[2023-03-17 05:01:06,760] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,760] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg87e46169-ca22-4362-8138-c4b77abcd191/dqc_reference
[2023-03-17 05:01:08,508] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:08,508] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,508] [INFO] Running command: cat /var/lib/cwl/stg3d28b9ad-2c99-4ab3-bb3d-dfbd75071d95/OceanDNA-b14064.fa | prodigal -d OceanDNA-b14064/cds.fna -a OceanDNA-b14064/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:16,332] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:16,333] [INFO] Task started: HMMsearch
[2023-03-17 05:01:16,333] [INFO] Running command: hmmsearch --tblout OceanDNA-b14064/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87e46169-ca22-4362-8138-c4b77abcd191/dqc_reference/reference_markers.hmm OceanDNA-b14064/protein.faa > /dev/null
[2023-03-17 05:01:16,483] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:16,484] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3d28b9ad-2c99-4ab3-bb3d-dfbd75071d95/OceanDNA-b14064.fa]
[2023-03-17 05:01:16,497] [INFO] Query marker FASTA was written to OceanDNA-b14064/markers.fasta
[2023-03-17 05:01:16,498] [INFO] Task started: Blastn
[2023-03-17 05:01:16,498] [INFO] Running command: blastn -query OceanDNA-b14064/markers.fasta -db /var/lib/cwl/stg87e46169-ca22-4362-8138-c4b77abcd191/dqc_reference/reference_markers.fasta -out OceanDNA-b14064/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:16,997] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:16,998] [INFO] Selected 10 target genomes.
[2023-03-17 05:01:16,998] [INFO] Target genome list was writen to OceanDNA-b14064/target_genomes.txt
[2023-03-17 05:01:17,005] [INFO] Task started: fastANI
[2023-03-17 05:01:17,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d28b9ad-2c99-4ab3-bb3d-dfbd75071d95/OceanDNA-b14064.fa --refList OceanDNA-b14064/target_genomes.txt --output OceanDNA-b14064/fastani_result.tsv --threads 1
[2023-03-17 05:01:19,776] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:19,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87e46169-ca22-4362-8138-c4b77abcd191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:19,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87e46169-ca22-4362-8138-c4b77abcd191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:19,776] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:01:19,776] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:01:19,776] [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 05:01:19,777] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14064/tc_result.tsv
[2023-03-17 05:01:19,777] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:19,777] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:19,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87e46169-ca22-4362-8138-c4b77abcd191/dqc_reference/checkm_data
[2023-03-17 05:01:19,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:19,786] [INFO] Task started: CheckM
[2023-03-17 05:01:19,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14064/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14064/checkm_input OceanDNA-b14064/checkm_result
[2023-03-17 05:01:44,640] [INFO] Task succeeded: CheckM
[2023-03-17 05:01:44,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.77%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:01:44,643] [INFO] ===== Completeness check finished =====
[2023-03-17 05:01:44,643] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:01:44,643] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14064/markers.fasta)
[2023-03-17 05:01:44,643] [INFO] Task started: Blastn
[2023-03-17 05:01:44,643] [INFO] Running command: blastn -query OceanDNA-b14064/markers.fasta -db /var/lib/cwl/stg87e46169-ca22-4362-8138-c4b77abcd191/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14064/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:45,340] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:45,341] [INFO] Selected 12 target genomes.
[2023-03-17 05:01:45,341] [INFO] Target genome list was writen to OceanDNA-b14064/target_genomes_gtdb.txt
[2023-03-17 05:01:45,660] [INFO] Task started: fastANI
[2023-03-17 05:01:45,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d28b9ad-2c99-4ab3-bb3d-dfbd75071d95/OceanDNA-b14064.fa --refList OceanDNA-b14064/target_genomes_gtdb.txt --output OceanDNA-b14064/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:01:50,336] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:50,339] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:01:50,339] [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_009392815.1	s__GCA-002712965 sp009392815	99.1352	403	459	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__GCA-002712965	95.0	99.65	99.65	0.80	0.80	2	conclusive
GCA_009391195.1	s__GCA-002712965 sp009391195	81.4909	209	459	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__GCA-002712965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696685.1	s__GCA-002712965 sp002696685	79.8996	288	459	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__GCA-002712965	95.0	98.93	98.49	0.85	0.81	3	-
--------------------------------------------------------------------------------
[2023-03-17 05:01:50,340] [INFO] GTDB search result was written to OceanDNA-b14064/result_gtdb.tsv
[2023-03-17 05:01:50,340] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:01:50,340] [INFO] DFAST_QC result json was written to OceanDNA-b14064/dqc_result.json
[2023-03-17 05:01:50,340] [INFO] DFAST_QC completed!
[2023-03-17 05:01:50,340] [INFO] Total running time: 0h0m44s