[2023-03-16 04:05:20,068] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,068] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a12073e-ca60-4b27-8afb-2ca0f68a79ca/dqc_reference
[2023-03-16 04:05:21,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:21,202] [INFO] Task started: Prodigal
[2023-03-16 04:05:21,203] [INFO] Running command: cat /var/lib/cwl/stgc3625330-8ca3-4cf6-b84d-2803def2a35f/OceanDNA-b11469.fa | prodigal -d OceanDNA-b11469/cds.fna -a OceanDNA-b11469/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:38,672] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:38,672] [INFO] Task started: HMMsearch
[2023-03-16 04:05:38,672] [INFO] Running command: hmmsearch --tblout OceanDNA-b11469/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a12073e-ca60-4b27-8afb-2ca0f68a79ca/dqc_reference/reference_markers.hmm OceanDNA-b11469/protein.faa > /dev/null
[2023-03-16 04:05:38,871] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:38,872] [INFO] Found 6/6 markers.
[2023-03-16 04:05:38,889] [INFO] Query marker FASTA was written to OceanDNA-b11469/markers.fasta
[2023-03-16 04:05:38,889] [INFO] Task started: Blastn
[2023-03-16 04:05:38,889] [INFO] Running command: blastn -query OceanDNA-b11469/markers.fasta -db /var/lib/cwl/stg0a12073e-ca60-4b27-8afb-2ca0f68a79ca/dqc_reference/reference_markers.fasta -out OceanDNA-b11469/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:39,417] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:39,418] [INFO] Selected 28 target genomes.
[2023-03-16 04:05:39,418] [INFO] Target genome list was writen to OceanDNA-b11469/target_genomes.txt
[2023-03-16 04:05:39,427] [INFO] Task started: fastANI
[2023-03-16 04:05:39,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3625330-8ca3-4cf6-b84d-2803def2a35f/OceanDNA-b11469.fa --refList OceanDNA-b11469/target_genomes.txt --output OceanDNA-b11469/fastani_result.tsv --threads 1
[2023-03-16 04:05:54,143] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:54,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a12073e-ca60-4b27-8afb-2ca0f68a79ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:54,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a12073e-ca60-4b27-8afb-2ca0f68a79ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:54,146] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:54,146] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:05:54,146] [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
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.3482	53	947	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:05:54,146] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11469/tc_result.tsv
[2023-03-16 04:05:54,146] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:54,146] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:54,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a12073e-ca60-4b27-8afb-2ca0f68a79ca/dqc_reference/checkm_data
[2023-03-16 04:05:54,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:54,151] [INFO] Task started: CheckM
[2023-03-16 04:05:54,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11469/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11469/checkm_input OceanDNA-b11469/checkm_result
[2023-03-16 04:06:39,722] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:39,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:39,724] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:39,724] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:39,725] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11469/markers.fasta)
[2023-03-16 04:06:39,725] [INFO] Task started: Blastn
[2023-03-16 04:06:39,725] [INFO] Running command: blastn -query OceanDNA-b11469/markers.fasta -db /var/lib/cwl/stg0a12073e-ca60-4b27-8afb-2ca0f68a79ca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11469/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:40,450] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:40,451] [INFO] Selected 27 target genomes.
[2023-03-16 04:06:40,451] [INFO] Target genome list was writen to OceanDNA-b11469/target_genomes_gtdb.txt
[2023-03-16 04:06:40,486] [INFO] Task started: fastANI
[2023-03-16 04:06:40,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3625330-8ca3-4cf6-b84d-2803def2a35f/OceanDNA-b11469.fa --refList OceanDNA-b11469/target_genomes_gtdb.txt --output OceanDNA-b11469/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:55,520] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:55,524] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:06:55,524] [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_905182585.1	s__GCA-002722245 sp905182585	99.6755	443	947	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002722245.1	s__GCA-002722245 sp002722245	76.9974	130	947	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720635.1	s__GCA-002722245 sp002720635	76.7652	98	947	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717515.1	s__GCA-002722245 sp002717515	76.7609	124	947	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	99.42	99.42	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:55,524] [INFO] GTDB search result was written to OceanDNA-b11469/result_gtdb.tsv
[2023-03-16 04:06:55,524] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:55,525] [INFO] DFAST_QC result json was written to OceanDNA-b11469/dqc_result.json
[2023-03-16 04:06:55,525] [INFO] DFAST_QC completed!
[2023-03-16 04:06:55,525] [INFO] Total running time: 0h1m35s