[2023-03-18 00:24:19,470] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:24:19,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:24:19,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a5dec5a-48c9-4d74-8f93-b086e51d16eb/dqc_reference
[2023-03-18 00:24:20,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:24:20,576] [INFO] Task started: Prodigal
[2023-03-18 00:24:20,576] [INFO] Running command: cat /var/lib/cwl/stg5a6e29c6-0584-41a5-9e27-efedf1bb7005/OceanDNA-b31152.fa | prodigal -d OceanDNA-b31152/cds.fna -a OceanDNA-b31152/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:24:34,664] [INFO] Task succeeded: Prodigal
[2023-03-18 00:24:34,664] [INFO] Task started: HMMsearch
[2023-03-18 00:24:34,664] [INFO] Running command: hmmsearch --tblout OceanDNA-b31152/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a5dec5a-48c9-4d74-8f93-b086e51d16eb/dqc_reference/reference_markers.hmm OceanDNA-b31152/protein.faa > /dev/null
[2023-03-18 00:24:34,867] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:24:34,867] [INFO] Found 6/6 markers.
[2023-03-18 00:24:34,886] [INFO] Query marker FASTA was written to OceanDNA-b31152/markers.fasta
[2023-03-18 00:24:34,887] [INFO] Task started: Blastn
[2023-03-18 00:24:34,887] [INFO] Running command: blastn -query OceanDNA-b31152/markers.fasta -db /var/lib/cwl/stg0a5dec5a-48c9-4d74-8f93-b086e51d16eb/dqc_reference/reference_markers.fasta -out OceanDNA-b31152/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:24:35,441] [INFO] Task succeeded: Blastn
[2023-03-18 00:24:35,442] [INFO] Selected 26 target genomes.
[2023-03-18 00:24:35,442] [INFO] Target genome list was writen to OceanDNA-b31152/target_genomes.txt
[2023-03-18 00:24:35,552] [INFO] Task started: fastANI
[2023-03-18 00:24:35,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6e29c6-0584-41a5-9e27-efedf1bb7005/OceanDNA-b31152.fa --refList OceanDNA-b31152/target_genomes.txt --output OceanDNA-b31152/fastani_result.tsv --threads 1
[2023-03-18 00:24:50,896] [INFO] Task succeeded: fastANI
[2023-03-18 00:24:50,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a5dec5a-48c9-4d74-8f93-b086e51d16eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:24:50,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a5dec5a-48c9-4d74-8f93-b086e51d16eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:24:50,897] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:24:50,897] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:24:50,897] [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
--------------------------------------------------------------------------------
[2023-03-18 00:24:50,897] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31152/tc_result.tsv
[2023-03-18 00:24:50,898] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:24:50,898] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:24:50,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a5dec5a-48c9-4d74-8f93-b086e51d16eb/dqc_reference/checkm_data
[2023-03-18 00:24:50,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:24:50,905] [INFO] Task started: CheckM
[2023-03-18 00:24:50,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31152/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31152/checkm_input OceanDNA-b31152/checkm_result
[2023-03-18 00:25:29,077] [INFO] Task succeeded: CheckM
[2023-03-18 00:25:29,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:25:29,287] [INFO] ===== Completeness check finished =====
[2023-03-18 00:25:29,287] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:25:29,287] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31152/markers.fasta)
[2023-03-18 00:25:29,288] [INFO] Task started: Blastn
[2023-03-18 00:25:29,288] [INFO] Running command: blastn -query OceanDNA-b31152/markers.fasta -db /var/lib/cwl/stg0a5dec5a-48c9-4d74-8f93-b086e51d16eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31152/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:25:30,162] [INFO] Task succeeded: Blastn
[2023-03-18 00:25:30,163] [INFO] Selected 25 target genomes.
[2023-03-18 00:25:30,163] [INFO] Target genome list was writen to OceanDNA-b31152/target_genomes_gtdb.txt
[2023-03-18 00:25:30,331] [INFO] Task started: fastANI
[2023-03-18 00:25:30,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6e29c6-0584-41a5-9e27-efedf1bb7005/OceanDNA-b31152.fa --refList OceanDNA-b31152/target_genomes_gtdb.txt --output OceanDNA-b31152/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:25:42,297] [INFO] Task succeeded: fastANI
[2023-03-18 00:25:42,300] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:25:42,300] [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_018649725.1	s__TMED23 sp018649725	76.5415	123	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__TMED23	95.0	99.78	99.75	0.87	0.87	3	-
GCA_002327565.1	s__UBA2165 sp002327565	76.2736	69	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__UBA2165	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018649245.1	s__UBA2165 sp018649245	76.1053	50	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__UBA2165	95.0	99.23	99.23	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:25:42,300] [INFO] GTDB search result was written to OceanDNA-b31152/result_gtdb.tsv
[2023-03-18 00:25:42,301] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:25:42,301] [INFO] DFAST_QC result json was written to OceanDNA-b31152/dqc_result.json
[2023-03-18 00:25:42,301] [INFO] DFAST_QC completed!
[2023-03-18 00:25:42,302] [INFO] Total running time: 0h1m23s