[2023-03-16 03:47:34,617] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:34,617] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:34,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg99ecb8fb-bc8a-4004-acbb-d0b87fcf3df4/dqc_reference
[2023-03-16 03:47:35,712] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:35,712] [INFO] Task started: Prodigal
[2023-03-16 03:47:35,712] [INFO] Running command: cat /var/lib/cwl/stg60f5555c-b2f9-43f2-a6b5-f9d8ba470262/OceanDNA-b31327.fa | prodigal -d OceanDNA-b31327/cds.fna -a OceanDNA-b31327/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:39,373] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:39,373] [INFO] Task started: HMMsearch
[2023-03-16 03:47:39,373] [INFO] Running command: hmmsearch --tblout OceanDNA-b31327/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99ecb8fb-bc8a-4004-acbb-d0b87fcf3df4/dqc_reference/reference_markers.hmm OceanDNA-b31327/protein.faa > /dev/null
[2023-03-16 03:47:39,514] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:39,514] [INFO] Found 6/6 markers.
[2023-03-16 03:47:39,523] [INFO] Query marker FASTA was written to OceanDNA-b31327/markers.fasta
[2023-03-16 03:47:39,523] [INFO] Task started: Blastn
[2023-03-16 03:47:39,523] [INFO] Running command: blastn -query OceanDNA-b31327/markers.fasta -db /var/lib/cwl/stg99ecb8fb-bc8a-4004-acbb-d0b87fcf3df4/dqc_reference/reference_markers.fasta -out OceanDNA-b31327/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:40,023] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:40,024] [INFO] Selected 6 target genomes.
[2023-03-16 03:47:40,024] [INFO] Target genome list was writen to OceanDNA-b31327/target_genomes.txt
[2023-03-16 03:47:40,028] [INFO] Task started: fastANI
[2023-03-16 03:47:40,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg60f5555c-b2f9-43f2-a6b5-f9d8ba470262/OceanDNA-b31327.fa --refList OceanDNA-b31327/target_genomes.txt --output OceanDNA-b31327/fastani_result.tsv --threads 1
[2023-03-16 03:47:41,447] [INFO] Task succeeded: fastANI
[2023-03-16 03:47:41,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99ecb8fb-bc8a-4004-acbb-d0b87fcf3df4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:47:41,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99ecb8fb-bc8a-4004-acbb-d0b87fcf3df4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:47:41,447] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:47:41,448] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:47:41,448] [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
--------------------------------------------------------------------------------
[2023-03-16 03:47:41,604] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31327/tc_result.tsv
[2023-03-16 03:47:41,604] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:47:41,604] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:47:41,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99ecb8fb-bc8a-4004-acbb-d0b87fcf3df4/dqc_reference/checkm_data
[2023-03-16 03:47:41,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:47:41,620] [INFO] Task started: CheckM
[2023-03-16 03:47:41,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31327/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31327/checkm_input OceanDNA-b31327/checkm_result
[2023-03-16 03:47:59,154] [INFO] Task succeeded: CheckM
[2023-03-16 03:47:59,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:47:59,156] [INFO] ===== Completeness check finished =====
[2023-03-16 03:47:59,156] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:47:59,157] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31327/markers.fasta)
[2023-03-16 03:47:59,157] [INFO] Task started: Blastn
[2023-03-16 03:47:59,157] [INFO] Running command: blastn -query OceanDNA-b31327/markers.fasta -db /var/lib/cwl/stg99ecb8fb-bc8a-4004-acbb-d0b87fcf3df4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31327/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:59,827] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:59,828] [INFO] Selected 13 target genomes.
[2023-03-16 03:47:59,828] [INFO] Target genome list was writen to OceanDNA-b31327/target_genomes_gtdb.txt
[2023-03-16 03:47:59,906] [INFO] Task started: fastANI
[2023-03-16 03:47:59,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg60f5555c-b2f9-43f2-a6b5-f9d8ba470262/OceanDNA-b31327.fa --refList OceanDNA-b31327/target_genomes_gtdb.txt --output OceanDNA-b31327/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:02,803] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:02,806] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:48:02,806] [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_905479795.1	s__Aquarickettsia sp905479795	91.563	110	184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Midichloriaceae;g__Aquarickettsia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887235.1	s__Aquarickettsia sp903887235	82.2016	128	184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Midichloriaceae;g__Aquarickettsia	95.0	99.94	99.90	0.95	0.94	8	-
GCF_003953955.1	s__Aquarickettsia rohweri	77.0127	63	184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Midichloriaceae;g__Aquarickettsia	95.0	98.47	98.47	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:02,806] [INFO] GTDB search result was written to OceanDNA-b31327/result_gtdb.tsv
[2023-03-16 03:48:02,807] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:02,807] [INFO] DFAST_QC result json was written to OceanDNA-b31327/dqc_result.json
[2023-03-16 03:48:02,807] [INFO] DFAST_QC completed!
[2023-03-16 03:48:02,807] [INFO] Total running time: 0h0m28s