceanDNA-b11602/dqc_result.json
[2023-03-15 13:04:50,317] [INFO] DFAST_QC completed!
[2023-03-15 13:04:50,317] [INFO] Total running time: 0h0m57s