[2023-03-18 07:54:30,541] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:30,541] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:30,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg76b3fb2e-4407-4746-ab10-db2062298eba/dqc_reference
[2023-03-18 07:54:32,272] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:32,273] [INFO] Task started: Prodigal
[2023-03-18 07:54:32,273] [INFO] Running command: cat /var/lib/cwl/stg068aa232-7570-4869-8f48-1b53904d7b80/OceanDNA-b14184.fa | prodigal -d OceanDNA-b14184/cds.fna -a OceanDNA-b14184/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:41,882] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:41,882] [INFO] Task started: HMMsearch
[2023-03-18 07:54:41,882] [INFO] Running command: hmmsearch --tblout OceanDNA-b14184/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76b3fb2e-4407-4746-ab10-db2062298eba/dqc_reference/reference_markers.hmm OceanDNA-b14184/protein.faa > /dev/null
[2023-03-18 07:54:42,032] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:42,032] [INFO] Found 6/6 markers.
[2023-03-18 07:54:42,046] [INFO] Query marker FASTA was written to OceanDNA-b14184/markers.fasta
[2023-03-18 07:54:42,047] [INFO] Task started: Blastn
[2023-03-18 07:54:42,047] [INFO] Running command: blastn -query OceanDNA-b14184/markers.fasta -db /var/lib/cwl/stg76b3fb2e-4407-4746-ab10-db2062298eba/dqc_reference/reference_markers.fasta -out OceanDNA-b14184/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:42,525] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:42,526] [INFO] Selected 3 target genomes.
[2023-03-18 07:54:42,526] [INFO] Target genome list was writen to OceanDNA-b14184/target_genomes.txt
[2023-03-18 07:54:42,528] [INFO] Task started: fastANI
[2023-03-18 07:54:42,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg068aa232-7570-4869-8f48-1b53904d7b80/OceanDNA-b14184.fa --refList OceanDNA-b14184/target_genomes.txt --output OceanDNA-b14184/fastani_result.tsv --threads 1
[2023-03-18 07:54:43,680] [INFO] Task succeeded: fastANI
[2023-03-18 07:54:43,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76b3fb2e-4407-4746-ab10-db2062298eba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:54:43,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76b3fb2e-4407-4746-ab10-db2062298eba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:54:43,680] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:54:43,681] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:54:43,681] [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 07:54:43,681] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14184/tc_result.tsv
[2023-03-18 07:54:43,681] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:54:43,681] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:54:43,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76b3fb2e-4407-4746-ab10-db2062298eba/dqc_reference/checkm_data
[2023-03-18 07:54:43,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:54:43,793] [INFO] Task started: CheckM
[2023-03-18 07:54:43,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14184/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14184/checkm_input OceanDNA-b14184/checkm_result
[2023-03-18 07:55:14,030] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:14,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 5.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:55:14,032] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:14,033] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:14,033] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14184/markers.fasta)
[2023-03-18 07:55:14,034] [INFO] Task started: Blastn
[2023-03-18 07:55:14,034] [INFO] Running command: blastn -query OceanDNA-b14184/markers.fasta -db /var/lib/cwl/stg76b3fb2e-4407-4746-ab10-db2062298eba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14184/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:14,651] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:14,652] [INFO] Selected 5 target genomes.
[2023-03-18 07:55:14,652] [INFO] Target genome list was writen to OceanDNA-b14184/target_genomes_gtdb.txt
[2023-03-18 07:55:14,678] [INFO] Task started: fastANI
[2023-03-18 07:55:14,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg068aa232-7570-4869-8f48-1b53904d7b80/OceanDNA-b14184.fa --refList OceanDNA-b14184/target_genomes_gtdb.txt --output OceanDNA-b14184/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:55:16,572] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:16,574] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:55:16,574] [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_002708065.1	s__UBA11795 sp002708065	91.0823	390	584	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11795	95.0	98.64	98.22	0.73	0.71	4	-
--------------------------------------------------------------------------------
[2023-03-18 07:55:16,574] [INFO] GTDB search result was written to OceanDNA-b14184/result_gtdb.tsv
[2023-03-18 07:55:16,574] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:55:16,575] [INFO] DFAST_QC result json was written to OceanDNA-b14184/dqc_result.json
[2023-03-18 07:55:16,575] [INFO] DFAST_QC completed!
[2023-03-18 07:55:16,575] [INFO] Total running time: 0h0m46s