[2023-03-15 05:56:37,386] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:56:37,401] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:56:37,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg65c3c00e-d1aa-492a-bd92-a23e4f139f5d/dqc_reference
[2023-03-15 05:56:39,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:56:39,381] [INFO] Task started: Prodigal
[2023-03-15 05:56:39,381] [INFO] Running command: cat /var/lib/cwl/stg136c9895-b109-40ac-b9d1-afb16c085b8e/OceanDNA-b2939.fa | prodigal -d OceanDNA-b2939/cds.fna -a OceanDNA-b2939/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:56:45,352] [INFO] Task succeeded: Prodigal
[2023-03-15 05:56:45,353] [INFO] Task started: HMMsearch
[2023-03-15 05:56:45,353] [INFO] Running command: hmmsearch --tblout OceanDNA-b2939/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65c3c00e-d1aa-492a-bd92-a23e4f139f5d/dqc_reference/reference_markers.hmm OceanDNA-b2939/protein.faa > /dev/null
[2023-03-15 05:56:45,584] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:56:45,585] [INFO] Found 6/6 markers.
[2023-03-15 05:56:45,610] [INFO] Query marker FASTA was written to OceanDNA-b2939/markers.fasta
[2023-03-15 05:56:45,611] [INFO] Task started: Blastn
[2023-03-15 05:56:45,611] [INFO] Running command: blastn -query OceanDNA-b2939/markers.fasta -db /var/lib/cwl/stg65c3c00e-d1aa-492a-bd92-a23e4f139f5d/dqc_reference/reference_markers.fasta -out OceanDNA-b2939/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:56:49,208] [INFO] Task succeeded: Blastn
[2023-03-15 05:56:49,219] [INFO] Selected 27 target genomes.
[2023-03-15 05:56:49,219] [INFO] Target genome list was writen to OceanDNA-b2939/target_genomes.txt
[2023-03-15 05:56:49,236] [INFO] Task started: fastANI
[2023-03-15 05:56:49,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg136c9895-b109-40ac-b9d1-afb16c085b8e/OceanDNA-b2939.fa --refList OceanDNA-b2939/target_genomes.txt --output OceanDNA-b2939/fastani_result.tsv --threads 1
[2023-03-15 05:56:58,408] [INFO] Task succeeded: fastANI
[2023-03-15 05:56:58,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65c3c00e-d1aa-492a-bd92-a23e4f139f5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:56:58,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65c3c00e-d1aa-492a-bd92-a23e4f139f5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:56:58,409] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:56:58,409] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:56:58,409] [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 05:56:58,415] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2939/tc_result.tsv
[2023-03-15 05:56:58,415] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:56:58,415] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:56:58,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65c3c00e-d1aa-492a-bd92-a23e4f139f5d/dqc_reference/checkm_data
[2023-03-15 05:56:58,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:56:58,508] [INFO] Task started: CheckM
[2023-03-15 05:56:58,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2939/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2939/checkm_input OceanDNA-b2939/checkm_result
[2023-03-15 05:57:19,405] [INFO] Task succeeded: CheckM
[2023-03-15 05:57:19,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.84%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 05:57:19,543] [INFO] ===== Completeness check finished =====
[2023-03-15 05:57:19,543] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:57:19,543] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2939/markers.fasta)
[2023-03-15 05:57:19,545] [INFO] Task started: Blastn
[2023-03-15 05:57:19,545] [INFO] Running command: blastn -query OceanDNA-b2939/markers.fasta -db /var/lib/cwl/stg65c3c00e-d1aa-492a-bd92-a23e4f139f5d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2939/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:57:20,244] [INFO] Task succeeded: Blastn
[2023-03-15 05:57:20,251] [INFO] Selected 21 target genomes.
[2023-03-15 05:57:20,251] [INFO] Target genome list was writen to OceanDNA-b2939/target_genomes_gtdb.txt
[2023-03-15 05:57:20,277] [INFO] Task started: fastANI
[2023-03-15 05:57:20,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg136c9895-b109-40ac-b9d1-afb16c085b8e/OceanDNA-b2939.fa --refList OceanDNA-b2939/target_genomes_gtdb.txt --output OceanDNA-b2939/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:57:25,996] [INFO] Task succeeded: fastANI
[2023-03-15 05:57:25,999] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:57:26,000] [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_005789325.1	s__ATZT02 sp005789325	83.048	156	353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__ATZT02	95.0	96.56	96.56	0.80	0.80	2	-
GCA_014190035.1	s__ATZT02 sp014190035	82.6883	238	353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__ATZT02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000428345.2	s__ATZT02 sp000428345	82.5628	159	353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__ATZT02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463095.1	s__ATZT02 sp016463095	81.7146	236	353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__ATZT02	95.0	98.85	98.85	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:57:26,004] [INFO] GTDB search result was written to OceanDNA-b2939/result_gtdb.tsv
[2023-03-15 05:57:26,013] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:57:26,020] [INFO] DFAST_QC result json was written to OceanDNA-b2939/dqc_result.json
[2023-03-15 05:57:26,020] [INFO] DFAST_QC completed!
[2023-03-15 05:57:26,020] [INFO] Total running time: 0h0m49s