[2023-03-15 04:45:50,372] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:50,374] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:50,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a2da428-db82-4f8f-8dff-943508cb5728/dqc_reference
[2023-03-15 04:45:51,462] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:51,463] [INFO] Task started: Prodigal
[2023-03-15 04:45:51,463] [INFO] Running command: cat /var/lib/cwl/stgc916c5ce-7203-4ad1-a844-2ebdf94d98b9/OceanDNA-b31223.fa | prodigal -d OceanDNA-b31223/cds.fna -a OceanDNA-b31223/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:46:08,101] [INFO] Task succeeded: Prodigal
[2023-03-15 04:46:08,101] [INFO] Task started: HMMsearch
[2023-03-15 04:46:08,101] [INFO] Running command: hmmsearch --tblout OceanDNA-b31223/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a2da428-db82-4f8f-8dff-943508cb5728/dqc_reference/reference_markers.hmm OceanDNA-b31223/protein.faa > /dev/null
[2023-03-15 04:46:08,290] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:46:08,291] [INFO] Found 6/6 markers.
[2023-03-15 04:46:08,330] [INFO] Query marker FASTA was written to OceanDNA-b31223/markers.fasta
[2023-03-15 04:46:08,331] [INFO] Task started: Blastn
[2023-03-15 04:46:08,331] [INFO] Running command: blastn -query OceanDNA-b31223/markers.fasta -db /var/lib/cwl/stg3a2da428-db82-4f8f-8dff-943508cb5728/dqc_reference/reference_markers.fasta -out OceanDNA-b31223/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:08,896] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:08,898] [INFO] Selected 21 target genomes.
[2023-03-15 04:46:08,899] [INFO] Target genome list was writen to OceanDNA-b31223/target_genomes.txt
[2023-03-15 04:46:08,912] [INFO] Task started: fastANI
[2023-03-15 04:46:08,912] [INFO] Running command: fastANI --query /var/lib/cwl/stgc916c5ce-7203-4ad1-a844-2ebdf94d98b9/OceanDNA-b31223.fa --refList OceanDNA-b31223/target_genomes.txt --output OceanDNA-b31223/fastani_result.tsv --threads 1
[2023-03-15 04:46:19,431] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:19,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a2da428-db82-4f8f-8dff-943508cb5728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:46:19,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a2da428-db82-4f8f-8dff-943508cb5728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:46:19,432] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:46:19,432] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:46:19,432] [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 04:46:19,438] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31223/tc_result.tsv
[2023-03-15 04:46:19,443] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:46:19,443] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:46:19,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a2da428-db82-4f8f-8dff-943508cb5728/dqc_reference/checkm_data
[2023-03-15 04:46:19,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:46:19,453] [INFO] Task started: CheckM
[2023-03-15 04:46:19,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31223/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31223/checkm_input OceanDNA-b31223/checkm_result
[2023-03-15 04:47:03,016] [INFO] Task succeeded: CheckM
[2023-03-15 04:47:03,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:47:03,043] [INFO] ===== Completeness check finished =====
[2023-03-15 04:47:03,043] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:47:03,043] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31223/markers.fasta)
[2023-03-15 04:47:03,044] [INFO] Task started: Blastn
[2023-03-15 04:47:03,045] [INFO] Running command: blastn -query OceanDNA-b31223/markers.fasta -db /var/lib/cwl/stg3a2da428-db82-4f8f-8dff-943508cb5728/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31223/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:47:03,992] [INFO] Task succeeded: Blastn
[2023-03-15 04:47:03,996] [INFO] Selected 23 target genomes.
[2023-03-15 04:47:03,997] [INFO] Target genome list was writen to OceanDNA-b31223/target_genomes_gtdb.txt
[2023-03-15 04:47:04,019] [INFO] Task started: fastANI
[2023-03-15 04:47:04,020] [INFO] Running command: fastANI --query /var/lib/cwl/stgc916c5ce-7203-4ad1-a844-2ebdf94d98b9/OceanDNA-b31223.fa --refList OceanDNA-b31223/target_genomes_gtdb.txt --output OceanDNA-b31223/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:47:13,944] [INFO] Task succeeded: fastANI
[2023-03-15 04:47:13,946] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:47:13,946] [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_002690705.1	s__TMED8 sp002690705	99.9705	953	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__TMED8	95.0	99.94	99.88	0.93	0.87	3	conclusive
--------------------------------------------------------------------------------
[2023-03-15 04:47:13,949] [INFO] GTDB search result was written to OceanDNA-b31223/result_gtdb.tsv
[2023-03-15 04:47:13,953] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:47:13,954] [INFO] DFAST_QC result json was written to OceanDNA-b31223/dqc_result.json
[2023-03-15 04:47:13,954] [INFO] DFAST_QC completed!
[2023-03-15 04:47:13,954] [INFO] Total running time: 0h1m24s