[2023-03-16 14:26:33,890] [INFO] DFAST_QC pipeline started.
[2023-03-16 14:26:33,890] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 14:26:33,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg95360a10-708b-4a67-a09f-5a38e6ad0888/dqc_reference
[2023-03-16 14:26:36,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 14:26:36,565] [INFO] Task started: Prodigal
[2023-03-16 14:26:36,565] [INFO] Running command: cat /var/lib/cwl/stgc85b4e27-8ce7-4dfc-8d1f-697b3748fd13/OceanDNA-b24174.fa | prodigal -d OceanDNA-b24174/cds.fna -a OceanDNA-b24174/protein.faa -g 11 -q > /dev/null
[2023-03-16 14:26:40,567] [INFO] Task succeeded: Prodigal
[2023-03-16 14:26:40,568] [INFO] Task started: HMMsearch
[2023-03-16 14:26:40,568] [INFO] Running command: hmmsearch --tblout OceanDNA-b24174/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95360a10-708b-4a67-a09f-5a38e6ad0888/dqc_reference/reference_markers.hmm OceanDNA-b24174/protein.faa > /dev/null
[2023-03-16 14:26:40,793] [INFO] Task succeeded: HMMsearch
[2023-03-16 14:26:40,793] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc85b4e27-8ce7-4dfc-8d1f-697b3748fd13/OceanDNA-b24174.fa]
[2023-03-16 14:26:40,800] [INFO] Query marker FASTA was written to OceanDNA-b24174/markers.fasta
[2023-03-16 14:26:40,800] [INFO] Task started: Blastn
[2023-03-16 14:26:40,800] [INFO] Running command: blastn -query OceanDNA-b24174/markers.fasta -db /var/lib/cwl/stg95360a10-708b-4a67-a09f-5a38e6ad0888/dqc_reference/reference_markers.fasta -out OceanDNA-b24174/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:26:44,545] [INFO] Task succeeded: Blastn
[2023-03-16 14:26:44,546] [INFO] Selected 12 target genomes.
[2023-03-16 14:26:44,546] [INFO] Target genome list was writen to OceanDNA-b24174/target_genomes.txt
[2023-03-16 14:26:44,554] [INFO] Task started: fastANI
[2023-03-16 14:26:44,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgc85b4e27-8ce7-4dfc-8d1f-697b3748fd13/OceanDNA-b24174.fa --refList OceanDNA-b24174/target_genomes.txt --output OceanDNA-b24174/fastani_result.tsv --threads 1
[2023-03-16 14:26:48,238] [INFO] Task succeeded: fastANI
[2023-03-16 14:26:48,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95360a10-708b-4a67-a09f-5a38e6ad0888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 14:26:48,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95360a10-708b-4a67-a09f-5a38e6ad0888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 14:26:48,473] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 14:26:48,473] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 14:26:48,473] [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
Fusobacterium perfoetens	strain=ATCC 29250	GCA_000622245.1	852	852	type	True	74.6558	52	238	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 14:26:48,473] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24174/tc_result.tsv
[2023-03-16 14:26:48,474] [INFO] ===== Taxonomy check completed =====
[2023-03-16 14:26:48,474] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 14:26:48,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95360a10-708b-4a67-a09f-5a38e6ad0888/dqc_reference/checkm_data
[2023-03-16 14:26:48,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 14:26:48,477] [INFO] Task started: CheckM
[2023-03-16 14:26:48,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24174/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24174/checkm_input OceanDNA-b24174/checkm_result
[2023-03-16 14:27:15,644] [INFO] Task succeeded: CheckM
[2023-03-16 14:27:15,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 14:27:15,646] [INFO] ===== Completeness check finished =====
[2023-03-16 14:27:15,646] [INFO] ===== Start GTDB Search =====
[2023-03-16 14:27:15,646] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24174/markers.fasta)
[2023-03-16 14:27:15,648] [INFO] Task started: Blastn
[2023-03-16 14:27:15,648] [INFO] Running command: blastn -query OceanDNA-b24174/markers.fasta -db /var/lib/cwl/stg95360a10-708b-4a67-a09f-5a38e6ad0888/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24174/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:27:18,042] [INFO] Task succeeded: Blastn
[2023-03-16 14:27:18,043] [INFO] Selected 17 target genomes.
[2023-03-16 14:27:18,043] [INFO] Target genome list was writen to OceanDNA-b24174/target_genomes_gtdb.txt
[2023-03-16 14:27:18,834] [INFO] Task started: fastANI
[2023-03-16 14:27:18,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgc85b4e27-8ce7-4dfc-8d1f-697b3748fd13/OceanDNA-b24174.fa --refList OceanDNA-b24174/target_genomes_gtdb.txt --output OceanDNA-b24174/fastani_result_gtdb.tsv --threads 1
[2023-03-16 14:27:27,761] [INFO] Task succeeded: fastANI
[2023-03-16 14:27:27,763] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 14:27:27,764] [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_002717245.1	s__GCA-002720895 sp002717245	79.4613	166	238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.29	99.29	0.96	0.96	2	-
GCA_002938195.1	s__MarineAlpha5-Bin7 sp002938195	74.7331	51	238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin7	95.0	99.81	99.67	0.81	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-16 14:27:27,764] [INFO] GTDB search result was written to OceanDNA-b24174/result_gtdb.tsv
[2023-03-16 14:27:27,764] [INFO] ===== GTDB Search completed =====
[2023-03-16 14:27:27,764] [INFO] DFAST_QC result json was written to OceanDNA-b24174/dqc_result.json
[2023-03-16 14:27:27,765] [INFO] DFAST_QC completed!
[2023-03-16 14:27:27,765] [INFO] Total running time: 0h0m54s