[2023-03-14 10:55:58,921] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,942] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg2510c3e1-e932-40c9-802a-9c1162862e39/dqc_reference
[2023-03-14 10:56:00,679] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,679] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,679] [INFO] Running command: cat /var/lib/cwl/stgc4a55bed-7f6b-4d6f-8858-1ecc8d9fe033/OceanDNA-b7194.fa | prodigal -d OceanDNA-b7194/cds.fna -a OceanDNA-b7194/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:23,505] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:23,505] [INFO] Task started: HMMsearch
[2023-03-14 10:56:23,505] [INFO] Running command: hmmsearch --tblout OceanDNA-b7194/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2510c3e1-e932-40c9-802a-9c1162862e39/dqc_reference/reference_markers.hmm OceanDNA-b7194/protein.faa > /dev/null
[2023-03-14 10:56:23,799] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:23,799] [INFO] Found 6/6 markers.
[2023-03-14 10:56:23,821] [INFO] Query marker FASTA was written to OceanDNA-b7194/markers.fasta
[2023-03-14 10:56:23,822] [INFO] Task started: Blastn
[2023-03-14 10:56:23,822] [INFO] Running command: blastn -query OceanDNA-b7194/markers.fasta -db /var/lib/cwl/stg2510c3e1-e932-40c9-802a-9c1162862e39/dqc_reference/reference_markers.fasta -out OceanDNA-b7194/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:24,419] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:24,420] [INFO] Selected 29 target genomes.
[2023-03-14 10:56:24,420] [INFO] Target genome list was writen to OceanDNA-b7194/target_genomes.txt
[2023-03-14 10:56:24,433] [INFO] Task started: fastANI
[2023-03-14 10:56:24,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a55bed-7f6b-4d6f-8858-1ecc8d9fe033/OceanDNA-b7194.fa --refList OceanDNA-b7194/target_genomes.txt --output OceanDNA-b7194/fastani_result.tsv --threads 1
[2023-03-14 10:56:41,097] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:41,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2510c3e1-e932-40c9-802a-9c1162862e39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:41,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2510c3e1-e932-40c9-802a-9c1162862e39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:41,102] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:41,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:41,102] [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
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	75.8075	50	1039	95	below_threshold
Aureitalea marina	strain=NBRC 107741	GCA_002943755.1	930804	930804	type	True	75.7677	54	1039	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	75.7343	55	1039	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:41,102] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7194/tc_result.tsv
[2023-03-14 10:56:41,102] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:41,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:41,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2510c3e1-e932-40c9-802a-9c1162862e39/dqc_reference/checkm_data
[2023-03-14 10:56:41,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:41,152] [INFO] Task started: CheckM
[2023-03-14 10:56:41,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7194/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7194/checkm_input OceanDNA-b7194/checkm_result
[2023-03-14 10:57:38,860] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:38,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:38,863] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:38,863] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:38,863] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7194/markers.fasta)
[2023-03-14 10:57:38,863] [INFO] Task started: Blastn
[2023-03-14 10:57:38,863] [INFO] Running command: blastn -query OceanDNA-b7194/markers.fasta -db /var/lib/cwl/stg2510c3e1-e932-40c9-802a-9c1162862e39/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7194/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:39,642] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:39,643] [INFO] Selected 28 target genomes.
[2023-03-14 10:57:39,643] [INFO] Target genome list was writen to OceanDNA-b7194/target_genomes_gtdb.txt
[2023-03-14 10:57:39,684] [INFO] Task started: fastANI
[2023-03-14 10:57:39,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a55bed-7f6b-4d6f-8858-1ecc8d9fe033/OceanDNA-b7194.fa --refList OceanDNA-b7194/target_genomes_gtdb.txt --output OceanDNA-b7194/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:55,460] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:55,464] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:57:55,464] [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_013214815.1	s__Gilvibacter sp013214815	78.6356	368	1039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163875.1	s__Gilvibacter sp002163875	78.5069	410	1039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966125.1	s__Pukyongia salina	75.8075	50	1039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943755.1	s__Aureitalea marina	75.7677	54	1039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295415.1	s__Altibacter sp014295415	75.7157	54	1039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:55,464] [INFO] GTDB search result was written to OceanDNA-b7194/result_gtdb.tsv
[2023-03-14 10:57:55,465] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:55,465] [INFO] DFAST_QC result json was written to OceanDNA-b7194/dqc_result.json
[2023-03-14 10:57:55,465] [INFO] DFAST_QC completed!
[2023-03-14 10:57:55,465] [INFO] Total running time: 0h1m57s