[2023-03-16 06:03:26,025] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:03:26,025] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:03:26,025] [INFO] DQC Reference Directory: /var/lib/cwl/stg37e448be-58d3-4769-b339-d849e84d8f00/dqc_reference
[2023-03-16 06:03:27,124] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:03:27,124] [INFO] Task started: Prodigal
[2023-03-16 06:03:27,124] [INFO] Running command: cat /var/lib/cwl/stg436a5a0d-86db-4c7e-ad74-ae7cba83be10/OceanDNA-b33555.fa | prodigal -d OceanDNA-b33555/cds.fna -a OceanDNA-b33555/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:03:43,298] [INFO] Task succeeded: Prodigal
[2023-03-16 06:03:43,298] [INFO] Task started: HMMsearch
[2023-03-16 06:03:43,298] [INFO] Running command: hmmsearch --tblout OceanDNA-b33555/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37e448be-58d3-4769-b339-d849e84d8f00/dqc_reference/reference_markers.hmm OceanDNA-b33555/protein.faa > /dev/null
[2023-03-16 06:03:43,497] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:03:43,498] [INFO] Found 6/6 markers.
[2023-03-16 06:03:43,516] [INFO] Query marker FASTA was written to OceanDNA-b33555/markers.fasta
[2023-03-16 06:03:43,518] [INFO] Task started: Blastn
[2023-03-16 06:03:43,518] [INFO] Running command: blastn -query OceanDNA-b33555/markers.fasta -db /var/lib/cwl/stg37e448be-58d3-4769-b339-d849e84d8f00/dqc_reference/reference_markers.fasta -out OceanDNA-b33555/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:44,110] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:44,111] [INFO] Selected 26 target genomes.
[2023-03-16 06:03:44,111] [INFO] Target genome list was writen to OceanDNA-b33555/target_genomes.txt
[2023-03-16 06:03:44,129] [INFO] Task started: fastANI
[2023-03-16 06:03:44,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg436a5a0d-86db-4c7e-ad74-ae7cba83be10/OceanDNA-b33555.fa --refList OceanDNA-b33555/target_genomes.txt --output OceanDNA-b33555/fastani_result.tsv --threads 1
[2023-03-16 06:03:56,816] [INFO] Task succeeded: fastANI
[2023-03-16 06:03:56,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37e448be-58d3-4769-b339-d849e84d8f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:03:56,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37e448be-58d3-4769-b339-d849e84d8f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:03:56,819] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:03:56,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:03:56,820] [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
Zwartia hollandica	strain=LF4-65	GCA_019923725.1	324606	324606	type	True	76.7207	60	850	95	below_threshold
Orrella marina	strain=HZ20	GCA_003058465.1	2163011	2163011	type	True	76.145	68	850	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:03:56,820] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33555/tc_result.tsv
[2023-03-16 06:03:56,820] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:03:56,820] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:03:56,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37e448be-58d3-4769-b339-d849e84d8f00/dqc_reference/checkm_data
[2023-03-16 06:03:56,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:03:56,825] [INFO] Task started: CheckM
[2023-03-16 06:03:56,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33555/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33555/checkm_input OceanDNA-b33555/checkm_result
[2023-03-16 06:04:40,513] [INFO] Task succeeded: CheckM
[2023-03-16 06:04:40,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:04:40,538] [INFO] ===== Completeness check finished =====
[2023-03-16 06:04:40,538] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:04:40,539] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33555/markers.fasta)
[2023-03-16 06:04:40,540] [INFO] Task started: Blastn
[2023-03-16 06:04:40,540] [INFO] Running command: blastn -query OceanDNA-b33555/markers.fasta -db /var/lib/cwl/stg37e448be-58d3-4769-b339-d849e84d8f00/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33555/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:04:41,530] [INFO] Task succeeded: Blastn
[2023-03-16 06:04:41,531] [INFO] Selected 23 target genomes.
[2023-03-16 06:04:41,531] [INFO] Target genome list was writen to OceanDNA-b33555/target_genomes_gtdb.txt
[2023-03-16 06:04:41,635] [INFO] Task started: fastANI
[2023-03-16 06:04:41,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg436a5a0d-86db-4c7e-ad74-ae7cba83be10/OceanDNA-b33555.fa --refList OceanDNA-b33555/target_genomes_gtdb.txt --output OceanDNA-b33555/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:04:55,930] [INFO] Task succeeded: fastANI
[2023-03-16 06:04:55,934] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:04:55,934] [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_017857895.1	s__Algicoccus sp017857895	95.6014	616	850	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Algicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903958565.1	s__NBD-18 sp903958565	76.2707	54	850	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.16	98.92	0.86	0.85	5	-
GCF_003058465.1	s__Algicoccus marinus	76.145	68	850	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Algicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:04:55,934] [INFO] GTDB search result was written to OceanDNA-b33555/result_gtdb.tsv
[2023-03-16 06:04:55,934] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:04:55,935] [INFO] DFAST_QC result json was written to OceanDNA-b33555/dqc_result.json
[2023-03-16 06:04:55,935] [INFO] DFAST_QC completed!
[2023-03-16 06:04:55,935] [INFO] Total running time: 0h1m30s