[2023-03-17 08:39:29,318] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:29,318] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:29,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg6448d28d-c5cd-45c3-9334-e41b9ba280d5/dqc_reference
[2023-03-17 08:39:30,392] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:30,393] [INFO] Task started: Prodigal
[2023-03-17 08:39:30,393] [INFO] Running command: cat /var/lib/cwl/stg12173f55-8639-4b1a-b517-5e56add04c1c/OceanDNA-b41618.fa | prodigal -d OceanDNA-b41618/cds.fna -a OceanDNA-b41618/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:39:41,632] [INFO] Task succeeded: Prodigal
[2023-03-17 08:39:41,632] [INFO] Task started: HMMsearch
[2023-03-17 08:39:41,632] [INFO] Running command: hmmsearch --tblout OceanDNA-b41618/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6448d28d-c5cd-45c3-9334-e41b9ba280d5/dqc_reference/reference_markers.hmm OceanDNA-b41618/protein.faa > /dev/null
[2023-03-17 08:39:41,819] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:39:41,820] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg12173f55-8639-4b1a-b517-5e56add04c1c/OceanDNA-b41618.fa]
[2023-03-17 08:39:41,834] [INFO] Query marker FASTA was written to OceanDNA-b41618/markers.fasta
[2023-03-17 08:39:41,835] [INFO] Task started: Blastn
[2023-03-17 08:39:41,835] [INFO] Running command: blastn -query OceanDNA-b41618/markers.fasta -db /var/lib/cwl/stg6448d28d-c5cd-45c3-9334-e41b9ba280d5/dqc_reference/reference_markers.fasta -out OceanDNA-b41618/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:42,372] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:42,373] [INFO] Selected 27 target genomes.
[2023-03-17 08:39:42,373] [INFO] Target genome list was writen to OceanDNA-b41618/target_genomes.txt
[2023-03-17 08:39:42,534] [INFO] Task started: fastANI
[2023-03-17 08:39:42,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg12173f55-8639-4b1a-b517-5e56add04c1c/OceanDNA-b41618.fa --refList OceanDNA-b41618/target_genomes.txt --output OceanDNA-b41618/fastani_result.tsv --threads 1
[2023-03-17 08:39:58,248] [INFO] Task succeeded: fastANI
[2023-03-17 08:39:58,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6448d28d-c5cd-45c3-9334-e41b9ba280d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:39:58,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6448d28d-c5cd-45c3-9334-e41b9ba280d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:39:58,249] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:39:58,249] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:39:58,249] [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 08:39:58,249] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41618/tc_result.tsv
[2023-03-17 08:39:58,249] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:39:58,249] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:39:58,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6448d28d-c5cd-45c3-9334-e41b9ba280d5/dqc_reference/checkm_data
[2023-03-17 08:39:58,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:39:58,255] [INFO] Task started: CheckM
[2023-03-17 08:39:58,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41618/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41618/checkm_input OceanDNA-b41618/checkm_result
[2023-03-17 08:40:30,073] [INFO] Task succeeded: CheckM
[2023-03-17 08:40:30,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:40:30,671] [INFO] ===== Completeness check finished =====
[2023-03-17 08:40:30,672] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:40:30,672] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41618/markers.fasta)
[2023-03-17 08:40:30,673] [INFO] Task started: Blastn
[2023-03-17 08:40:30,673] [INFO] Running command: blastn -query OceanDNA-b41618/markers.fasta -db /var/lib/cwl/stg6448d28d-c5cd-45c3-9334-e41b9ba280d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41618/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:40:31,406] [INFO] Task succeeded: Blastn
[2023-03-17 08:40:31,407] [INFO] Selected 21 target genomes.
[2023-03-17 08:40:31,407] [INFO] Target genome list was writen to OceanDNA-b41618/target_genomes_gtdb.txt
[2023-03-17 08:40:31,869] [INFO] Task started: fastANI
[2023-03-17 08:40:31,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg12173f55-8639-4b1a-b517-5e56add04c1c/OceanDNA-b41618.fa --refList OceanDNA-b41618/target_genomes_gtdb.txt --output OceanDNA-b41618/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:40:41,974] [INFO] Task succeeded: fastANI
[2023-03-17 08:40:41,978] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:40:41,979] [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_018668095.1	s__UBA7434 sp018668095	80.7108	375	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	98.20	98.20	0.79	0.79	2	-
GCA_003492055.1	s__UBA7434 sp003492055	80.6076	247	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	98.70	98.70	0.91	0.91	2	-
GCA_905480475.1	s__UBA7434 sp905480475	77.1829	138	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726445.1	s__UBA7434 sp002726445	76.8145	62	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.17	99.17	0.72	0.72	2	-
GCA_002336035.1	s__UBA7434 sp002336035	76.538	68	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478995.1	s__UBA7434 sp002480045	76.3387	51	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.42	99.16	0.91	0.89	7	-
GCA_002339085.1	s__UBA7434 sp002339085	76.2986	84	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.78	99.78	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-17 08:40:41,979] [INFO] GTDB search result was written to OceanDNA-b41618/result_gtdb.tsv
[2023-03-17 08:40:41,979] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:40:41,980] [INFO] DFAST_QC result json was written to OceanDNA-b41618/dqc_result.json
[2023-03-17 08:40:41,980] [INFO] DFAST_QC completed!
[2023-03-17 08:40:41,981] [INFO] Total running time: 0h1m13s