[2023-03-15 21:24:38,469] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:38,469] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:38,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c648b52-9c1d-4291-9d92-2f1e021b6beb/dqc_reference
[2023-03-15 21:24:39,546] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:39,546] [INFO] Task started: Prodigal
[2023-03-15 21:24:39,546] [INFO] Running command: cat /var/lib/cwl/stgb5090bdd-283c-4849-a27e-ed716b601f2c/OceanDNA-a1245.fa | prodigal -d OceanDNA-a1245/cds.fna -a OceanDNA-a1245/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:42,617] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:42,617] [INFO] Task started: HMMsearch
[2023-03-15 21:24:42,617] [INFO] Running command: hmmsearch --tblout OceanDNA-a1245/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c648b52-9c1d-4291-9d92-2f1e021b6beb/dqc_reference/reference_markers.hmm OceanDNA-a1245/protein.faa > /dev/null
[2023-03-15 21:24:42,750] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:42,750] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb5090bdd-283c-4849-a27e-ed716b601f2c/OceanDNA-a1245.fa]
[2023-03-15 21:24:42,755] [INFO] Query marker FASTA was written to OceanDNA-a1245/markers.fasta
[2023-03-15 21:24:42,755] [INFO] Task started: Blastn
[2023-03-15 21:24:42,755] [INFO] Running command: blastn -query OceanDNA-a1245/markers.fasta -db /var/lib/cwl/stg5c648b52-9c1d-4291-9d92-2f1e021b6beb/dqc_reference/reference_markers.fasta -out OceanDNA-a1245/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:43,209] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:43,210] [INFO] Selected 5 target genomes.
[2023-03-15 21:24:43,210] [INFO] Target genome list was writen to OceanDNA-a1245/target_genomes.txt
[2023-03-15 21:24:43,213] [INFO] Task started: fastANI
[2023-03-15 21:24:43,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5090bdd-283c-4849-a27e-ed716b601f2c/OceanDNA-a1245.fa --refList OceanDNA-a1245/target_genomes.txt --output OceanDNA-a1245/fastani_result.tsv --threads 1
[2023-03-15 21:24:43,756] [INFO] Task succeeded: fastANI
[2023-03-15 21:24:43,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c648b52-9c1d-4291-9d92-2f1e021b6beb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:24:43,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c648b52-9c1d-4291-9d92-2f1e021b6beb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:24:43,757] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:24:43,757] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:24:43,757] [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 21:24:43,757] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1245/tc_result.tsv
[2023-03-15 21:24:43,758] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:24:43,758] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:24:43,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c648b52-9c1d-4291-9d92-2f1e021b6beb/dqc_reference/checkm_data
[2023-03-15 21:24:43,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:24:43,860] [INFO] Task started: CheckM
[2023-03-15 21:24:43,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1245/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1245/checkm_input OceanDNA-a1245/checkm_result
[2023-03-15 21:24:59,576] [INFO] Task succeeded: CheckM
[2023-03-15 21:24:59,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:24:59,578] [INFO] ===== Completeness check finished =====
[2023-03-15 21:24:59,578] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:24:59,578] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1245/markers.fasta)
[2023-03-15 21:24:59,580] [INFO] Task started: Blastn
[2023-03-15 21:24:59,580] [INFO] Running command: blastn -query OceanDNA-a1245/markers.fasta -db /var/lib/cwl/stg5c648b52-9c1d-4291-9d92-2f1e021b6beb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1245/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:00,550] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:00,551] [INFO] Selected 8 target genomes.
[2023-03-15 21:25:00,551] [INFO] Target genome list was writen to OceanDNA-a1245/target_genomes_gtdb.txt
[2023-03-15 21:25:00,685] [INFO] Task started: fastANI
[2023-03-15 21:25:00,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5090bdd-283c-4849-a27e-ed716b601f2c/OceanDNA-a1245.fa --refList OceanDNA-a1245/target_genomes_gtdb.txt --output OceanDNA-a1245/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:25:02,251] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:02,254] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:25:02,254] [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_018658955.1	s__JABIKK01 sp018658955	99.6872	170	198	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__UBA489;g__JABIKK01	95.0	99.81	99.70	0.91	0.85	13	conclusive
GCA_016845225.1	s__JABIKK01 sp016845225	87.9024	177	198	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__UBA489;g__JABIKK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:25:02,254] [INFO] GTDB search result was written to OceanDNA-a1245/result_gtdb.tsv
[2023-03-15 21:25:02,254] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:25:02,255] [INFO] DFAST_QC result json was written to OceanDNA-a1245/dqc_result.json
[2023-03-15 21:25:02,255] [INFO] DFAST_QC completed!
[2023-03-15 21:25:02,255] [INFO] Total running time: 0h0m24s