[2023-03-14 12:25:41,530] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,530] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg31dc20c6-62d7-45ef-a37a-3f90be17f9ee/dqc_reference
[2023-03-14 12:25:42,755] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,755] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,755] [INFO] Running command: cat /var/lib/cwl/stg3cf51109-3288-442b-bf69-95cb90363e7f/OceanDNA-b3611.fa | prodigal -d OceanDNA-b3611/cds.fna -a OceanDNA-b3611/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:26:11,081] [INFO] Task succeeded: Prodigal
[2023-03-14 12:26:11,081] [INFO] Task started: HMMsearch
[2023-03-14 12:26:11,081] [INFO] Running command: hmmsearch --tblout OceanDNA-b3611/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31dc20c6-62d7-45ef-a37a-3f90be17f9ee/dqc_reference/reference_markers.hmm OceanDNA-b3611/protein.faa > /dev/null
[2023-03-14 12:26:11,301] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:26:11,302] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3cf51109-3288-442b-bf69-95cb90363e7f/OceanDNA-b3611.fa]
[2023-03-14 12:26:11,326] [INFO] Query marker FASTA was written to OceanDNA-b3611/markers.fasta
[2023-03-14 12:26:11,327] [INFO] Task started: Blastn
[2023-03-14 12:26:11,327] [INFO] Running command: blastn -query OceanDNA-b3611/markers.fasta -db /var/lib/cwl/stg31dc20c6-62d7-45ef-a37a-3f90be17f9ee/dqc_reference/reference_markers.fasta -out OceanDNA-b3611/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:11,872] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:11,873] [INFO] Selected 23 target genomes.
[2023-03-14 12:26:11,873] [INFO] Target genome list was writen to OceanDNA-b3611/target_genomes.txt
[2023-03-14 12:26:11,888] [INFO] Task started: fastANI
[2023-03-14 12:26:11,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cf51109-3288-442b-bf69-95cb90363e7f/OceanDNA-b3611.fa --refList OceanDNA-b3611/target_genomes.txt --output OceanDNA-b3611/fastani_result.tsv --threads 1
[2023-03-14 12:26:26,394] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:26,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31dc20c6-62d7-45ef-a37a-3f90be17f9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:26,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31dc20c6-62d7-45ef-a37a-3f90be17f9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:26,399] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:26,399] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:26:26,399] [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
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	75.3603	53	1034	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	75.3603	53	1034	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:26:26,399] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3611/tc_result.tsv
[2023-03-14 12:26:26,399] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:26,399] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:26,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31dc20c6-62d7-45ef-a37a-3f90be17f9ee/dqc_reference/checkm_data
[2023-03-14 12:26:26,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:26,441] [INFO] Task started: CheckM
[2023-03-14 12:26:26,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3611/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3611/checkm_input OceanDNA-b3611/checkm_result
[2023-03-14 12:27:37,403] [INFO] Task succeeded: CheckM
[2023-03-14 12:27:37,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.30%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:27:37,407] [INFO] ===== Completeness check finished =====
[2023-03-14 12:27:37,407] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:27:37,407] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3611/markers.fasta)
[2023-03-14 12:27:37,409] [INFO] Task started: Blastn
[2023-03-14 12:27:37,409] [INFO] Running command: blastn -query OceanDNA-b3611/markers.fasta -db /var/lib/cwl/stg31dc20c6-62d7-45ef-a37a-3f90be17f9ee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3611/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:27:38,145] [INFO] Task succeeded: Blastn
[2023-03-14 12:27:38,146] [INFO] Selected 28 target genomes.
[2023-03-14 12:27:38,146] [INFO] Target genome list was writen to OceanDNA-b3611/target_genomes_gtdb.txt
[2023-03-14 12:27:38,163] [INFO] Task started: fastANI
[2023-03-14 12:27:38,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cf51109-3288-442b-bf69-95cb90363e7f/OceanDNA-b3611.fa --refList OceanDNA-b3611/target_genomes_gtdb.txt --output OceanDNA-b3611/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:27:59,231] [INFO] Task succeeded: fastANI
[2023-03-14 12:27:59,234] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:27:59,234] [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
GCF_002631205.1	s__Lewinella_A marina	75.3603	53	1034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015490175.1	s__WFYJ01 sp015490175	75.2163	68	1034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WFYJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:27:59,234] [INFO] GTDB search result was written to OceanDNA-b3611/result_gtdb.tsv
[2023-03-14 12:27:59,234] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:27:59,235] [INFO] DFAST_QC result json was written to OceanDNA-b3611/dqc_result.json
[2023-03-14 12:27:59,235] [INFO] DFAST_QC completed!
[2023-03-14 12:27:59,235] [INFO] Total running time: 0h2m18s