[2023-03-17 03:50:13,822] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,822] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,822] [INFO] DQC Reference Directory: /var/lib/cwl/stg69792307-573a-4924-a776-235c10129ecf/dqc_reference
[2023-03-17 03:50:15,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,102] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,102] [INFO] Running command: cat /var/lib/cwl/stgc3315935-d43d-4261-a945-2e94ac30fabf/OceanDNA-b46121.fa | prodigal -d OceanDNA-b46121/cds.fna -a OceanDNA-b46121/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:21,660] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:21,660] [INFO] Task started: HMMsearch
[2023-03-17 03:50:21,660] [INFO] Running command: hmmsearch --tblout OceanDNA-b46121/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69792307-573a-4924-a776-235c10129ecf/dqc_reference/reference_markers.hmm OceanDNA-b46121/protein.faa > /dev/null
[2023-03-17 03:50:21,832] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:21,832] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc3315935-d43d-4261-a945-2e94ac30fabf/OceanDNA-b46121.fa]
[2023-03-17 03:50:21,840] [INFO] Query marker FASTA was written to OceanDNA-b46121/markers.fasta
[2023-03-17 03:50:21,840] [INFO] Task started: Blastn
[2023-03-17 03:50:21,840] [INFO] Running command: blastn -query OceanDNA-b46121/markers.fasta -db /var/lib/cwl/stg69792307-573a-4924-a776-235c10129ecf/dqc_reference/reference_markers.fasta -out OceanDNA-b46121/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:22,335] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:22,336] [INFO] Selected 11 target genomes.
[2023-03-17 03:50:22,336] [INFO] Target genome list was writen to OceanDNA-b46121/target_genomes.txt
[2023-03-17 03:50:22,372] [INFO] Task started: fastANI
[2023-03-17 03:50:22,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3315935-d43d-4261-a945-2e94ac30fabf/OceanDNA-b46121.fa --refList OceanDNA-b46121/target_genomes.txt --output OceanDNA-b46121/fastani_result.tsv --threads 1
[2023-03-17 03:50:29,220] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:29,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69792307-573a-4924-a776-235c10129ecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:29,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69792307-573a-4924-a776-235c10129ecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:29,221] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:29,221] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:50:29,221] [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 03:50:29,221] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46121/tc_result.tsv
[2023-03-17 03:50:29,221] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:29,221] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:29,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69792307-573a-4924-a776-235c10129ecf/dqc_reference/checkm_data
[2023-03-17 03:50:29,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:29,226] [INFO] Task started: CheckM
[2023-03-17 03:50:29,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46121/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46121/checkm_input OceanDNA-b46121/checkm_result
[2023-03-17 03:50:51,828] [INFO] Task succeeded: CheckM
[2023-03-17 03:50:51,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:50:51,830] [INFO] ===== Completeness check finished =====
[2023-03-17 03:50:51,830] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:50:51,830] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46121/markers.fasta)
[2023-03-17 03:50:51,831] [INFO] Task started: Blastn
[2023-03-17 03:50:51,831] [INFO] Running command: blastn -query OceanDNA-b46121/markers.fasta -db /var/lib/cwl/stg69792307-573a-4924-a776-235c10129ecf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46121/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:52,564] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:52,564] [INFO] Selected 14 target genomes.
[2023-03-17 03:50:52,564] [INFO] Target genome list was writen to OceanDNA-b46121/target_genomes_gtdb.txt
[2023-03-17 03:50:52,878] [INFO] Task started: fastANI
[2023-03-17 03:50:52,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3315935-d43d-4261-a945-2e94ac30fabf/OceanDNA-b46121.fa --refList OceanDNA-b46121/target_genomes_gtdb.txt --output OceanDNA-b46121/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:50:59,065] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:59,067] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:50:59,067] [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_002457235.1	s__GCA-2690565 sp002457235	82.8205	154	314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__GCA-2690565	95.0	99.55	99.48	0.94	0.91	3	-
GCA_011522825.1	s__GCA-2690565 sp011522825	81.9701	141	314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__GCA-2690565	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:50:59,068] [INFO] GTDB search result was written to OceanDNA-b46121/result_gtdb.tsv
[2023-03-17 03:50:59,068] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:50:59,068] [INFO] DFAST_QC result json was written to OceanDNA-b46121/dqc_result.json
[2023-03-17 03:50:59,068] [INFO] DFAST_QC completed!
[2023-03-17 03:50:59,068] [INFO] Total running time: 0h0m45s